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...
1719
Leo Chavas
cnshnaalas@...
Aug 4, 2008 6:13 am
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...
1720
wmeining
Aug 4, 2008 4:29 pm
... Subject: Re: Annealing before complete model building! Date: Mon, 04 Aug 2008 12:12:49 -0000 From: mark.abrooks <mark.abrooks@...> To:...
1721
Tatsuya KAMINISHI
kami@...
Aug 4, 2008 9:24 pm
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...
1722
Tatsuya KAMINISHI
kami@...
Aug 4, 2008 10:42 pm
Dear Prof. Axel Brunger, Thank you very much for your suggestion! ... enabled the program to run and terminate normally. Best regards, kami...
1723
rupi_navdeep
Aug 6, 2008 6:04 pm
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...
1724
Daniel Schlieper
daniel_schli...
Aug 7, 2008 10:14 am
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...
1725
Terry Dowd
dowdtldowd
Aug 7, 2008 3:55 pm
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...
1726
i_m_subh
Aug 8, 2008 7:25 am
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...
1727
bashan.anat
Aug 12, 2008 12:45 pm
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...
1728
Axel Brunger
brunger@...
Aug 12, 2008 2:41 pm
Please try the most recent version (1.21). Axel Brunger ... Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular...
1729
sivaphy
Aug 12, 2008 3:39 pm
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...
1730
Filip Van Petegem
filip.vanpetegem@...
Aug 18, 2008 5:36 am
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...
1731
Axel Brunger
brunger@...
Aug 18, 2008 2:48 pm
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 ...
1732
Axel Brunger
brunger@...
Aug 18, 2008 11:11 pm
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...
1733
Filip Van Petegem
filip.vanpetegem@...
Aug 19, 2008 5:22 am
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 ...
1734
rupi_navdeep
Aug 19, 2008 6:53 am
Hi I want to convert "car and mdf" or "msi" files generated using materials studio to "pdb and psf" files. Please help me in doing so. Thanks...
1735
Christian Biertuempfel
cbiertue
Aug 19, 2008 3:52 pm
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, ...
1736
proclus@...
Aug 20, 2008 4:51 am
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...
1737
Molecules@... site in...
proclus@...
Aug 21, 2008 6:16 pm
I am starting to get questions about how the Molecules site was constructed. http://molecules.gnu-darwin.org/ I think that it is a good example of what is...
1738
rupi_navdeep
Aug 21, 2008 6:37 pm
Hi all I am trying to generate psf file for carbon nanotubes but the atom types are not defined on the force field files. How can I generate these files. ...
1739
vkabas
Aug 23, 2008 12:25 am
Hi I am trying to refine the experimental model (few helices) using cns1.1 and cns rigid body and model map throw away the model out of the density and map...
1740
albumns
Aug 25, 2008 7:25 am
I am a CNS 1.21 user. Recently I want to check if there is a small molecule in my protein and I did the sa_omit_map.inp in CNS.But when I opened the...
1741
Leo Chavas
cnshnaalas@...
Aug 25, 2008 11:19 am
Dear Albumns -- ... This is a question for the Coot mailing list I guess. Anyway, in this case I think I can give a hint... it should depend on your resolution...
1742
Katya Heldwein
katya.heldwein
Sep 9, 2008 7:18 pm
Hi all, When I run generate.inp script in CNS 1.21, I get the message "Segmentation fault". The last lines in the output file are CNSsolve> do...
1743
Axel Brunger
brunger@...
Sep 9, 2008 9:12 pm
This sounds to me like a compiler problem on your linux computer. Please use the latest Intel ifort, Portland Group pgf95, or Gfortran compilers on linux. I...
1744
Axel Brunger
brunger@...
Sep 9, 2008 9:13 pm
One more thing: please make sure you set limit stacksize unlimited on your machine. The default stacksize is often too small, causing unpredictable...
1745
quiquine77
Sep 22, 2008 9:27 pm
Hi all I have seen several messages without answer concerning how to deal with atoms on special position. Can somebody tell clearly what is going on when atoms...
1746
albumns
Sep 22, 2008 9:27 pm
Dear all: Rcently I want to judge if there is a ligand in my structure, and make 2fo-fc and omit map by CNS1.21. When I opened then in Coot, it found that:...
1747
ce_deli
Sep 22, 2008 9:27 pm
Deal all CNS users, I want to refine a solution NMR structure with CNS 1.2. The final CNS energy of this struture is shown below: REMARK overall = 532.641 ...
