Is there a way to copy a value of a standard parameter into a new symbol
in CNS?. Something like

	 newvalue = oldvalue.
I tried
	 evaluate($newsegid=segid)

The symbol 'newsegid' is not assigned the value of segid from the pdb
file, but the literal string 'segid' is assigned.

[I am not trying to change the segid. So please do not refer me to
'rename_segid.inp'. I need a way to copy the value into a temporary
variable]

Please reply to sundar@...

Thanks
Sundar

--
------------------------------------------------------------------------------
M. Sundaramoorthy, Ph.D.  E-mail: msundar@...
University of Kansas Medical Center Phone: (913) 588-6574
Department of Biochemistry & 	 Fax  : (913) 588-7007

try: evaluate($newsegid=$segid)

--dvd

On 24 Mar 2001, M Sundaramoorthy wrote:

> Is there a way to copy a value of a standard parameter into a new symbol
> in CNS?. Something like
>
>  newvalue = oldvalue.
> I tried
>  evaluate($newsegid=segid)
>
> The symbol 'newsegid' is not assigned the value of segid from the pdb
> file, but the literal string 'segid' is assigned.
>
> [I am not trying to change the segid. So please do not refer me to
> 'rename_segid.inp'. I need a way to copy the value into a temporary
> variable]
>
> Please reply to sundar@...
>
> Thanks
> Sundar
>
> --
> ------------------------------------------------------------------------------
> M. Sundaramoorthy, Ph.D.  E-mail: msundar@...
> University of Kansas Medical Center Phone: (913) 588-6574
> Department of Biochemistry & 	 Fax  : (913) 588-7007
>


--gerard

******************************************************************
                         Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshevik 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.
******************************************************************


---

Dear All,

I would like to clarify the position of MSI regarding X-PLOR/CNS/CNX and to
clear up any misunderstandings that were reported in an email recently
posted to this list. MSI is strongly committed to the development and
enhancement of CNX.    As you may know, CNX is the result of the merger of
the code basis of X-PLOR 98/98.1 from MSI and CNS from Yale.  MSI has
continued to make regular releases of CNX with the first release CNX 2000
in early 2000, followed by the recently release of CNX 2000.1 For more
information about what was included in these releases please see the
following web page: http://www.msi.com/life/products/cnx/

We have developed these releases both through internal development efforts
and external collaborations. In addition, we are currently developing CNX
2001 which will include new functionality.  We expect CNX 2001 to be
released in Fall 2001.  CNX will extend further the functionality of CNS
and we will try to follow closely needs of crystallographic and NMR
community to develop new functionality in CNX according to these needs.

On MSI's website you can download a one-month trial of the current release
CNX 2000.1:  http://www.msi.com/download/cnx/cnx_download.html (Academic
users can obtain this downloadable version for a nominal fee).

MSI remains committed to developing and supporting CNX. If you have any
questions/concerns related to CNX, please feel free to contact me at
cnx@...

Regards

David Edwards
--------------------------------------------------------------------------------\
---------

David J. Edwards, Ph.D.                                 dje@...
Senior Product Manager, Structural Proteomics   Tel: (858) 799 5374
Simulations & Modeling Product Division         Fax: (858) 458 0136
Molecular Simulations Inc.                              http://www.msi.com
9685 Scranton Road
San Diego, CA 92121-3752.
--------------------------------------------------------------------------------\
----------

---

Hi there,

As a starting crystallographer, I 'm encoutering problems with adding
hydrogens to my protein structure, using CNS... in particular,
hydrogens on histidines (these are all charged) are often not in the
plane of the histidine, which should be the case for an aromatic
residue. All suggestions are highly appreciated...



--
Stefan Loverix
Vrije Universiteit Brussel
Instituut voor Moleculaire Biologie/Biotechnologie
Dienst Ultrastruktuur
Paardenstraat 65,
B- 1640 Sint-Genesius-Rode
Belgium
Tel: 32/2/359 02 68
Fax: 32/2/359 02 89
Email: SLOVERIX@...

i suspect that this is due to the initial
B-factor correction (default is 'anisotropic'
but you can change this to 'no' if you like)

--dvd


On 28 Mar 2001, Markus Meier wrote:

> Dear all
>
> Using the provided script minimize.inp of CNS Ver. 1.0, the B-factors
> are changed comparing input and output file by a small amount of 0.01
> (they are supposed to be constant).
> If I use the script bindividual.inp and fix part of the B-factors in the
> structure the output B-factors are even changed by a larger amount
> (0.11) in the fixed part.
>
> I am not happy about this, even though the changes are small. Did anyone
> else have the same problem (and has probably a fix for it)?
>
> Thanks
> Markus
>
> Markus Meier
> MIH
> Biozentrum der Universitaet Basel
> Basel
> Switzerland
>
> ---
>


--gerard

******************************************************************
                         Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshevik 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.
******************************************************************


---

ICMSB2001
International Conference on Molecular Structural Biology
    Vienna, Austria  September 5.-9. 2001

              !!! Call for Abstracts !!!

You can now register for the ICMSB2001 via the homepage at

http://pharmchem.kfunigraz.ac.at/icmsb2001/

Abstracts can be sent electronically or by post.
Visit the homepage to view the entire scientific programme,
with sessions on:

Structural Molecular Biology: Ad Bax (NIH), Venki Ramakrishnan
                 (MRC Cambridge), Brian Sykes (University of Alberta)

The Protein Factory: Pirkko Vihko (University of Helsinki)

Macromolecular Structures: Johann Deisenhofer (Texas University),
                 Dino Moras (Université Louis Pasteur), John Walker (MRC
Cambridge),
                 Ian Wilson (Scripps Institute)

Folding and Function: Brian Matthews (University of Oregon), Eugene
Shakhnovich
                 (Harvard University), Manfred Sippl (University of Salzburg)

Structure-Based Design: Torben Borchert (Novozymes), Ursula Egner
(Schering),
                  Kal Ramnarayan (Structural Bioinformatics Inc.), Myriam
Altamirano
                  (MRC, Cambridge)

Structural Genomics: Barry Honig (Columbia University), Malcolm Weir
(Inpharmatica Ltd.),
                 Tom Peat (Structural GenomiX Inc.), Andrej Sali (Rockefeller
University)

If you need any further information please contact the conference
secretariat:

Dr. Andreas Kungl
Austrian Chemical Society (GÖCH),
Biochemistry Subgroup
c/o Institute of Pharmaceutical Chemistry,
University of Graz, Universitätsplatz 1,
A-8010 Graz
Tel.: +43 316 380 5373
Fax: +43 316 382541
E-Mail: andreas.kungl@...


---

Dear all

Using the provided script minimize.inp of CNS Ver. 1.0, the B-factors
are changed comparing input and output file by a small amount of 0.01
(they are supposed to be constant).
If I use the script bindividual.inp and fix part of the B-factors in the
structure the output B-factors are even changed by a larger amount
(0.11) in the fixed part.

I am not happy about this, even though the changes are small. Did anyone
else have the same problem (and has probably a fix for it)?

Thanks
Markus

Markus Meier
MIH
Biozentrum der Universitaet Basel
Basel
Switzerland

---

I am not being successful in generating in CNS the mtf and pdb file for a carbohydrate (gal(alpha1-3)-gal). I am not being able to do the alpha1-3 link. I also did not find Gal-Alpha in the topology file for carbohydrates (only Gal beta). I wonder if I will have to create a new topology file.
I would appreciate any help.

Regards

Fabio

-- 
___________________________________________________________
Prof. Fabio C. L. Almeida
Centro Nacional de Ressonancia Magnetica Nuclear - CNRMN
Departamento de Bioquimica Medica - ICB
Universidade Federal do Rio de Janeiro
Av.Brig. Trompowiski s/n CCS - Sala E10
Cidade Universitaria - Rio de Janeiro- RJ, 21941-590
tel. +55-21-280-6041 /103          Fax: +55-21-270-8647
falmeida@...  http://cnrmn.bioqmed.ufrj.br
------------------------------------------------------------

Hi,
	 If anyone has any tips on how to avoid NMR structure calculations
getting trapped in knotted states using torsion angle dynamics in CNS, I
would love to hear them.  I've tried protocols à la anneal.inp from the
standard release and also along the lines used in the ARIA protocols from
Michael Nilges' lab. My case is perhaps trickier than average - two module
fragment using plenty of ambiguous NOEs.  In the initial stages at high
temp, the two modules collapse together satisfying the NOEs, but as the
Van der Waals repulsion comes up and the modules push apart knots get
trapped - particularly the inter-modular linker sticking through the
middle of an adjacent loop.  I can calculate respectable structures using
cartesian space dynamics, but TAD is supposed to be more efficient ain't
it?

Any ideas?

Brian Smith

Dr. Brian O. Smith ----------------------- Brian.O.Smith@...
Institute of Cell and Molecular Biology, University of Edinburgh,
             King's Buildings, Edinburgh EH9 3JR, UK.
Tel: 0131 650 7051/7045/4704                   Fax: 0131 650 7055

I would like to post the following opening for a postdoctoral fellowship
in protein crystallography:

An NSF-supported postdoctoral position is available on a project
involving the incorporation of unnatural amino acids to alter the
specificity of existing enzymes and to create new enzyme catalysts. A
motivated candidate with expertise in protein crystallography is sought
who is also interested in expanding their knowledge of enzymology. Our
laboratories are well-equipped for enzyme purification and
characterization, and for molecular and structural biology studies. The
Chemistry Department at the University of Toledo is housed in Wolfe
Hall, a modern research laboratory that is also the home of the Ohio
Crystallography consortium, and is equipped with both small molecule CCD
and R-Axis diffractometers and a network of SGI workstations for data
analysis.  Interested and qualified applicants should send a CV and a
summary of research experiences and interests to: Dr. Ronald E. Viola,
Department of Chemistry, University of Toledo, Toledo, OH 43606 or
electronically at: ron.viola@...

Thank you for any help that you can provide in making this position
known to the crystallography community.

Sincerely,
Dr. Ronald Viola


---

I think the "misunderstandings that were reported in an email recently" may
be a vague reference to the suggestion that CNS is a dieing program. It may
not have been explicitly stated in the "recent email" but it was implicit
that CNS would be dieing due to it's being commercialized. I suspect that
MSI will no longer distribute this for free to academic users, as Brunger
did, and I presume that the source will no longer be distributed. Perhaps
David will clarify these points.

-----Original Message-----
From: owner-x-plor@... [mailto:owner-x-plor@...]On
Behalf Of David Edwards
Sent: Sunday, March 25, 2001 5:49 PM
To: x-plor@...
Subject: RE: Help with obtaining/resurrecting x-plor/cns



Dear All,

I would like to clarify the position of MSI regarding X-PLOR/CNS/CNX and to
clear up any misunderstandings that were reported in an email recently
posted to this list. MSI is strongly committed to the development and
enhancement of CNX.    As you may know, CNX is the result of the merger of
the code basis of X-PLOR 98/98.1 from MSI and CNS from Yale.  MSI has
continued to make regular releases of CNX with the first release CNX 2000
in early 2000, followed by the recently release of CNX 2000.1 For more
information about what was included in these releases please see the
following web page: http://www.msi.com/life/products/cnx/

We have developed these releases both through internal development efforts
and external collaborations. In addition, we are currently developing CNX
2001 which will include new functionality.  We expect CNX 2001 to be
released in Fall 2001.  CNX will extend further the functionality of CNS
and we will try to follow closely needs of crystallographic and NMR
community to develop new functionality in CNX according to these needs.

On MSI's website you can download a one-month trial of the current release
CNX 2000.1:  http://www.msi.com/download/cnx/cnx_download.html (Academic
users can obtain this downloadable version for a nominal fee).

MSI remains committed to developing and supporting CNX. If you have any
questions/concerns related to CNX, please feel free to contact me at
cnx@...

Regards

David Edwards
----------------------------------------------------------------------------
-------------

David J. Edwards, Ph.D.                                 dje@...
Senior Product Manager, Structural Proteomics   Tel: (858) 799 5374
Simulations & Modeling Product Division         Fax: (858) 458 0136
Molecular Simulations Inc.                              http://www.msi.com
9685 Scranton Road
San Diego, CA 92121-3752.
----------------------------------------------------------------------------
--------------

---


---

Add the following line to your CONFIG.SYS:

SHELL=C:\WINDOWS\COMMAND.COM C:\ /E:8192 /P

then reboot and try again, should work. :)

XF

----- Original Message -----
From: ""matt meyer"" <mgm10@...>
To: <x-plor@...>
Sent: Wednesday, April 04, 2001 4:45 PM
Subject: cns win98


> Strangely, when I run cns_solve_env.bat on this machine running windows 98
> SE
> It replies:
> "Bad command or file name"
> "Out of environment space" (9 times)
> I must have some windows setting wrong
> Any PC users, who've had this problem?
> Thanks in advance
>
>
> -------------------------------------------
> Matthew G. Meyer
> 6 Althouse Laboratory
> Dept of Biochemistry & Molecular Biology
> Penn State University
> University Park, PA 16802
> (814) 865-8383
>
> ---
>
>

---

Strangely, when I run cns_solve_env.bat on this machine running windows 98
SE
It replies:
"Bad command or file name"
"Out of environment space" (9 times)
I must have some windows setting wrong
Any PC users, who've had this problem?
Thanks in advance


-------------------------------------------
Matthew G. Meyer
6 Althouse Laboratory
Dept of Biochemistry & Molecular Biology
Penn State University
University Park, PA 16802
(814) 865-8383

---

Dear CNS/X-plor users,

The X-plor/CNS support newsgroup bionet.software.x-plor
(simultaneously a mailing list x-plor@...) has in recent
years increasingly been target for unrelated postings ("spam"). Many
users and CNS-experts have therefore unsubscribed from the list
and/or use it rarely.

I took the freedom to create a new moderated mailing list, which
forwards messages from bionet.software.x-plor. Messages not related
to Structural Biology are manually filtered out and only then
forwarded to the list members. This way one can again "dare" to
follow and participate in discussions on CNS/X-plor.

The list address of the moderated list is cnsbb@yahoogroups.com. To
subscribe to this list send an e-mail to
cnsbb-subscribe@yahoogroups.com. The homepage of the list is
http://groups.yahoo.com/group/cnsbb. If you hate advertisements,
you'll find an ads-free list archive at
http://chips.csb.ki.se/cnsbb/. Please be aware that postings to this
new list are not forwarded to bionet.software.x-plor /
x-plor@.... Moderating is very easy, but requires manual
interaction. If you would be ready to co-moderate the list let me
please know.

I'm not sure about the level of support, which will be offered on the
X-plor list in the future, even if there would be no spam anymore.
The intensity of discussions or rather the lack of them are somewhat
disillusioning ... We use CNS a lot in our group and would certainly
have benefit of a functioning support forum.

Regards,

Winfried Meining


--------------------------------------------
Dr. Winfried Meining
Södertörns Högskola & Karolinska Institutet
Dept. of Biosciences at NOVUM, CSB
S-14157 Huddinge, Sweden
Tel.: +46-(0)8-6083-336
Fax : +46-(0)8-6089-290
http://www.csb.ki.se/xray/
--------------------------------------------

---

Dear all,

I am winding up the refinement with R_cryst=19.2% and R_free=23.8% for a
2.2A data.  Everything is fine except few residues (about 2%) having large
deviation for N-Ca-C angle (some are more than +/- 10degrees).  (2fo-fc)
maps hav good density for these residues.  I have used CNS 1.0 for
refinement.  I have used the default weights throughout the refinement.

Is it ok to have that many deviations? If not, how to minimize the
numbers?  Manipulating weights could be a way out. But are there any
otherthings which I should look into?

regards,
Anil

  _______________________________________________________________________
    Anil K. Padyana, Department of Physics, Indian Institute of Science,
    Bangalore - 560 012, INDIA Phone:+91-80-3092718 FAX:+91-80-3602602
  _______________________________________________________________________

Dear all,
can I download the articles posted before on the www.bio.net/hypermail/X-PLOR//?
I think I can learn much from the questions asked and the answers before.

I want to download them on my local computer and can read them locally, needing
not to access to the www web.

thanks,
Rong-Jin Guan

On 9 Apr 2001, at 19:03, you wrote:

> Dear all,
> can I download the articles posted before on the
> www.bio.net/hypermail/X-PLOR//? I think I can learn much from the
> questions asked and the answers before.

Just connect via anonymous ftp to ftp.bio.net and go to
/pub/BIOSCI/ARCHIVE/x-plor

You will find monthwise filed archives of bionet.software.x-plor.

Best regards,
Winfried


>
> I want to download them on my local computer and can read them locally,
needing
> not to access to the www web.
>
> thanks,
> Rong-Jin Guan
>
> ---------------------------------------------------------------------------
> To unsubscribe from this group, send an email to:
> cnsbb-unsubscribe@yahoogroups.com. Postings to cnsbb@yahoogroups.com are
> not re-forwarded to bionet.software.x-plor.
>
>
> Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
>
>



-------------------------------------------
Dr. Winfried Meining
Södertörns Högskola & Karolinska Institutet
Department of Biosciences, NOVUM
Center for Structural Biochemistry
S-14157 Huddinge, Sweden
Tel.: +46-(0)8-6083-336
Fax : +46-(0)8-6089-290

Dear all,

Some of you might still wonder how to unsubscribe from
x-plor@@hgmp.mrc.ac.uk or x-plor@....

Here is some information pertaining requests to unsubscribe:

----

If the subscribed e-mail address is the same as your current e-mail
address simply send an e-mail to majordomo@... with the
line

unsubscribe x-plor

in the body of the message.

----

For the case that the subscribed e-mail address is not the same as
your current e-mail address Jurgen F. Doreleijers has given an useful
advice:

" ...
I subscribed with an email address: jurgen@... where
bmrb.wisc.edu is actually an alias for the machine
yola.bmrb.wisc.edu.

The solution (thanks to Jeff Vargason) is to manually set the
outgoing domain name of the unsubscribing email message for the
unsubscribing email. This can be done in pine by setting the option
[S (Setup), C (Config)] "user-domain" to, in my case:
"bmrb.wisc.edu". I don't know of other email programs that can do
this though.
..."

----

Please do not send administrative commands to
x-plor@.../x-plor@....

To subscribe to cnsbb@yahoogroups.com just send an e-mail (can be an
empty e-mail) to cnsbb-subscribe@yahoogroups.com.

Best regards,
Winfried



-------------------------------------------
Dr. Winfried Meining
Södertörns Högskola & Karolinska Institutet
Department of Biosciences, NOVUM
Center for Structural Biochemistry
S-14157 Huddinge, Sweden
Tel.: +46-(0)8-6083-336
Fax : +46-(0)8-6089-290
http://www.csb.ki.se/xray/

---

Dear all,

When I am trying to run average_map.inp on a map from density_modify.inp or
on a map from model_map.inp, I get the error message "unit cell parameters
incompatible" and the information that my unit cell parameters are 107.9800
107.9800  172.7200  instead of expected  107.9820  107.9820  172.7250. Does
anybody know how to overcome this problem?

Regards, Mikael Karlström
------------------------------------------------------------
Mikael Karlström, Ph.D. Student
Karolinska Institute, Center for Structural Biochemistry
Department of Biosciences at Novum
Haelsovaegen 7-9, S-14157 Huddinge, SWEDEN
phone  :   +46-8-6089-178           Fax :  +46-8-6089-290
e-mail :   mikael.karlstrom@...
Internet : http://www.csb.ki.se/xray/micke/mikael.html
------------------------------------------------------------

i don't know, but i suspect that cns has the good
sense to distrust cell axes with an apparent
precision of 6 digits and cuts them at 0.01 A
(and with axes > 100 A even that may be too
optimistic). precision should be determined
by your experiment, not by FORMAT statements

--dvd

> When I am trying to run average_map.inp on a map from density_modify.inp or
> on a map from model_map.inp, I get the error message "unit cell parameters
> incompatible" and the information that my unit cell parameters are 107.9800
> 107.9800  172.7200  instead of expected  107.9820  107.9820  172.7250. Does
> anybody know how to overcome this problem?

******************************************************************
                         Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshevik 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.
******************************************************************

Hello,

I am using anomalous data in the refinement of a Se-Met protein. I have
noticed that there is a libraries for anomalous data collected at the
wavelengths of Cu and Mo anodes:

cns_solve_1.0/libraries/xray/anom_cu.lib
cns_solve_1.0/libraries/xray/anom_mo.lib

But what about lambda=0.97945 A. Is there a program that can generate
the anom_desired_lambda.lib.

Thanks, joao.

--
Joao Alexandre R G Barbosa
National Research Council (NRC)
Biotechnology Research Institute (BRI)
6100 Royalmount Ave.
Montreal, Quebec, Canada
H4P 2R2

phone : (514) 496-6173
fax   : (514) 496-5143
e-mail: joao@...

When I try to run the fix_dna_rna utility I get the following error
message:

"resconv" may clash with future reserved word at
/usr2/local/bin/CNS/cns_solve_1.0/sgi-r4k5k-irix-6.3/utils/fix_dna_rna
line 15.
Syntax error in file
/usr2/local/bin/CNS/cns_solve_1.0/sgi-r4k5k-irix-6.3/utils/fix_dna_rna
at line 15, next 2 tokens "resconv("
"my" may clash with future reserved word at
/usr2/local/bin/CNS/cns_solve_1.0/sgi-r4k5k-irix-6.3/utils/fix_dna_rna
line 28.
Syntax error in file
/usr2/local/bin/CNS/cns_solve_1.0/sgi-r4k5k-irix-6.3/utils/fix_dna_rna
at line 28, next 2 tokens "my $rn "
Syntax error in file
/usr2/local/bin/CNS/cns_solve_1.0/sgi-r4k5k-irix-6.3/utils/fix_dna_rna
at line 32, next 2 tokens "=>"
Execution of
/usr2/local/bin/CNS/cns_solve_1.0/sgi-r4k5k-irix-6.3/utils/fix_dna_rna
aborted due to compilation errors.


Any suggestions as to how to fix this would be greatly appreciated.

--
*****************************************
Angela Toms
Department of Chemistry
The University of Manitoba
Winnipeg, Manitoba  R3T 2N2

Phone (204) 474-6267
FAX   (204) 474-7608
*****************************************

i suspect you have an old version of perl
(try: perl -v)

i suspect you need perl 5

--gerard

******************************************************************
                         Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshevik 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.
******************************************************************


---

Dear all,
I have two molecules in the asymmetric unit, one have very good
density in the map, while some residues of the other molecule have
poor density. I have refined the structure to R=17% and Rf=19% using
CNS.
Now shall I average the density of the two molecules to improve the
second molecule's density?

Thanks in advance.

Rong-Jin Guan

1) You can't unsubscribe by sending an unsubscribe message to the mail
    reflector. There's an administration address reserved for this
    purpose. It should not require a Ph.D. to find out what it is.

2) By sending administratory messages to the main list you're
    contaminating our mailboxes and offer your addresses to spam
    spiders trawling the mirror USENET newsgroup. This is probably
    not what you want, unless you're posting from a sacrificial
    account.

Jeez.

On 11 Apr 2001, Silvia Spinelli wrote:

> unsubscribe
>
> --
> silvia SPINELLI                        Tel: 33.491164512
> AFMB-UMR 6098-CNRS-IFR1                FAX: 33.491164536
> 31, Chemin Joseph AIGUIER              e-mail:spinelli@...
> 13402 MARSEILLE, CX 20, France
> my home page: http://afmb.cnrs-mrs.fr/teams/spinelli.html

---

Hello,
I have started an NMR spectroscopic structure determination of a
calcium-binding protein with CNS. Now I am wondering how I can include
distance restraints between calcium ions and the protein?
I have first tried to generate the structure file (.mtf, with
sequences of the protein and the Ca2+-ions as the two input files)
with generate_seq.inp, then to create the extended structure (.pdb)
with generate_extended.inp and finally to anneal the extended
structure with NOE restraints.

My .mtf file looks like:
...
2627 'A' '176' 'GLY' 'OT1' 'OC' -0.570000 15.9990
2628 'A' '176' 'GLY' 'OT2' 'OC' -0.570000 15.9990
2629 'I' '1' 'CA2' 'CA+2' 'CA+2' 2.00000 40.0800
2630 'I' '2' 'CA2' 'CA+2' 'CA+2' 2.00000 40.0800
2631 'I' '3' 'CA2' 'CA+2' 'CA+2' 2.00000 40.0800
...

And my .pdb file has the form:
...
ATOM   2627  OT1 GLY   176     525.793  -4.793   3.500  1.00
0.00      A
ATOM   2628  OT2 GLY   176     525.227  -4.484   1.399  1.00
0.00      A
ATOM   2629 CA+2 CA2     1     534.168   4.300  13.304  1.00
0.00      I
ATOM   2630 CA+2 CA2     2     540.774   1.876   5.853  1.00
0.00      I
ATOM   2631 CA+2 CA2     3     542.746   8.443   0.941  1.00
0.00      I
...

What I get with an input restraint of the form:

assign (resid 65 and name OD1) (resid 1 and name CA2) 2.40 0.40 0.40

is an error message:

reading restraint     1
  %NOESET-ERR: error in selection - no atoms spec.
  %NOE-ERR: problem at     1  -999.000  -999.000  -999.000  -999.000

Does anyone know what I'm doing wrong?

Thank you in advance,

Helena Aitio
Institute of biotechnology
University of Helsinki, Finland

hi !
I think your statement should read as
assign (resid 65 and atmnam OD1) (resid 1 and atmnam CA2) 2.40 0.40
0.40

regards

jawahar



On Thu, 12 Apr 2001 helena.aitio@... wrote:

  >Hello,
  >I have started an NMR spectroscopic structure determination of a
  >calcium-binding protein with CNS. Now I am wondering how I can include
  >distance restraints between calcium ions and the protein?
  >I have first tried to generate the structure file (.mtf, with
  >sequences of the protein and the Ca2+-ions as the two input files)
  >with generate_seq.inp, then to create the extended structure (.pdb)
  >with generate_extended.inp and finally to anneal the extended
  >structure with NOE restraints.
  >
  >My .mtf file looks like:
  >...
  >2627 'A' '176' 'GLY' 'OT1' 'OC' -0.570000 15.9990
  >2628 'A' '176' 'GLY' 'OT2' 'OC' -0.570000 15.9990
  >2629 'I' '1' 'CA2' 'CA+2' 'CA+2' 2.00000 40.0800
  >2630 'I' '2' 'CA2' 'CA+2' 'CA+2' 2.00000 40.0800
  >2631 'I' '3' 'CA2' 'CA+2' 'CA+2' 2.00000 40.0800
  >...
  >
  >And my .pdb file has the form:
  >...
  >ATOM   2627  OT1 GLY   176     525.793  -4.793   3.500  1.00
  >0.00      A
  >ATOM   2628  OT2 GLY   176     525.227  -4.484   1.399  1.00
  >0.00      A
  >ATOM   2629 CA+2 CA2     1     534.168   4.300  13.304  1.00
  >0.00      I
  >ATOM   2630 CA+2 CA2     2     540.774   1.876   5.853  1.00
  >0.00      I
  >ATOM   2631 CA+2 CA2     3     542.746   8.443   0.941  1.00
  >0.00      I
  >...
  >
  >What I get with an input restraint of the form:
  >
  >assign (resid 65 and name OD1) (resid 1 and name CA2) 2.40 0.40 0.40
  >
  >is an error message:
  >
  >reading restraint     1
  > %NOESET-ERR: error in selection - no atoms spec.
  > %NOE-ERR: problem at     1  -999.000  -999.000  -999.000  -999.000
  >
  >Does anyone know what I'm doing wrong?
  >
  >Thank you in advance,
  >
  >Helena Aitio
  >Institute of biotechnology
  >University of Helsinki, Finland
  >
  >
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hej !

> ATOM   2631 CA+2 CA2     3     542.746   8.443   0.941  1.00
> 0.00      I

you call the atoms "CA+2" and the "residues" CA2; hence in:

> assign (resid 65 and name OD1) (resid 1 and name CA2) 2.40 0.40 0.40

you need to say ... (resid 1 and name CA+2) ...

(in general it might also be a good idea to throw
the segment id in the selection statement to be
sure that you are unambiguous)

--gerard

******************************************************************
                         Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshevik 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.
******************************************************************

Dear all,
in refinement, when seting free_R test, how many reflections are
suitable for test set? someone tole me it should be 500-2000. I
think the percentage should depend on the total number of reflections
and should have a reasonable range.

Thanks,
Rong-Jin Guan

Dear Crystallographer,

I have a heterocompound in my structure and I was not able to directly use
the topology and parameter files that I download directly from HIC-UP server
in CNS. Can anyone give me suggestions how to convert an Xplor topology and
parameter file to CNS files? Thanks.

Xiaoshan Min
UT Southwestern Medical Center at Dallas