Hi all, As part of its recent winter update, the Protein Data Bank in Europe (PDBe; http://pdbe.org/) has improved its facility that allows for tandem searches...
2056
Gerard DVD Kleywegt
gerard@...
Apr 20, 2011 4:04 pm
In June 1999, staff of the Macromolecular Structure Database (MSD; nowadays known as the Protein Data Bank in Europe, http://pdbe.org/) at the European ...
2057
Gerard DVD Kleywegt
gerard@...
Apr 20, 2011 4:44 pm
Hi all, The Protein Data Bank in Europe (PDBe; http://pdbe.org) has vacancies for a (possibly junior) scientific programmer and for a system ...
2058
tublu bose
bose.tubl@...
Apr 24, 2011 4:41 pm
Dear all, I have a ligand molecule sitting across a symmetry axis. According to the FAQ, I should be able to modify the input files so that the symmetry...
2059
tublu bose
bose.tubl@...
Apr 25, 2011 7:24 pm
I did two separate rounds if annealing, one with the igroup statement and one without. The output pdb's are exactly superimposable, at least in the region of...
2060
b.nescaffe
May 2, 2011 12:29 pm
Hi CNS users i am downloading the cns and when i try to install the CNS then i facing some problem.My problem is there written first edit the file...
2061
chitayat920
May 6, 2011 5:17 am
Hi, Does anyone know of a way to tweak the anneal.inp script used for NMR protein structure calculation so that it spreads the job over multiple processors? I...
2062
wrouane@...
wrouane
May 12, 2011 5:59 am
... I am having a similar problem. When I enter into the command line $source cns_solve_env, after changing the directory listing at the top, nothing happens,...
2063
Ed Pozharski
pozharski
May 12, 2011 1:34 pm
... Try tcsh, not csh. That is, imho, one of the (many) problems with csh - some "csh-scripts" actually use extended functionality of tcsh. Since most modern...
2064
wrouane@...
wrouane
May 12, 2011 8:25 pm
... I tried $source cns_solve_env while in tcsh, and while in bash using Ed Pozharski's bash version of cns_solve_env which I found at...
2065
Ed Pozharski
pozharski
May 12, 2011 9:24 pm
By which you mean that 'which cns' returns nothing? You probably have the issue with the architecture determination. After sourcing cns_solve_env, try this...
2066
wrouane@...
wrouane
May 13, 2011 3:44 am
Dear Ed, When I enter %which cns, I get back, cns:Command not found. By nothing happening, I meant when I type %source cns_solve_env, I simply get the command...
2067
wrouane@...
wrouane
May 13, 2011 3:44 am
... I made sure the cns_solve_env file has the right directory listing, which in my case is setenv CNS_SOLVE '/home/joyce/Downloads/cns_solve_1.3' When I...
2068
Edward A. Berry
edwardaber
May 13, 2011 4:29 am
... ../bin is a directory, and even when executable you get the "permission denied" error when trying to execute a directory. try ls the directory, and execute...
2069
Ed Pozharski
pozharski
May 13, 2011 4:41 am
Just for the complete picture, how does your PATH look like? One obvious problem is that you appear to be trying to run 64-bit cns on 32-bit OS. Did you do...
2070
wrouane@...
wrouane
May 13, 2011 5:29 pm
This is the output of PATH: ...
2071
Ben Eisenbraun
bpeisenbraun
May 13, 2011 6:18 pm
... That's useful; in the future it's cleaner to do this: echo $PATH | tr : '\n' | grep cns Which will either output any directories with the word 'cns' in...
2072
wrouane@...
wrouane
May 13, 2011 7:19 pm
I am now currently trying to compile a 32-bit version of cns. I initial problem was probably that my Ubuntu didn't have a fortran compiler, since the output of...
2073
Ben Eisenbraun
bpeisenbraun
May 13, 2011 7:54 pm
Hello Joyce, It looks like your CNS environment set via cns_solve_env is not correct. ... Is the 'getarch' script in /home/joyce/Downloads/cns_solve_1.3/bin? I...
2074
sitaram686
May 21, 2011 11:21 am
Hello every one I am using UBUNTU 10.04 and it uses BASH shell by default and their is no source script like .sh in the new version of the CNS and its creating...
2075
Ed Pozharski
pozharski
May 23, 2011 1:37 pm
You can find one here http://tinyurl.com/3omk368 just edit the CNS_SOLVE line and you should be good to go. ... -- Edwin Pozharski, PhD, Assistant Professor ...
2076
Gerard DVD Kleywegt
gerard@...
Jun 14, 2011 10:34 am
Hi all, A fresh installment of Quips (interactive stories about interesting entries from the PDB) is now available on the PDBe website. It is called "Getting a...
2077
Robert Sweet
sweet@...
Jun 20, 2011 1:54 pm
Summer X-rays at the NSLS The PXRR operates five beamlines at the NSLS: http://www.px.nsls.bnl.gov/. Two of these are the undulator beamlines X25 and X29. The...
2078
Gerard DVD Kleywegt
gerard@...
Jul 6, 2011 7:15 pm
Hi all, As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org) carried out a substantial make-over of its website last summer, including...
2079
Gerard DVD Kleywegt
gerard@...
Jul 7, 2011 6:01 pm
The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is organising a scientific symposium in Cold Spring Harbor this autumn to celebrate the 40th anniversary of...
2080
Gerard DVD Kleywegt
gerard@...
Jul 8, 2011 2:09 pm
Hi all, From 14-18 November, an EMBO Practical Course on "Computational structural biology - from data to structure to function" will be held at the EBI in ...
2081
Gerard DVD Kleywegt
gerard@...
Jul 14, 2011 7:00 pm
Hi all, The Protein Data Bank in Europe (PDBe; http://pdbe.org/) continues to improve its services to the scientific community. As part of our recent website ...
2082
akz_uom
Jul 18, 2011 7:47 am
Dear all, I'm trying to perform water refinement for the very first time (new CNS user), on an NMR ensemble of CYANA calculated protein structures but the end...
2083
Gerard DVD Kleywegt
gerard@...
Jul 21, 2011 5:51 pm
Hi all, As part of its recent summer update, the Protein Data Bank in Europe (PDBe; http://pdbe.org) introduced UniPDB (http://pdbe.org/unipdb), a widget for ...
2084
Julie Fisher
j.fisher@...
Jul 26, 2011 12:55 pm
Dear All We are using cns_solve_1.1 to generate structures for a DNA duplex. Everything is fine until the end of the 'accept' procedure when a '.dat' file is...
