We have 4 million small molecules in pdb format, with many more to come. Check it out. http://molecules.gnu-darwin.org/ Be sure and scroll down to the News...
proclus@...
Aug 20, 2008 4:51 am
1735
Hi Rupi, I have never converted these files myself but have a look into the openbabel project. It might do what you need. http://openbabel.org Cheers, ...
Hello, I'm not using an external mask, but the problem goes away when I switch off bulk solvent scaling and truncate at 8A. Because my data at low resolution ...
Filip Van Petegem
filip.vanpetegem@...
Aug 19, 2008 5:22 am
1732
Your test case ran fine on my mac. So I suspect it is a machine/compilation problem. How did you compile CNS on your linux computer? Which compiler did you...
Axel Brunger
brunger@...
Aug 18, 2008 11:11 pm
1731
Are you using an external solvent mask? Your external mask may not be properly defined. Try to use an internal mask. Axel Brunger ... Axel T. Brunger ...
Axel Brunger
brunger@...
Aug 18, 2008 2:48 pm
1730
Hello, while trying to run a 'standard' refine.inp script, I got the following message: MAPResolution= 2.1500 GRIDsize= 0.33330 grid parameter for solvent...
Filip Van Petegem
filip.vanpetegem@...
Aug 18, 2008 5:36 am
1729
Hello Everyone, Can anyone suggest me how to calculate average structure and rmsd of an ensemble of structures (say 10) obtained from simulated annealing? I...
Please try the most recent version (1.21). Axel Brunger ... Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular...
Axel Brunger
brunger@...
Aug 12, 2008 2:41 pm
1727
Hi , running minimize.inp in cns 1.2 I get the output .pdb file I need but at the end of the .log file I get this error : %FREHP error encountered: corrupt...
Hi Thanks for to Dr. Chavas, Dr. Mark and Dr Shaanan for your suggestions. I want to run make_cv.inp to start refinement in CNS.I have converted my mtz data...
Hi, I am a new member to this group and have a calculation problem with CNS 1.2. When proton chemical shifts are added as a constraint, the overall energy in...
Hi Navdeep, I had the same problems on an openSUSE machine. Try the Intel compiler ifort. http://www.intel.com/cd/software/products/asmo-na/eng/282048.htm Also...
Hi all I am getting this error while installing CNS in kubuntu 8.02... Installation directory: /usr/local/bin/cns_solve_1.21/intel-i686-linux copying files in...
Dear Prof. Axel Brunger, Thank you very much for your suggestion! ... enabled the program to run and terminate normally. Best regards, kami...
Tatsuya KAMINISHI
kami@...
Aug 4, 2008 10:42 pm
1721
Hi, I've recently compiled an OpenMP version of CNS 1.21 using ifort (version 10.1.0.15). It works nicely with minimize.inp and bindividual.inp, and total time...
Tatsuya KAMINISHI
kami@...
Aug 4, 2008 9:24 pm
1720
... Subject: Re: Annealing before complete model building! Date: Mon, 04 Aug 2008 12:12:49 -0000 From: mark.abrooks <mark.abrooks@...> To:...
Dear Subhendu -- ... It might help your modeling, but I quite sure it will not make the density of the loops appear, or at least not completely. Have you tried...
Leo Chavas
cnshnaalas@...
Aug 4, 2008 6:13 am
1718
Hi, I have built an almost complete model with some refinement but I am still unable to build two small loops (5-6 residues)using "coot" or "O" even after some...
Hello, I have a 2.4 A dataset from a perfect merohedral twin. From this, I have refined a structure to R=18%, Rfree=20% using CNS 1.0 and the routines...
Hello, we just found that cns_solve 1.21 does not compile under SGI IRIX. We tried on a Fuel system (R14000) running IRIX 6.5.30 as well as on an Octane...
o.h.weiergraeber@...
Jul 24, 2008 12:08 pm
1715
An openmp multi-processor version of CNS 1.21 is now available at the CNS download site (see http://cns-online.org/cns_request/ to obtain downloading ...
Axel Brunger
brunger@...
Jul 23, 2008 10:03 pm
1714
Hi Everyone, I am trying to refine a structure that contains F atom , but am running into the following error: SELRPN: 2081 atoms have been selected out of...
Hi all, I am using the plot_patterson utility of CNS 1.2. after I type #plot_patterson #patterson map file -> *.map #patterson plane (x/y/z) -> I just want to...
Hi, Sorry to continuing with the subjec "viewing map files" There is an utility in CNS plot_patterson that can be used to convert postscript plots from...
CNS 1.21 is now available. A particular highlight is automatic dimensioning of torsion angle dynamics arrays (e.g., MAXTREE), so no user intervention is...
Axel Brunger
brunger@...
Jul 11, 2008 6:29 pm
1709
It looks to me that the ligand is in a very tight conformation or fit that causes the close contacts. Eventually, the annealing job becomes unstable and the ...
Hi again, Actually the maps prepared from the self_rotaion.inp are patterson maps. those are self_rotation_p1.map                     and...
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