Hello All: I am having a problem with refine.inp. Actually, it is the map building part that is causing the problem. The refinement is carried out and .pdb...
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Gerard DVD Kleywegt
gerard@...
Feb 2, 2004 8:56 pm
... the combination of your a-axis length, the resolution and the map grid makes that cns feels that the grid along x is too coarse. in the refine.inp file ...
860
Zhenya
fadeev
Feb 3, 2004 4:50 am
hi, i am trying to calculate certain stats about my structures and print them out in a separate file, not in the main output stream. i would appreciate if...
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James Stroud
stroudj@...
Feb 3, 2004 5:49 am
Use STDERR. You can send the STDOUT of "command" to one file ("file1") and STDERR to another ("file2") with this construct: ( command > file1 ) >& file2...
862
brian.o.smith@...
brian_o_smith
Feb 3, 2004 9:22 am
... You want something like: set print_file filename end and to return to the stdout: set print_file=OUTPUT end ... b.smith at bio.gla.ac.uk...
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Zhenya
fadeev
Feb 3, 2004 5:51 pm
also if you need to link this group in a special way different from peptide links, you'll need to build a patch residue (topology presidue) similar to PEPT (in...
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Zhenya
fadeev
Feb 3, 2004 5:52 pm
i think it is not too important how you'd define the formyl proton. if you look into parallhdg.pro file you will see that almost all the parameters are the...
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Zhenya
fadeev
Feb 3, 2004 5:53 pm
set display=file end works! thanks for your responses! evgeny...
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Rakesh Dabas
dabasrk
Feb 5, 2004 4:11 pm
Dear all, Hereby i am inviting for the 8th World Multi-Conference on Systemics, Cybernetics and Informatics 2004 (SCI-2004) from July 18-21, 2004 at Orlando,...
867
Paul Paukstelis
paul@...
Feb 6, 2004 2:42 pm
I've been using NOE distance restraints (based on biochemical data) in CNS to try and dock an RNA structure onto a protein structure. I would like to try...
868
Paul Paukstelis
paul@...
Feb 6, 2004 5:26 pm
Sorry folks, I figured out how to do this, minus one little thing. How do I call random numbers in CNS?...
869
K. Anderson
khristine_an...
Feb 9, 2004 5:38 pm
Post-doctoral/Research Scientist - Toronto, ON, Canada I've been asked to assist in recruiting a Post-doctoral/Research Scientist for a biopharmaceutical...
870
Evgeny Fadeev
fadeev
Feb 12, 2004 7:05 am
either way would work, but i think presidue is more economical in terms of typing(in addition you might need to define some parameters for the formyl; xplor ...
871
Zhenya
fadeev
Feb 12, 2004 7:05 am
to get random number use evaluate ($a=random()) that will set $a to a number within (0;1) interval you can also use set seed=$n end to use a different random...
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Zhenya
fadeev
Feb 12, 2004 7:05 am
Hi, i just have a small question about the use of <R-3> noe distance averaging option. i understand that this option calculates the distance between a proton...
873
Robert Sweet
sweet@...
Feb 13, 2004 6:25 pm
There are still positions available, especially for Experimenters. If some who applied as Observers would like to apply also as Experimenters, please do so,...
874
Sanishvili, Ruslan
rsanishvili@...
Feb 16, 2004 4:41 pm
Dear PX beamline users, Here at APS, as most probably at other synchrotrons as well, attempts will be made to standardize the user software for beamline...
875
lenize@...
Feb 17, 2004 4:10 pm
Hi everybody, I need to use the cross-validation method to evaluate the degree of conformational variability of my structures and I am trying to use the script...
876
=?gb2312?B??=
ydyu@...
Feb 18, 2004 10:49 am
hi, all, I am refining a structure whose lattice packing is very tight. Automatic water picking run in CNS yielded waters around one molecule but also many...
877
Gerard DVD Kleywegt
gerard@...
Feb 18, 2004 10:52 am
... if you run what_check you will find that this is one of the tests it carries out. it will identify such waters and provide you with the new coordinates....
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M. Kirsten Frank
kirstenfrank2
Feb 18, 2004 2:27 pm
Has anybody tried this in Xplor? I am documenting Xplor-NIh and I would like to add an example like this to the standard examples. Sincerely, Kirsten Frank...
879
Gerard DVD Kleywegt
gerard@...
Feb 20, 2004 5:31 pm
Dear structural(-ly interested) biologist ! HIC-Up, the Hetero-compound Information Centre - Uppsala, has been updated and now contains information on 4,669...
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Nuno S.L.S. Ferreira
nunolf2003
Feb 20, 2004 8:42 pm
Hi all I've read in the Xplor-NIH homepage (did not knew this soft, till yesterday; ups, not doing my everyday search :), that: "CNS is no longer under...
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Ganapathy Sarma
sarma@...
Feb 21, 2004 8:08 am
Hello all- This might be a very FAQ! Is there a way to refine over-oxidized cysteines in CNS? Any help is appreciated. Thanks, Sarma. ... Ganapathy Sarma ...
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florent.barbault
flotchinson
Feb 23, 2004 8:32 am
Hi all Personally I tried XPLOR-NIH and CNS for NMR structure determination. There is no real difference for me. In fact, it is the same Torsion Angle ...
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Gerard DVD Kleywegt
gerard@...
Feb 23, 2004 4:42 pm
... i assume you mean things like S-hydroxycysteine (http://xray.bmc.uu.se/hicup/CSO) etc. ? you can either define them as new residue types, or (probably ...
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Haydyn Mertens
haydyn_mertens
Feb 24, 2004 12:53 am
Hi guys, although the torsion angle dynamics protocols for both Xplor-NIH and CNS are the same (the original TAD/Cartesian Stein, Rice and Brunger protocol), a...
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florent.barbault
flotchinson
Feb 24, 2004 9:30 am
Hi Frank and Haydyn, In fact I didn't use the internal dynamics. It sounds like better even if I didn't have a good souvenir of dyana calculation. I was using...
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Robert Sweet
sweet@...
Feb 26, 2004 4:25 pm
On 15 March there will be a workshop to discuss the possibilities for a new synchrotron radiation source at Brookhaven National Laboratory. This is the same...
887
rim3r
Feb 27, 2004 8:07 am
On the CNS web site (http://cns.csb.yale.edu/v1.1/), they have a poorly detailed "syntax manual". Under which there is a description of: topology...
