We are offering RapiData 2010, the twelvth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in...
1871
Kay Diederichs
kay.diederichs@...
Dec 15, 2009 4:26 pm
Dear all, we've been using the *allhdg topology and parameter files in the hope of being able to minimize some models (without experimental data). However we...
1872
Ed Pozharski
pozharski
Dec 15, 2009 5:04 pm
Kay, are you using model_minimize.inp or something homemade? Ed. ... -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ... When...
1873
Kay Diederichs
kay.diederichs@...
Dec 16, 2009 6:37 pm
... thanks to Fred Dyda, I inspected my parameter files and found a nbonds repel statement - this prevents the electrostatics from being calculated. Thanks to...
1874
Venkataraman
vkabas
Dec 29, 2009 5:00 pm
Hi, Is there anyway to do molecular simulation using cns both by fixing main chain and flexible side chain and both flexible. Also how can I get a final energy...
1875
Venkataraman
vkabas
Dec 29, 2009 10:44 pm
hi all I am trying to minimize the model with chain ID as A and residues are 100-200 , 300-400, 500-600. I did generate pdb and mtf seems fine and takes the...
1876
Ed Pozharski
pozharski
Dec 30, 2009 5:31 pm
{===>} atom_fixed=(name c or name n or name ca or name o or name ot+); to fix the backbone. To get energy values: energy end See here for more details and/or...
1877
Robert Sweet
sweet@...
Jan 4, 2010 1:18 pm
We are offering RapiData 2010, the twelfth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in...
1878
Venkataraman
vkabas
Jan 5, 2010 9:24 am
Hi I wanted to do ncs restrain for only main chain. I do have six monomer and wanted to do the ncs restrain for main chain. I mutated many residues to alanine...
1879
Ed Pozharski
pozharski
Jan 5, 2010 2:43 pm
http://cns.csb.yale.edu/v1.2/tutorial/language/atom_sele_basic/text.html http://cns.csb.yale.edu/v1.2/tutorial/language/atom_sele/text.html These parts of...
1880
Axel Brunger
brunger@...
Jan 21, 2010 11:32 pm
... Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular Physiology Stanford University Web:...
1881
Robert Sweet
sweet@...
Jan 26, 2010 1:47 am
We are offering RapiData 2010, the twelfth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in...
1882
Christian Biertuempfel
cbiertue
Jan 27, 2010 2:43 am
Dear all, I am refining a crystal structure with a modified DNA base. I tried to input the modification via a patch in cns (1.2). So, I modified generate.inp,...
1883
stan_124
Jan 27, 2010 4:02 pm
Hey, How do I type the logic AND operator? I tried '&&' and '&' and 'and' and nothing works. Can you help me understand how to put 'and' 'or' and 'not' in...
1884
Ed Pozharski
pozharski
Jan 27, 2010 6:45 pm
Simple, yet interesting. It may be described somewhere in the XPLOR manual, but a quick look at the .inp files reveals no examples of what you are trying to...
1885
amitd_01
Feb 5, 2010 10:54 am
Hello everybody, When using refine.inp of CNS ver 1.2 the rsmd bonds and angles outputs are 0.000 and very low values of wa=2x10-2 and rweight= 0.02 resptly....
1886
Ed Pozharski
pozharski
Feb 5, 2010 10:40 pm
Just to verify, you are using the *latest* version, 1.21 (not 1.2)? This is really strange. Do both R and Rfree go up when you weaken restraints? And how...
1887
amitd_01
Feb 8, 2010 6:11 am
Yes I am using 1.21 version. Forcing the wa to higher than automatic value of wa= 7.230911E-02, increases the r and rfree to above 50! ... rweight= 0.0100 r=...
1888
Satyabrata Das
satyabratadas
Feb 9, 2010 6:03 am
Dear All, I want to install CNS in a PC running on Windows-Vista (32bit). Is it possible? if yes, How to do it? Ideal thing if executable file is available. ...
1889
Ed Pozharski
pozharski
Feb 10, 2010 7:18 am
Did you try the Windows executables from CNS website? If that doesn't work, consider running linux version in a virtual machine. Or break with the dark side...
1890
AMIT
amitd_01
Feb 11, 2010 9:07 am
Yes I was puzzled. I tried the same refinements using CNS 1.1 (I switched to this version now) which works fine gives following pdb output file: REMARK...
1891
Axel Brunger
brunger@...
Feb 11, 2010 4:13 pm
This could be a compilation problem. Please try the pre-compiled linux binaries that you can download from the CNS download site. Axel Brunger ... Axel T....
1892
Ed Pozharski
pozharski
Feb 12, 2010 10:23 pm
OK, this clearly indicates that there is something wrong with the CNS 1.21 binaries that you use. Where did you get them and what OS you are running? ... -- ...
1893
AMIT
amitd_01
Feb 13, 2010 2:28 pm
CNS is downloaded from the yale website and installed in a linux workstation , ver is RHEL WS4.0. The one which is working fine is CNS ver 1.1 installed on a...
1894
Axel Brunger
brunger@...
Feb 13, 2010 3:09 pm
Please try the pre-compiled linux binary (follow instructions in the Installation section of the cns website). Axel Brunger ... Axel T. Brunger Investigator,...
1895
Ed Pozharski
pozharski
Feb 14, 2010 7:15 am
Hmm... Is your Linux OS 64-bit or 32-bit? Did you compile your own binaries or used pre-compiled ones? On a side note, I highly recommend the parallel...
1896
AMIT
amitd_01
Feb 15, 2010 6:03 pm
The linux OS is a 64-bit one. CNS was compiled on the machine. We have Xeon dual core processors. I will download the mp version and install it now to solve...
1897
Ed Pozharski
pozharski
Feb 16, 2010 4:19 pm
Hope it works :) As for windows, I assume that you tried ms-dos binaries and they don't work? I always thought that CNS is the program which is not really ...
1898
Sanishvili, Ruslan
rsanishvili@...
Feb 24, 2010 3:52 pm
Dear Colleagues, Building on the success of the past 2 years, we are pleased to announce the third annual CCP4 workshop at Advanced Photon Source (APS),...
1899
Julie Fisher
j.fisher@...
Feb 25, 2010 11:36 am
Dear All We are using cns_solve 1.1 to structure generate from NMR parameters. We note during the annealing process the following message: %NOESET-ERR: error...
