HI all, does anyone have a script to convert dyana input restraint files (file.aco, file.upl used for NMR structure calculation) to CNS restraints files. ...
HI all, NMR calculation of protein structures: In th case of methyls of Val or Leu which are sometimes degenerate in the NMR spectrum, the structure...
HI, I am doing a NMR structure calculation on a protein I like to inroduce a cis-proline in my protein. I did not find it in the topology files. can someone...
Prem, Here is what we do for cis-prolines in CNS. Maybe you could repost this at the CNS users site. Dealing with Cis-Prolines in both DYANA and CNS for...
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Pilar Saiz Vela
psaiz@...
Aug 12, 2003 3:20 pm
Hi all! Does anybody know where/how can I find the correct values of dihedral and impropers for a naphthyl ring? I have tried the Dundee PRODRG Server and the...
744
Daan van Aalten
vdava@...
Aug 12, 2003 3:54 pm
Dear Pilar Sounds to me if PRODRG/HICUP were both right with proper/improper dihedral angles of 0.0 for a completely flat, aromatic, compound like a naphthyl ...
I would like to thank everyone that helped with suggestions for my recompiling and linking of my new CNS source code. I now have a rather trivial question. I...
Hello, I am using torsion angle dynamics in CNS 1.1 to solve the NMR structures of an RNA (running under windows). I am getting a strange error and was hoping...
Hello, I have a system running Redhat 9.0 and I'm trying to install CNS and X-Plor. But as some of you may know, there is a problem with the fort77 compiler. ...
748
Charles@...
Aug 15, 2003 1:05 pm
... Hash: SHA1 Hi-- ... Xplor-NIH (http://nmr.cit.nih.gov/xplor-nih/) version 2.9.1 runs (and compiles) fine on redhat 9 systems. The binary package ...
749
Harry M. Greenblatt
harry.greenblatt@...
Aug 17, 2003 6:35 am
BS"D ... It would be helpful to know the error. If the problem occurs during the initial compiler tests, it could be a simple problem of not finding the...
I am trying to use the "vector" option to do rigid body refinement. The rigid.inp requires the phases input from a reflection file containing complex array. I...
751
Mei-I Su
msu@...
Aug 21, 2003 4:08 pm
I was trying to calculate DNA structures which has 3 strands in it. There is a template, primer and downstream strand so it formed a gapped DNA. When I tried...
hi, all: I have no problem installing CNS on Redhat 9.0 linux. I downloaded both f2c and fort77 and used fort77 to compile. However, I have a problem with...
Dear Members, Give me your two cents... We are using a software which can read ONLY standard format PDB files (i.e. downloaded PDB files from...
754
rohini qamra
rohiniq@...
Aug 25, 2003 1:31 pm
Dear all, I have been facing a few problems while using cns for refinement. 1) The rigid body refinement does not seem to make any difference to the movements...
755
Daan van Aalten
vdava@...
Aug 25, 2003 3:58 pm
Hi Rohini Take a careful look at the logic behind your rigid domain definition. How can a residue be in the range (segid A and residue 1:20) AND AT THE SAME ...
756
rohini qamra
rohiniq@...
Aug 26, 2003 6:18 am
Dear All, I have a two fold symmetry for two molecules in an asu. The ncs matrix is however not identical for the various domains of the protein. I need to...
Dear all, is there any software to find out the SNPs of a particular gene. when i submitted to the SNP consortium i get different locus in the chromosomes and...
758
Gerard DVD Kleywegt
gerard@...
Aug 26, 2003 6:17 pm
... which aspects of x-plor-style pdb files does your software object to ? alternatively, which things does it expect but not encounter in such files ? ...
759
Sacha Uljon
uljon@...
Aug 27, 2003 5:04 am
During minimization, the following message appears in the log file: "Line search terminated LBFGS: maximum number of function evaluations reached CNSsolve>...
hi, all: Does anyone know how to set up the energy minimization for nmr structures in water bath using Xplor, or has the macro file that can share with me? I ...
Hello, Though there exist "pdbset" in ccp4 and "XPAND" they are not generating the symmetry related molecule in the proximity of the actual molecule. In O I...
Hello, Is there any program to generate the symmetry related molecule and give the output in PDB format? If yes,please let me know abt this. Thanks in advance....
763
Pilar Saiz Vela
psaiz@...
Sep 4, 2003 3:21 pm
Hi All, I have problems opening a .crd file with VMD. Can anybody explain me what this file exactly contain to know wether the problem is in my .crd file or, ...
hi, all: Does anyone know how to set up the energy minimization for nmr structures in water bath using Xplor, or has the macro file that can share with me? I ...
Hi there, Recently, I collected data on my protein in complex with an inhibitor to 2.65A resolution. The structure of the same protien has been solved before...
767
Olaf Gaiser
ogaiser@...
Sep 9, 2003 6:24 am
Dear all, I am using CNS (1.0) for NMR structure calculations. When comparing the best structures with the NOE distance restraints it turned out that a few of...
768
renhuai huang
huangrenhuai@...
Sep 9, 2003 3:46 pm
Dear Olaf, There are several average modes about the ambiguous Noe restraints of prochiral atoms. You can just have a look at the website: ...
