cnsbb : Messages : 1676-1705 of 2224

Dear All,

At last I am able to install cns in openSUSE 10.3. I don't know which
compiler is playing the role but I am mentioning the libraries and
compilers I have installed.

gcc-fortran.ymp
libgfortran41.ymp
libgfortran42.ymp
libgfortrna43.ymp
gcc33.ymp
gcc33-fortran.ymp
libgcc33.ymp
and INTEL FORTRAN compiler ifort with registration.

although i have got many remarks while the installation procedure was
going on

those are

remark: "file_name" has been targeted for automatic cpu dispatch
remark: LOOP WAS VECTORIZED

probably those are the warning messages like in C

I fix it up after reuntarring the cns_solve_1.2_all.tar an did make
install. But before doing all these thing I install all the compilers.

Thank you
Debajyoti Dutta

#1677

From: "smith.uab35243" <smith.uab35243@...>
Date: Thu May 1, 2008 4:43 pm
Subject: abnomally small B factors

smith.uab35243

I have a structure solved by molecular replacement and refines pretty
well.  It's low resolution 3.2A and high solvent content 75%.  But the
MR solution went smoothly and is refining to 23% and 28% Rfree with 25-
3.2A data.  Two molecules in ASU and saw significant diff. density in
both that I've put two sulfate ions in eacn monomer and saw some
residues that were missing in the model and put them in.
Initially I did rigid, then anneal, then bgroup refinements and finally
refine all with isotropic B factor refinement.
The unusual thing is that without restricting B, there are several
residues in each monomer where the B factor refined to 1.0.  So I've
been restricting them to be between 15 and 150.  Everything else looks
good and the density is pretty good with only a little noise.  It's
P3121 SpGrp and Rmerge of the data was around 9.8% with I/sigma around
9 or so.  Am doing automatic Bulk solvent corrections.  Other Bfactors
look very normal from 20s to about 120s for a few terminal residues.
With the restrictions the B factors what want dive stop at 15.0.
Theres are about 10 of them in each monomer of 250 residues each.
I've never seen this happen.
Has anyone seen this and can give me a clue as to what is happening and
what to do about it.

Thanks,  Craig

#1678

From: "sean_c_gay" <sean_c_gay@...>
Date: Fri May 2, 2008 5:33 pm
Subject: generate easy errors

sean_c_gay

Despite having my ligand (ADP) named exactly as it is in my topology
and parameter files, I am getting errors when running generate easy
and the pdb output does not contain my ligand. The errors are:


%ADDST-ERR: STMAX too small. Check code

and then further down:

MAPIC: Atom numbers being modified
  %GENRES-ERR: residue ADP  not found in topology file
  %PATCH-ERR: to be deleted bond -C    +N    not found in molecular
structure.
  %PATCH-ERR: to be deleted angle -CA   -C    +N    not found in
molecular structure.
  %PATCH-ERR: to be deleted angle -O    -C    +N    not found in
molecular structure.
  %PATCH-ERR: to be deleted angle -C    +N    +CA   not found in
molecular structure.
  %PATCH-ERR: to be deleted angle -C    +N    +H    not found in
molecular structure.
  %PATCH-ERR: to be deleted dihedral -C    +N    +CA   +C    not found
in molecular structure.
  %PATCH-ERR: to be deleted dihedral -N    -CA   -C    +N    not found
in molecular structure.
  %PATCH-ERR: to be deleted dihedral -CA   -C    +N    +CA   not found
in molecular structure.
  %PATCH-ERR: to be deleted improper -C    -CA   +N    -O    not found
in molecular structure.
  %PATCH-ERR: to be deleted improper +N    -C    +CA   +H    not found
in molecular structure.
  SEGMNT:   197 residues were inserted into segment "A   "

and even further down:

  %READC-ERR: atom A    1001 ADP  PB   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O1B  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O2B  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O3B  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  PA   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O1A  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O2A  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O3A  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O5*  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C5*  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C4*  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O4*  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C3*  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O3*  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C2*  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  O2*  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C1*  not found in molecular structure
  %READC-ERR: atom A    1001 ADP  N9   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C8   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  N7   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C5   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C6   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  N6   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  N1   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C2   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  N3   not found in molecular structure
  %READC-ERR: atom A    1001 ADP  C4   not found in molecular structure

i am at a total loss here. Any ideas?

Sean Gay
Fisher Lab
Department of Chemistry
University of California, Davis
Davis, CA USA

Reply | Messages in this Topic (3)

#1679

From: Christian Biertuempfel <biertumpfelc@...>
Date: Mon May 5, 2008 3:32 pm
Subject: Re: generate easy errors

cbiertue

Hi Sean,
Have a look into your pdb file again. Are chainids, segids and atom
labels correct? Has everything the correct position?

Hope this helps,
christian


sean_c_gay wrote:
>
>
> Despite having my ligand (ADP) named exactly as it is in my topology
> and parameter files, I am getting errors when running generate easy
> and the pdb output does not contain my ligand. The errors are:
>
> %ADDST-ERR: STMAX too small. Check code
>
> and then further down:
>
> MAPIC: Atom numbers being modified
> %GENRES-ERR: residue ADP not found in topology file
> %PATCH-ERR: to be deleted bond -C +N not found in molecular
> structure.
> %PATCH-ERR: to be deleted angle -CA -C +N not found in
> molecular structure.
> %PATCH-ERR: to be deleted angle -O -C +N not found in
> molecular structure.
> %PATCH-ERR: to be deleted angle -C +N +CA not found in
> molecular structure.
> %PATCH-ERR: to be deleted angle -C +N +H not found in
> molecular structure.
> %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found
> in molecular structure.
> %PATCH-ERR: to be deleted dihedral -N -CA -C +N not found
> in molecular structure.
> %PATCH-ERR: to be deleted dihedral -CA -C +N +CA not found
> in molecular structure.
> %PATCH-ERR: to be deleted improper -C -CA +N -O not found
> in molecular structure.
> %PATCH-ERR: to be deleted improper +N -C +CA +H not found
> in molecular structure.
> SEGMNT: 197 residues were inserted into segment "A "
>
> and even further down:
>
> %READC-ERR: atom A 1001 ADP PB not found in molecular structure
> %READC-ERR: atom A 1001 ADP O1B not found in molecular structure
> %READC-ERR: atom A 1001 ADP O2B not found in molecular structure
> %READC-ERR: atom A 1001 ADP O3B not found in molecular structure
> %READC-ERR: atom A 1001 ADP PA not found in molecular structure
> %READC-ERR: atom A 1001 ADP O1A not found in molecular structure
> %READC-ERR: atom A 1001 ADP O2A not found in molecular structure
> %READC-ERR: atom A 1001 ADP O3A not found in molecular structure
> %READC-ERR: atom A 1001 ADP O5* not found in molecular structure
> %READC-ERR: atom A 1001 ADP C5* not found in molecular structure
> %READC-ERR: atom A 1001 ADP C4* not found in molecular structure
> %READC-ERR: atom A 1001 ADP O4* not found in molecular structure
> %READC-ERR: atom A 1001 ADP C3* not found in molecular structure
> %READC-ERR: atom A 1001 ADP O3* not found in molecular structure
> %READC-ERR: atom A 1001 ADP C2* not found in molecular structure
> %READC-ERR: atom A 1001 ADP O2* not found in molecular structure
> %READC-ERR: atom A 1001 ADP C1* not found in molecular structure
> %READC-ERR: atom A 1001 ADP N9 not found in molecular structure
> %READC-ERR: atom A 1001 ADP C8 not found in molecular structure
> %READC-ERR: atom A 1001 ADP N7 not found in molecular structure
> %READC-ERR: atom A 1001 ADP C5 not found in molecular structure
> %READC-ERR: atom A 1001 ADP C6 not found in molecular structure
> %READC-ERR: atom A 1001 ADP N6 not found in molecular structure
> %READC-ERR: atom A 1001 ADP N1 not found in molecular structure
> %READC-ERR: atom A 1001 ADP C2 not found in molecular structure
> %READC-ERR: atom A 1001 ADP N3 not found in molecular structure
> %READC-ERR: atom A 1001 ADP C4 not found in molecular structure
>
> i am at a total loss here. Any ideas?
>
> Sean Gay
> Fisher Lab
> Department of Chemistry
> University of California, Davis
> Davis, CA USA
>
>

_______________________________________________________________________

Dr. Christian Biert�mpfel
Laboratory of Molecular Biology

NIDDK/National Institutes of Health              phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03          fax:   +1 301 496 0201
Bethesda, MD 20892-0580
USA
_______________________________________________________________________

Reply | Messages in this Topic (3)

#1680

From: Javier Gonz�lez <javierg@...>
Date: Mon May 5, 2008 8:52 pm
Subject: Cysteine sulfonic .top & .par files

biojmg

Hi all, I'm completely new to CNS and I'm trying to refine a protein
having an oxidized Cys residue, to Cys-sulfonate (ie, Cys-SH to Cys-SO3).
Does anyone know where I can get the corresponding topology and
parametrization files?

Thanks in advance.

Javier.

#1681

From: Calvin Steussy <csteussy@...>
Date: Tue May 6, 2008 9:34 am
Subject: Re: generate easy errors

nsteussy

I usually see that error when there is not an 'END' card/line at the
bottom of the pdb file.

Nic out


Christian Biertuempfel wrote:
> Hi Sean,
> Have a look into your pdb file again. Are chainids, segids and atom
> labels correct? Has everything the correct position?
>
> Hope this helps,
> christian
>
>
> sean_c_gay wrote:
>
>> Despite having my ligand (ADP) named exactly as it is in my topology
>> and parameter files, I am getting errors when running generate easy
>> and the pdb output does not contain my ligand. The errors are:
>>
>> %ADDST-ERR: STMAX too small. Check code
>>
>> and then further down:
>>
>> MAPIC: Atom numbers being modified
>> %GENRES-ERR: residue ADP not found in topology file
>> %PATCH-ERR: to be deleted bond -C +N not found in molecular
>> structure.
>> %PATCH-ERR: to be deleted angle -CA -C +N not found in
>> molecular structure.
>> %PATCH-ERR: to be deleted angle -O -C +N not found in
>> molecular structure.
>> %PATCH-ERR: to be deleted angle -C +N +CA not found in
>> molecular structure.
>> %PATCH-ERR: to be deleted angle -C +N +H not found in
>> molecular structure.
>> %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found
>> in molecular structure.
>> %PATCH-ERR: to be deleted dihedral -N -CA -C +N not found
>> in molecular structure.
>> %PATCH-ERR: to be deleted dihedral -CA -C +N +CA not found
>> in molecular structure.
>> %PATCH-ERR: to be deleted improper -C -CA +N -O not found
>> in molecular structure.
>> %PATCH-ERR: to be deleted improper +N -C +CA +H not found
>> in molecular structure.
>> SEGMNT: 197 residues were inserted into segment "A "
>>
>> and even further down:
>>
>> %READC-ERR: atom A 1001 ADP PB not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O1B not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O2B not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O3B not found in molecular structure
>> %READC-ERR: atom A 1001 ADP PA not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O1A not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O2A not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O3A not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O5* not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C5* not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C4* not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O4* not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C3* not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O3* not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C2* not found in molecular structure
>> %READC-ERR: atom A 1001 ADP O2* not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C1* not found in molecular structure
>> %READC-ERR: atom A 1001 ADP N9 not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C8 not found in molecular structure
>> %READC-ERR: atom A 1001 ADP N7 not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C5 not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C6 not found in molecular structure
>> %READC-ERR: atom A 1001 ADP N6 not found in molecular structure
>> %READC-ERR: atom A 1001 ADP N1 not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C2 not found in molecular structure
>> %READC-ERR: atom A 1001 ADP N3 not found in molecular structure
>> %READC-ERR: atom A 1001 ADP C4 not found in molecular structure
>>
>> i am at a total loss here. Any ideas?
>>
>> Sean Gay
>> Fisher Lab
>> Department of Chemistry
>> University of California, Davis
>> Davis, CA USA
>>
>>
>>
>
> _______________________________________________________________________
>
> Dr. Christian Biert�mpfel
> Laboratory of Molecular Biology
>
> NIDDK/National Institutes of Health              phone: +1 301 402 4647
> 9000 Rockville Pike, Bldg. 5, Rm. B1-03          fax:   +1 301 496 0201
> Bethesda, MD 20892-0580
> USA
> _______________________________________________________________________
>
> ------------------------------------
>
> --------------------------------------------------------
> List information at http://groups.yahoo.com/group/cnsbb.
> Posting is only allowed for members of this list.
>
> Yahoo! Groups Links
>
>
>
>

Reply | Messages in this Topic (3)

#1682

From: "prasenjitcomm" <prasenjitcomm@...>
Date: Mon May 12, 2008 5:30 pm
Subject: How to calculate inter-atomic distance?

prasenjitcomm

Hi All,
Can CNS be used to calculate inter-atomic distance?
If yes, can someone please help me out.

I am using Ubuntu Linux, so if possible, please mention any
differences in command or options.

Thanks

#1683

From: "Joe Van Dyk" <joevandyk@...>
Date: Tue May 13, 2008 9:59 pm
Subject: Using CNS in commercial software

swimmar

According to http://cns-online.org/v1.2/, you need to have prior
written authorization from Yale in order to use CNS in a commercial
application.

Anyone know who to contact?

Thanks,
Joe Van Dyk

#1684

From: Christian Biertuempfel <biertumpfelc@...>
Date: Tue May 13, 2008 6:37 pm
Subject: Re: How to calculate inter-atomic distance?

cbiertue

Hi,
CNS has two input scripts which might be interesting for you:

contact.inp
difference_distance.inp

In addition moleman2 from the USF has very useful distance commands and
there is the differences distance matrix program from yale:

http://xray.bmc.uu.se/usf/moleman2_man.html#H22
http://freedom.bph.jhu.edu/fleming/ddmp/

Best regards,
christian


prasenjitcomm wrote:
>
>
> Hi All,
> Can CNS be used to calculate inter-atomic distance?
> If yes, can someone please help me out.
>
> I am using Ubuntu Linux, so if possible, please mention any
> differences in command or options.
>
> Thanks
>
>

--
_______________________________________________________________________

Dr. Christian Biert�mpfel
Laboratory of Molecular Biology

NIDDK/National Institutes of Health              phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03          fax:   +1 301 496 0201
Bethesda, MD 20892-0580
USA
_______________________________________________________________________

#1685

From: Debajyoti Dutta <molbiol349@...>
Date: Sun May 18, 2008 9:58 pm
Subject: Error in twinning detection

molbiol349

Hi,

I am trying to detect twining of my reflection data processed with d*trek. I have converted the reflection file dtscale.ref into dtscale.mtz and dtscale.hkl using to_cns command. But upon running

cns_solve <detect_twinning.inp I am getting the following error. Please help me solving the problem.

Sincerely
Debajyoti

REFLection>evaluate ($echo_old_sclib=$result)
EVALUATE: symbol $ECHO_OLD_SCLIB set to TRUE (logical)
REFLection>set echo=off message=off end
Program version= 1.2 File version= 1.2
%REFLection-ERR: unrecognized command:
SCATter
^^^^^^^
%REFLection-ERR: unrecognized command:
SCATter (
         ^
%REFLection-ERR: unrecognized command:
SCATter ( chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical H*
                    ^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical H* and
                       ^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical H* and not
                           ^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical H* and not (
                               ^
%REFLection-ERR: unrecognized command:
           chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "He"
                    ^^^^
%REFLection-ERR: unrecognized command:
           chemical "He" or
                         ^^
%REFLection-ERR: unrecognized command:
           chemical "He" or chemical
                            ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "He" or chemical "HE"
                                     ^^^^
%REFLection-ERR: unrecognized command:
           chemical "He" or chemical "HE" or
                                          ^^
%REFLection-ERR: unrecognized command:
           chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Ho"
                    ^^^^
%REFLection-ERR: unrecognized command:
           chemical "Ho" or
                         ^^
%REFLection-ERR: unrecognized command:
           chemical "Ho" or chemical
                            ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Ho" or chemical "HO"
                                     ^^^^
%REFLection-ERR: unrecognized command:
           chemical "Ho" or chemical "HO" or
                                          ^^
%REFLection-ERR: unrecognized command:
           chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Ho+3"
                    ^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Ho+3" or
                           ^^
%REFLection-ERR: unrecognized command:
           chemical "Ho+3" or chemical
                              ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Ho+3" or chemical "HO+3"
                                       ^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Ho+3" or chemical "HO+3" or
                                              ^^
%REFLection-ERR: unrecognized command:
           chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hf"
                    ^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hf" or
                         ^^
%REFLection-ERR: unrecognized command:
           chemical "Hf" or chemical
                            ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hf" or chemical "HF"
                                     ^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hf" or chemical "HF" or
                                          ^^
%REFLection-ERR: unrecognized command:
           chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hf+4"
                    ^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hf+4" or
                           ^^
%REFLection-ERR: unrecognized command:
           chemical "Hf+4" or chemical
                              ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hf+4" or chemical "HF+4"
                                       ^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hf+4" or chemical "HF+4" or
                                              ^^
%REFLection-ERR: unrecognized command:
           chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg"
                    ^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg" or
                         ^^
%REFLection-ERR: unrecognized command:
           chemical "Hg" or chemical
                            ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg" or chemical "HG"
                                     ^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg" or chemical "HG" or
                                          ^^
%REFLection-ERR: unrecognized command:
           chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+1"
                    ^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+1" or
                           ^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+1" or chemical
                              ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+1" or chemical "HG+1"
                                       ^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+1" or chemical "HG+1" or
                                              ^^
%REFLection-ERR: unrecognized command:
           chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+2"
                    ^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+2" or
                           ^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+2" or chemical
                              ^^^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+2" or chemical "HG+2"
                                       ^^^^^^
%REFLection-ERR: unrecognized command:
           chemical "Hg+2" or chemical "HG+2" ))
                                              ^
%REFLection-ERR: unrecognized command:
           chemical "Hg+2" or chemical "HG+2" ))
                                               ^
%REFLection-ERR: unrecognized command:
   0.489918
   ^^^^^^^^
%REFLection-ERR: unrecognized command:
   0.489918 20.6593
            ^^^^^^^
%REFLection-ERR: unrecognized command:
   0.489918 20.6593 0.262003
                    ^^^^^^^^
%REFLection-ERR: unrecognized command:
   0.489918 20.6593 0.262003 7.74039
                             ^^^^^^^
%REFLection-ERR: unrecognized command:
   0.489918 20.6593 0.262003 7.74039 0.196767
                                     ^^^^^^^^
%REFLection-ERR: unrecognized command:
   0.489918 20.6593 0.262003 7.74039 0.196767 49.5519
                                              ^^^^^^^
%REFLection-ERR: unrecognized command:
   0.489918 20.6593 0.262003 7.74039 0.196767 49.5519 0.049879
                                                      ^^^^^^^^
%REFLection-ERR: unrecognized command:
   0.489918 20.6593 0.262003 7.74039 0.196767 49.5519 0.049879 2.20159
                                                               ^^^^^^^
%REFLection-ERR: unrecognized command:
   0.489918 20.6593 0.262003 7.74039 0.196767 49.5519 0.049879 2.20159 0.001305
                                                                       ^^^^^^^^
%REFLection-ERR: unrecognized command:
SCATter
^^^^^^^
%REFLection-ERR: unrecognized command:
SCATter (
         ^
%REFLection-ERR: unrecognized command:
SCATter ( chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "He"
                    ^^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "He" or
                         ^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "He" or chemical
                            ^^^^^^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "He" or chemical "HE"
                                     ^^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "He" or chemical "HE" )
                                          ^
%REFLection-ERR: unrecognized command:
   0.8734
   ^^^^^^
%REFLection-ERR: unrecognized command:
   0.8734 9.1037
          ^^^^^^
%REFLection-ERR: unrecognized command:
   0.8734 9.1037 0.6309
                 ^^^^^^
%REFLection-ERR: unrecognized command:
   0.8734 9.1037 0.6309 3.3568
                        ^^^^^^
%REFLection-ERR: unrecognized command:
   0.8734 9.1037 0.6309 3.3568 0.3112
                               ^^^^^^
%REFLection-ERR: unrecognized command:
   0.8734 9.1037 0.6309 3.3568 0.3112 22.9276
                                      ^^^^^^^
%REFLection-ERR: unrecognized command:
   0.8734 9.1037 0.6309 3.3568 0.3112 22.9276 0.178
                                              ^^^^^
%REFLection-ERR: unrecognized command:
   0.8734 9.1037 0.6309 3.3568 0.3112 22.9276 0.178 0.9821
                                                    ^^^^^^
%REFLection-ERR: unrecognized command:
   0.8734 9.1037 0.6309 3.3568 0.3112 22.9276 0.178 0.9821 0.0064
                                                           ^^^^^^
%REFLection-ERR: unrecognized command:
SCATter
^^^^^^^
%REFLection-ERR: unrecognized command:
SCATter (
         ^
%REFLection-ERR: unrecognized command:
SCATter ( chemical
           ^^^^^^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "Li"
                    ^^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "Li" or
                         ^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "Li" or chemical
                            ^^^^^^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "Li" or chemical "LI"
                                     ^^^^
%REFLection-ERR: unrecognized command:
SCATter ( chemical "Li" or chemical "LI" )
                                          ^
%REFLection-ERR: unrecognized command:
   1.1282
   ^^^^^^
%REFLection-ERR: unrecognized command:
   1.1282 3.9546
          ^^^^^^
%REFLection-ERR: unrecognized command:
   1.1282 3.9546 0.7508
                 ^^^^^^
%REFLection-ERR: unrecognized command:
   1.1282 3.9546 0.7508 1.0524
                        ^^^^^^
%REFLection-ERR: unrecognized command:
   1.1282 3.9546 0.7508 1.0524 0.6175
                               ^^^^^^
%REFLection-ERR: unrecognized command:
   1.1282 3.9546 0.7508 1.0524 0.6175 85.3905
                                      ^^^^^^^
%REFLection-ERR: unrecognized command:
   1.1282 3.9546 0.7508 1.0524 0.6175 85.3905 0.4653
                                              ^^^^^^
%REFLection-ERR: unrecognized command:
   1.1282 3.9546 0.7508 1.0524 0.6175 85.3905 0.4653 168.261
                                                     ^^^^^^^
%PARSER error encountered: Encountered too many parsing errors.
   (CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.
          ============================================================
           Maximum dynamic memory allocation:      832744 bytes
           Maximum dynamic memory overhead:            72 bytes
           Program started at: 03:21:46 on 19-May-08
           Program stopped at: 03:21:46 on 19-May-08
           CPU time used:       0.1120 seconds
          ============================================================

What is your Emotional Quotient? Find out.

#1686

From: "i_m_subh" <i_m_subh@...>
Date: Mon May 19, 2008 7:15 pm
Subject: Energy Minimization for a Homology Model!

i_m_subh

Hi,
I joined the group today and I am very new to CNS.I want  to energy
minimize my homology model/models.

What  input files should I use?
  I could see that the anneal.inp,and minimize.inp have
crystallographic data inputs (resolution,shell dimensions etc)in the
script.I will obviously not supply these inputs.
Do I have to get rid of something while editing the scripts for a
Homology model?
Has anyone ever done energy minimisation of a homology Model by CNS?
It would be amazing to get some help and guidance.

Subh

#1687

From: "i_m_subh" <i_m_subh@...>
Date: Thu May 22, 2008 6:07 pm
Subject: Problem creating an mtf file!

i_m_subh

Hi,
Thanks for your help and guidance.As a non programmer I still have some questions which might sound a bit obvious to you guys.Thats why I need you help to explain me things which I can't understand after reading the stuff in CNS.I appreciate your help.

Here goes my question

I am trying to run generate_easy.inp to make an mtf file from my pdb file.The pdb file is created in MODELLER.
Its not working and it seems that its because I can't understand what these directions explicitly mean.

"Different chains in the structure must have either unique segid or chainid records. If this is no the case, the end of a chain must be delimited by a TER card.
A break in a chain can be detected automatically or should be delimited by a BREAK card. In this case no patch (head, tail or link) will be applied between the residues that bound the chain break.
NB. The input PDB file must finish with an END statement "

Could anyone tell me what changes do I have to make in the generate_easy.inp files to correctly run it.
Thanks a lot in advance.

Subhendu

#1688

From: "i_m_subh" <i_m_subh@...>
Date: Thu May 29, 2008 3:46 pm
Subject: Working with MODELLER pdb files!

i_m_subh

Hi,
Has anyone ever used the pdb files generated in MODELLER (A.Sali) as
inputs for CNS?
Please let me know if you have done so.

Thanks
Subh

#1689

From: Christian Biertuempfel <biertumpfelc@...>
Date: Thu May 29, 2008 8:47 pm
Subject: Re: Problem creating an mtf file!

cbiertue

Hi Subhendu,
The CNS tasks you want to look at are model_minimize.inp and
model_anneal.inp. However, be careful that you do not overfit your model
which can easily be done without experimental data. Maybe, someone else
can give you some more hints. As a rough estimation I reduce the number
of steps for the above mentioned tasks by a factor of 10 from the
default values.

Of course, you have to generate a pdb and mtf file first. It is
difficult to troubleshoot without your pdb file. One problem can be a
wrong assignment of the segids. Do you use the following in generate_easy?

{* convert chainid to segid if chainid is non-blank *}
{+ choice: true false +}
{===>} convert=true;

{* separate chains by segid - a new segid starts a new chain *}
{+ choice: true false +}
{===>} separate=true;

Sometimes, an easy fix is to read your pdb file into another program
like moleman2, o, coot, pymol, chimera, vmd, rasmol, pdbset or whatever
and write out a new pdb file. This helps in some cases to remove
problems with columns or format errors.

Is your chain continuous? If you introduce a lot of breaks with modeller
   it might lead to trouble.

If you want send me your file off list and I could try to make it work.

Best regards,
christian

i_m_subh wrote:
>
>
> Hi,
> Thanks for your help and guidance.As a non programmer I still have some
> questions which might sound a bit obvious to you guys.Thats why I need
> you help to explain me things which I can't understand after reading the
> stuff in CNS.I appreciate your help.
>
> Here goes my question
>
> I am trying to run generate_easy.inp to make an mtf file from my pdb
> file.The pdb file is created in MODELLER.
> Its not working and it seems that its because I can't understand what
> these directions explicitly mean.
>
>
>  *"Different chains in the structure must have either unique segid or
> chainid records. If this is no the case, the end of a chain must be
> delimited by a TER card.
> A break in a chain can be detected automatically or should be delimited
> by a BREAK card. In this case no patch (head, tail or link) will be
> applied between the residues that bound the chain break.
> NB. The input PDB file must finish with an END statement "
>
> *Could anyone tell me what changes do I have to make in the
> generate_easy.inp files to correctly run it.
> Thanks a lot in advance.
>
> Subhendu
>
>

_______________________________________________________________________

Dr. Christian Biert�mpfel
Laboratory of Molecular Biology

NIDDK/National Institutes of Health              phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03          fax:   +1 301 496 0201
Bethesda, MD 20892-0580
USA
_______________________________________________________________________

#1690

From: "ina_lindemann" <ina_lindemann@...>
Date: Mon Jun 2, 2008 12:15 pm
Subject: Patch for covalently bound ligand in generate.inp/CNS

ina_lindemann

Hey,
I got a problem during the refinement of my crystal structure in
CNS. The protein has a covalently bound inhibitor. I specified the
inhibitor's pdb in -ligand files- of the generate.pdb.
But I don't know how to write the patch for the covalent binding and
how to change the topology and parameter files.
For any help I would be very thankful.
Bye,
Ina

#1691

From: "Stephanie K�rber" <Stephie2801@...>
Date: Tue Jun 3, 2008 1:24 pm
Subject: installing CNS on windows

stephiekorber

Hi,

i am trying to install CNS on windows, so i downloaded the .exe file for
windows, but it seems that this is damaged. Is there an other way to install CNS
on windows machines??
Thank you for help!!

Viele Gr��e,
Stephie
--
GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen!
Jetzt dabei sein: http://www.shortview.de/?mc=sv_ext_mf@gmx

#1692

From: "i_m_subh" <i_m_subh@...>
Date: Tue Jun 17, 2008 5:13 pm
Subject: Cross_rotation.inp running problem!

i_m_subh

Hi,
I am trying to run cross_rotation.inp(Molecular Replacement) file but
it is giving an error everytime.The program basically halts just after
reading the first HKL data.I have checked my input files but I would
like to know whether my hkl file header is the problem.( I generated
the HKL file from CCP4i MTZ to others).

My HKL file header  looks like this


   NREFlection=         104433
  ANOMalous=FALSE

  DECLare NAME=FOBS         DOMAin=RECIprocal   TYPE=COMP END

  DECLare NAME=SIGMA        DOMAin=RECIprocal   TYPE=REAL END

  INDE   -45    0    2

  INDE   -45    0    3

Could you guys please throw some light on this?
Is thre anything else I am missing?

Subhendu

#1693

From: Gerard DVD Kleywegt <gerard@...>
Date: Thu Jun 19, 2008 1:19 pm
Subject: Re: Cross_rotation.inp running problem!

gerard@...

if your reflection lines only contain indices, it means there is no data ...
where are your FOBS and SIGMA values?

>  INDE   -45    0    2

--gerard

******************************************************************
                          Gerard J.  Kleywegt
      [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                  Biomedical Centre  Box 596
                  SE-751 24 Uppsala  SWEDEN

      http://xray.bmc.uu.se/gerard/  mailto:gerard@...
******************************************************************
     The opinions in this message are fictional.  Any similarity
     to actual opinions, living or dead, is purely coincidental.
******************************************************************

#1694

From: Christina Bourne <bournecr@...>
Date: Thu Jun 19, 2008 9:19 pm
Subject: problem installing 1.2 on Ubuntu hardy 8.04

bournecr

Hello,
I am trying to install version 1.2 on my Ubuntu 8.04 system. Typing "sudo make install" returns:
-clip-
C compiler passes test
compiling: gfortran -w -O3 -malign-double -funroll-loops -ffast-math
linking: gfortran -w
At line 2 of file test_f.f
Fortran runtime error: Missing initial left parenthesis in format
symbol=%s; lookup in file=%s [%lu]

***** ERROR: problem with Fortran compiler *****
make[3]: *** [fortran-test] Error 2
make[2]: *** [compiler-test] Error 2
make[1]: *** [compiler-test] Error 2
compiler problems - stopping installation
please check compilers before retrying installation
make: *** [install] Error 1

I have gfortran (4.1 and 4.2) installed. I see a similar error on the installation pages, but it's to do with fort77. Maybe I just haven't gotten that far, but I don't think the solution is the same as for my problem (to re-compile f2c, which I do have installed).??

I have two copies (at intel-i686-linux/compiler-test/ and instlib/compiler-test/) of test_f.f and they are identical:
      program hello
      write(6, '(1X,A)') 'Hello_FORTRAN_world'
      end

Any suggestions appreciated,
Christina Bourne

#1695

From: Debajyoti Dutta <molbiol349@...>
Date: Sat Jun 28, 2008 2:43 pm
Subject: viewing map files

molbiol349

Hi,

I have prepared two map files after running self_rotation.inp. Is there any viewer to see those map files. Can O be used in this purpose. Can I use the outputs of self rotation function in molrep.

Thanx in advance

Debajyoti Dutta

Bring your gang together. Do your thing. Find your favourite Yahoo! Group.

#1696

From: "prem_tezu_poly" <prem_tezu_poly@...>
Date: Mon Jun 30, 2008 7:47 am
Subject: CNS-1.2 RDC parameter

prem_tezu_poly

Dear All,

I am the youngest member of this group. Hi to all of you.

I am trying to incorporate RDC data into my structure calculation.

I generated the MTF file and at the end i added the lines
2277 ' ' '144' 'GLU' 'OT2' 'OC' -0.570000 15.9990
2278 ' ' '500' 'ANI' 'X' 'XXX' 0.000000E+00 10.0000
2279 ' ' '500' 'ANI' 'Y' 'YYY' 0.000000E+00 10.0000
2280 ' ' '500' 'ANI' 'Z' 'ZZZ' 0.000000E+00 10.0000
2281 ' ' '500' 'ANI' 'OO' 'OOO' 0.000000E+00 10.0000
-1 ' ' ' ' ' ' ' ' ' ' -1.00000 -1.00000

and bond
2275 2277
2281 2278
2281 2279
2281 2270

and angle

2276 2275 2277
2278 2281 2279
2278 2281 2280
2279 2281 2280
-1 -1 -1

but upon trying to generate the extended_pdb
i am getting the following error message
%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
   bond energy constant missing.
   target bond length missing.
   ATOM1: SEGId="    ",  RESId="500 ",  NAME="OO  ",  CHEMical="OOO "
   ATOM2: SEGId="    ",  RESId="144 ",  NAME="HG1 ",  CHEMical="HA  "
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  %CODBON error encountered: program will be aborted.
    (CNS is in mode: SET ABORT=NORMal END)

Will you please help me?

Regards to ALL
PremPrakash

#1697

From: Gerard DVD Kleywegt <gerard@...>
Date: Mon Jun 30, 2008 12:45 pm
Subject: Re: viewing map files

gerard@...

> I have prepared two map files after running self_rotation.inp. Is there any
viewer to see those map files. Can O be used in this purpose. Can I use the
outputs of self rotation function in molrep.

it's a long time ago i did MR with x-plor/cns but if the map format is the
standard x-plor/cns one, you should be able to convert the file into a ccp4 or
O map with mapman and thus be able to view with any program that allows you to
view maps

--gerard

******************************************************************
                          Gerard J.  Kleywegt
      [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                  Biomedical Centre  Box 596
                  SE-751 24 Uppsala  SWEDEN

      http://xray.bmc.uu.se/gerard/  mailto:gerard@...
******************************************************************
     The opinions in this message are fictional.  Any similarity
     to actual opinions, living or dead, is purely coincidental.
******************************************************************

#1698

From: Kevin Jude <kjude@...>
Date: Mon Jun 30, 2008 5:43 pm
Subject: Re: CNS-1.2 RDC parameter

kmjxxx

I see two problems.  Looks like you've made a typo in your bond
definitions - atom 2270 is a hydrogen atom.  After correcting this, you
will need to define a target bond length and weight if you haven't
already; look at $CNS_SOLVE/libraries/toppar/protein_rep.param for the
appropriate format.

Best wishes
Kevin Jude


prem_tezu_poly wrote:
>
>
> Dear All,
>
> I am the youngest member of this group. Hi to all of you.
>
> I am trying to incorporate RDC data into my structure calculation.
>
> I generated the MTF file and at the end i added the lines
> 2277 ' ' '144' 'GLU' 'OT2' 'OC' -0.570000 15.9990
> 2278 ' ' '500' 'ANI' 'X' 'XXX' 0.000000E+00 10.0000
> 2279 ' ' '500' 'ANI' 'Y' 'YYY' 0.000000E+00 10.0000
> 2280 ' ' '500' 'ANI' 'Z' 'ZZZ' 0.000000E+00 10.0000
> 2281 ' ' '500' 'ANI' 'OO' 'OOO' 0.000000E+00 10.0000
> -1 ' ' ' ' ' ' ' ' ' ' -1.00000 -1.00000
>
> and bond
> 2275 2277
> 2281 2278
> 2281 2279
> 2281 2270
>
> and angle
>
> 2276 2275 2277
> 2278 2281 2279
> 2278 2281 2280
> 2279 2281 2280
> -1 -1 -1
>
> but upon trying to generate the extended_pdb
> i am getting the following error message
> %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
> bond energy constant missing.
> target bond length missing.
> ATOM1: SEGId=" ", RESId="500 ", NAME="OO ", CHEMical="OOO "
> ATOM2: SEGId=" ", RESId="144 ", NAME="HG1 ", CHEMical="HA "
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %CODBON error encountered: program will be aborted.
> (CNS is in mode: SET ABORT=NORMal END)
>
> Will you please help me?
>
> Regards to ALL
> PremPrakash
>
>
>

#1699

From: Debajyoti Dutta <molbiol349@...>
Date: Wed Jul 2, 2008 5:24 am
Subject: Error from translation.inp

molbiol349

Hi All,

I am executing translation.inp for a 2.0A data. I have sucessfully got the cross rotation output peaks. But when trying to run the translation.inp I am getting the following errors

RIGID: main coordinates set to best minimum
%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
ATOM: SEGId="O   ", RESId="338 ", NAME="S   ", CHEMical="SUF "
%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
ATOM: SEGId="O   ", RESId="338 ", NAME="O1 ", CHEMical="OUF "

%NBUPDA error encountered: program will be aborted.
   (CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.

Does I have to change the model.pdb (all the residues are there: generated by generate_easy, and contain ligands and waters) file or I have to fix or limit some bond parameters. I have set the resolution limits 30A to 2.0A for both cross rotation and translation inp.

Please help me as I am very new CNS user.

Thank you for your suggestions in advance.

Yours Sincerely
Debajyoti Dutta

Best Jokes, Best Friends, Best Food. Get all this and more on Best of Yahoo! Groups.

#1700

From: Gerard DVD Kleywegt <gerard@...>
Date: Wed Jul 2, 2008 8:36 am
Subject: Re: Error from translation.inp

gerard@...

well, you could fix the *symptom* by defining top/par for the ligand(s), but
for molecular replacement calculations you should really remove all ligands
and waters. count yourself lucky: this is one of those rare cases in life
where fixing the problem is less work than fixing the symptoms ;-)

--gerard

******************************************************************
                          Gerard J.  Kleywegt
      [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                  Biomedical Centre  Box 596
                  SE-751 24 Uppsala  SWEDEN

      http://xray.bmc.uu.se/gerard/  mailto:gerard@...
******************************************************************
     The opinions in this message are fictional.  Any similarity
     to actual opinions, living or dead, is purely coincidental.
******************************************************************

#1701

From: Debajyoti Dutta <molbiol349@...>
Date: Wed Jul 2, 2008 3:48 pm
Subject: Re: Error from translation.inp

molbiol349

Hi again,

Thank you all for your suggestions. I am very sorry for my incomplete mail. Actually translation.inp is giving error for may atoms I have taken only two to save space as probably all errors are related to same reason.

Initially I had prepared my model with generate_easy.inp but unfortunately the input PDB contain ligans and waters. But before that I prepared my model with generate.inp giving
inputs of ligans, waters and model differently. That time also translation.inp is also giving
the same error.

But I don't know how to prepare the ligand parameter file
CNS_TOPPAR:protein_rep.param). Please guide me.

Yous Sincerely
Debajyoti

--- On Wed, 2/7/08, Ed Pozharski <epozh001@...> wrote:

From: Ed Pozharski <epozh001@...>
Subject: Re: [cnsbb] Error from translation.inp
To: molbiol349@...
Date: Wednesday, 2 July, 2008, 6:35 PM

Sounds like you don't have the parameter file for the ligand.  Another
strange thing is that you seem to have two atoms from the residue with
the same segid (O) and resid (338) but different resname (SUF and OUF).

On Wed, 2008-07-02 at 10:54 +0530, Debajyoti Dutta wrote:
> 
> Hi All,
> 
> I am executing translation.inp for a 2.0A data. I have sucessfully got
> the cross rotation output peaks. But when trying to run the
> translation.inp I am getting the following errors
> 
> RIGID: main coordinates set to best minimum
>  %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
>   ATOM: SEGId="O   ",  RESId="338 ",  NAME="S  
",  CHEMical="SUF "
>
  %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
>   ATOM: SEGId="O   ",  RESId="338 ",  NAME="O1 
",  CHEMical="OUF "
> 
> %NBUPDA error encountered: program will be aborted.
>    (CNS is in mode: SET ABORT=NORMal END)
>  *****************************************************
>  ABORT mode will terminate program execution. 
>  *****************************************************
>  Program will stop immediately.
> 
> Does I have to change the model.pdb (all the residues are there:
> generated by generate_easy, and contain ligands and waters) file or I
> have to fix or limit some bond parameters. I have set the resolution
> limits 30A to 2.0A for both cross rotation and translation inp.
> 
> Please help me as I am very new CNS user.
> 
> Thank you for your suggestions in advance.
> 
> Yours Sincerely
> Debajyoti
 Dutta
>  
> 
> 
> 
> 
> 
> ______________________________________________________________________
> Best Jokes, Best Friends, Best Food. Get all this and more on Best of
> Yahoo! Groups.
> 
> 
>  
-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then
 respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

Explore your hobbies and interests. Click here to begin.

#1702

From: "prem_tezu_poly" <prem_tezu_poly@...>
Date: Thu Jul 3, 2008 4:57 am
Subject: Calculating RDC data from PDB

prem_tezu_poly

Dear All,

is there any way to calculate theoretically Residual Dipoar Coupling
value given a PDB structure.

How does the RDC calculated the obtained.

regards

Prem

#1703

From: Debajyoti Dutta <molbiol349@...>
Date: Thu Jul 3, 2008 5:22 pm
Subject: Re: Error from translation.inp

molbiol349

Hi all,

Thank you for all replies, suggestions. All helped me a lot.

Sincerely
Debajyoti

--- On Wed, 2/7/08, Ed Pozharski <epozh001@...> wrote:

From: Ed Pozharski <epozh001@...>
Subject: Re: [cnsbb] Error from translation.inp
To: molbiol349@...
Date: Wednesday, 2 July, 2008, 10:52 PM

Why don't you remove ligand and waters from the pdb-file?  In fact, you
MUST remove thme for molecular replacement.

Topology/parameter files can be generated manually (see CNS tutorial),
using xplo2d (Uppsala Software Factory) or PRODRG server.

On Wed, 2008-07-02 at 21:18 +0530, Debajyoti Dutta wrote:
> 
> Hi again,
> 
> Thank you all
 for your suggestions. I am very sorry for my incomplete
> mail. Actually translation.inp is giving error for may atoms I have
> taken only two to save space as probably all errors are related to
> same reason.
> 
> Initially I had prepared my model with generate_easy.inp but
> unfortunately  the input PDB contain ligans and waters. But before
> that I prepared my model with generate.inp giving 
> inputs of ligans, waters and model differently. That time also
> translation.inp is also giving 
> the same error.
> 
> But I don't know how to prepare the ligand parameter file 
> CNS_TOPPAR:protein_rep.param). Please guide me. 
> 
> Yous Sincerely
> Debajyoti
> 
> 
> 
> 
> --- On Wed, 2/7/08, Ed Pozharski <epozh001@...> wrote:
>         From: Ed Pozharski <epozh001@...>
>         Subject: Re:
 [cnsbb] Error from translation.inp
>         To: molbiol349@...
>         Date: Wednesday, 2 July, 2008, 6:35 PM
>         
>         Sounds like you don't have the parameter file for the ligand. 
Another
>         strange thing is that you seem to have two atoms from the residue
with
>         the same segid (O) and resid (338) but different resname (SUF and
OUF).
>         
>         On Wed, 2008-07-02 at 10:54 +0530, Debajyoti Dutta wrote:
>         > 
>         > Hi All,
>         > 
>         > I am executing translation.inp for a 2.0A data. I have
sucessfully got
>         > the cross rotation output peaks. But when trying to run the
>         > translation.inp I am getting the following errors
>         > 
>         > RIGID: main coordinates set to best minimum
>         >  %NBUPDA-ERR: missing
 nonbonded Lennard-Jones parameters
%%%%%%%
>         >   ATOM: SEGId="O   ",  RESId="338 ", 
NAME="S  
>         ",  CHEMical="SUF "
>         >
>           %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%%
>         >   ATOM: SEGId="O   ",  RESId="338 ", 
NAME="O1 
>         ",  CHEMical="OUF "
>         > 
>         > %NBUPDA error encountered: program will be aborted.
>         >    (CNS is in mode: SET ABORT=NORMal END)
>         >  *****************************************************
>         >  ABORT mode will terminate program execution. 
>         >  *****************************************************
>         >  Program will stop immediately.
>         > 
>         > Does I have to change the model.pdb (all the residues are
there:
>         > generated by generate_easy, and contain
 ligands and waters)
file or I
>         > have to fix or limit some bond parameters. I have set the
resolution
>         > limits 30A to 2.0A for both cross rotation and translation
inp.
>         > 
>         > Please help me as I am very new CNS user.
>         > 
>         > Thank you for your suggestions in advance.
>         > 
>         > Yours Sincerely
>         > Debajyoti
>          Dutta
>         >  
>         > 
>         > 
>         > 
>         > 
>         > 
>         >
______________________________________________________________________
>         > Best Jokes, Best Friends, Best Food. Get all this and more on
Best of
>         > Yahoo! Groups.
>         > 
>         > 
>         >  
>         -- 
>         Edwin Pozharski, PhD, Assistant Professor
>         University of Maryland, Baltimore
>         ----------------------------------------------
>         When the Way is forgotten duty and justice appear;
>         Then knowledge and wisdom are born along with hypocrisy.
>         When harmonious relationships dissolve then
>          respect and devotion arise;
>         When a nation falls to chaos then loyalty and patriotism are born.
>         ------------------------------   / Lao Tse /
> 
> 
> ______________________________________________________________________
> Explore your hobbies and interests. Click here to begin.
-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and
 justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

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#1704

From: "i_m_subh" <i_m_subh@...>
Date: Sat Jul 5, 2008 1:44 am
Subject: Solved phases in a different Space group!

i_m_subh

Hi,
I have solved phases in a different space group than the one that was
in the synchrotron data.
Do I have to change the space group in the data file before I use
it(as input file) for model building in ARP/wARP now?

Thanks
subhendu

#1705

From: "i_m_subh" <i_m_subh@...>
Date: Sat Jul 5, 2008 9:43 pm
Subject: converting truncate.mtz to cns

i_m_subh

Hi,
I am tryting to convert truncated mtz data file to cns. The mtz header
looks like this
H K L IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-) F SIGF DANO SIGDANO
F(+) SIGF(+) F(-) SIGF(-) ISYM

As this data was supposed to be a derivative but I didn't get any
anomlous signal I want it to be used as Native.(it diffracted to 1.4A)

When I run mtz2cns after assigning the labels as follows

FP=IMEAN SIGFP=SIGIMEAN FPH=I(+) SIGFPH=SIGI(+) FC=I(-) PHIC=ISYM
FOM=SIGI(-) DP=F SIGDP=SIGF F(+)=F(+) SIGF(+)=SIGF(+) F(-)=F(-)
SIGF(-)=SIGF(-)

it fails to do the job with error like this below

From ccp4_lrassn: expected type F does not match file type J for
column IMEAN
From ccp4_lrassn: expected type F does not match file type K for
column I(+)
From ccp4_lrassn: expected type Q does not match file type M for
column SIGI(+)
From ccp4_lrassn: expected type F does not match file type K for
column I(-)
From ccp4_lrassn: expected type P does not match file type Y for
column ISYM
From ccp4_lrassn: expected type W does not match file type M for
column SIGI(-)
From ccp4_lrassn: expected type D does not match file type F for column F

Could you please help me out?

Thanks