Hi, all, I am learning the NMR structure calcuation procedures and have a beginner's question. I have to deal with very limited distance restraints and trying...
1019
J. Chen
afarnti
Jul 3, 2004 7:27 am
oops, I forgot to put a title previously. sorry. Hi, all, I am learning the NMR structure calcuation procedures and have a beginner's question. I have to deal...
1020
Samuel
zhenglin88
Jul 5, 2004 12:58 pm
Hello, Im having the same problem. If someone know the answer - I'll appreciate that much, Thanks, Shmulik...
Hello, i want to use the dna-rna_restraints.def from the folder /cns_solve_1.1/inputs/auxiliary to set several restraints. Can you tell me the correct use of...
1022
rbaxter@...
Jul 6, 2004 9:03 pm
Dear All, I ran xtal_pdbsubmission.inp on my finished model, and the number of reflections reported is 139458, which is close but not equal to the number of...
1023
Sangita Sinha
sangita@...
Jul 6, 2004 10:08 pm
Hi Richard, I believe this is because CNS imposes an automatic I/sigI > 0 data cutoff. If you grep your reflection file for reflections with I (or fobs) = 0, I...
1024
Afarnti J. Chen
afarnti
Jul 7, 2004 6:41 am
Hi, all, I have been trying to find out what kind of non-bonded interactions are used in the last cooling stage of CNS:anneal.inp for NMR structure ...
1025
Bryan W. Lepore
salmonrushdee
Jul 8, 2004 4:30 pm
i am confused by the error message average_map.inp reports after failing ... Map: a= 118.8900, b= 92.9250, c= 177.7300, alpha= 90.0000, beta= 96.7400, gamma=...
1026
yangna0831
Jul 12, 2004 10:24 am
To all: I want to have the toppar file of acetic, ACY.top. There's no information about ACY in the ion.top file in CNS. Thanks ... Do You Yahoo!? ...
1027
Bryan W. Lepore
salmonrushdee
Jul 12, 2004 8:39 pm
i am attempting to patch a particular prosthetic group into a protein. my other prosthetic groups work fine with the same generate script, but this one (zinc)...
1028
Bryan W. Lepore
salmonrushdee
Jul 12, 2004 9:13 pm
... before i get reprimanded, i should say that the reason i want to attach the zinc is to keep the cysteines from refining away from it as occurs if it is...
1029
Bryan W. Lepore
salmonrushdee
Jul 13, 2004 6:43 am
i have solved my problem. the answer is: each GROUP statement must conclude with an END statement. -bryan...
1030
Alan Purvis
purvis_alan
Jul 13, 2004 8:01 am
It took me so long to work out how to attach a ligand that I wrote it down on my website: http://www.personal.rdg.ac.uk/~sas01app/page32.html Good Luck Alan ...
1031
Yu Yadong
ydyu@...
Jul 13, 2004 8:23 am
Hi, there, I am refining a structure with a magnesium ion which is coordinated in a octahedral form, and I have difficulty to fit atoms in density map. I...
1032
Bryan W. Lepore
salmonrushdee
Jul 13, 2004 5:01 pm
i'm using non-crystallographic symmetry. i want to patch an NCS-related residue to the protomer atoms. is there such a way to do this e.g. like 'resid 100...
1033
Martyn Symmons
martyn@...
Jul 13, 2004 5:40 pm
hello everyone I am trying to refine a large RNA structure in CNS by annealing with distance restraints from fluorescence experiments. As well as these...
1034
Sarah Diane
sarahthenerd
Jul 14, 2004 7:28 pm
Hello Hopefully someone can help me out here. We are trying to install CNS on linux Fedora Core 2. We compiled using the g77 compiler because of the error in...
1035
Jiansheng Jiang
jiang@...
Jul 14, 2004 8:20 pm
Hi Sarah, You just need to change '[A-z]' to '[A-Za-z]' in several scripts where might have "sed -e" statements. Or, you may download the fixed cns for...
1036
Joe Krahn
joekrahn
Jul 15, 2004 4:43 am
I also found a significant bug in CNS on Fedora. Due to differences in memory management, this didn't show up. The variable MPACK is used as a HEAP index, a...
1037
Joel Tyndall
joel.tyndall@...
Jul 16, 2004 3:27 am
HI folks, I've recently got a new linux box to run CNS and all my groovy software on but as a relative novice to linux I'm a bit stuck. I've got an AMD 64-bit...
1038
Jiansheng Jiang
jiang@...
Jul 16, 2004 4:38 am
Hi Joel, CNS running on AMD64-bit machine with Fedora Core 2 (compiled with g77) indeed has a problem currently. The "cns_fc1.tar.gz" works on 32-bit linux...
1039
Charles@...
Jul 16, 2004 1:27 pm
... Hash: SHA1 Hi-- ... I developed an (architecture-dependent) fix for this problem in Xplor-NIH in which negative HEAP index values are rewritten as positive...
1040
S. Shanmuga Sundara Raj
raj_sss
Jul 16, 2004 6:42 pm
Hi All, How can I turn off nonbonded energies for side-chain of a paricular residue? Thanks in advance Raj ******************************************** ...
1041
Joe Krahn
joekrahn
Jul 17, 2004 5:30 pm
... I'm not sure what you mean. Fortran numbers are always signed. As long as HEAP array indices use the same integer size as memory pointers, the wrapping is...
1042
Lou Zhi-Yong
louzy@...
Jul 17, 2004 6:22 pm
Dear all, I am trying to convert a .hkl file to .mtz file. But I have met some problem with it. That is, this .hkl file which I have gotten from ...
1043
Mensur Dlakic
mdlakic@...
Jul 18, 2004 3:32 pm
Hi, This will help, assuming you have CCP4 and f2mtz installed: f2mtz HKLIN density_modify.hkl HKLOUT density_modify.mtz << EOF TITLE ANYTHING YOU WANT HERE ...
1044
William Scott
wgscott@...
Jul 18, 2004 4:27 pm
You might want to use sftools. It is interactive and you don't have to mess with fortran formatting and so on....
1045
Brow
brow0927@...
Jul 19, 2004 11:54 pm
1046
deodat
zhenglin88
Jul 20, 2004 8:48 am
Dear all, When I try to use Aria I don't know how to tell to this program that I want to find a dimer. I'am using Aria 1.2 and I just would like to know where...
1047
Akanksha Nagpal
gte977x@...
Jul 20, 2004 7:28 pm
Dear CNS users: I am using surface_plot.inp to calculate the solvent accessible area for the ligand in my protein. In the output file (surface_plot.list) the...
