Hi, I am calculating a symmetric dimer. I started with a monomer, and wonder how Ican generate a 180 rotated symmetric monomer pdb file from the current one?...
1505
Mark A. White
white@...
Oct 27, 2006 3:12 pm
Iain, This problem has come up several times on the CCP4BB and cnsbb news groups. Newer versions of sed require a different pattern-matching format. /a-Z/...
1504
iain_d_kerr
Oct 27, 2006 8:50 am
I just installed CNS v1.1 under Ubuntu Dapper using g77 compilers. The programs appear to run OK but everytime I open a shell, which in turn sources...
1503
Mark A. White
white@...
Oct 20, 2006 3:11 pm
Hello everyone, I just wanted to resend my original message from yesterday, so that everyone will know how to do this in CNS. VK, You can either tell CNS to...
1502
vkabs
Oct 20, 2006 2:37 pm
Hey all, I have found out immediately after posting this message {* selection of atoms other than hydrogens for which coordinates will be generated *} {* to...
1501
P. Manish Chandra
pmxtal@...
Oct 20, 2006 8:13 am
Hi VK, you may select only C-alpha atoms in a pdb file using this awk command. awk ' $3 == "CA" {print $0}' My_input.pdb > My_output.pdb This will select...
1500
Frank Murphy
fm@...
Oct 20, 2006 7:24 am
I have not tried this, but the easiest solution I can think of is to re-write the topology and parameter files such that every amino acid, no matter its name,...
1499
vkabs
Oct 19, 2006 5:39 pm
hey all I wanted to generate just main chain (backbone) topology with out changing the residue name as alanine in the pdb. How can I do that? cheers vk...
1498
Kay Diederichs
kay.diederichs@...
Oct 17, 2006 7:54 am
Now that you mention CNS - I have a OpenMP version of CNS 1.1 sourceode, which of course cuts down the time for omit maps and other crystallographic...
1497
Bryan W. Lepore
bryanlepore@...
Oct 16, 2006 5:12 pm
it looks like one must detwin prior to calculating maps with fourier_map.inp - i.e. give fourier_map.inp fobs_det, etc. - right? -bryan...
1496
Eddy Arnold
life_sciences
Oct 16, 2006 11:19 am
POSTDOCTORAL ASSOCIATE OR RESEARCH FACULTY POSITIONS AVAILABLE: STRUCTURE-BASED DRUG AND VACCINE DESIGN, STRUCTURAL STUDIES OF PROTEINS AND VIRUSES RELEVANT TO...
1495
Nicholas Noinaj
nicholas_noinaj
Oct 14, 2006 8:55 am
Hi, i was just wondering if anyone has successfully loaded CNS onto an AMD64 system? I have already tried all the suggestions from previous cnsbb posts, with...
1494
Gerard DVD Kleywegt
gerard@...
Oct 11, 2006 10:06 pm
... doing a grep in the source directory gives: PARAMETER (MXTITL=128,TITMAX=STRING_SIZE) apparently, it's the maximum nr of 'titles' (remark records ?) ...
1493
Leonard Thomas
thomasle@...
Oct 11, 2006 9:28 pm
One of our users is getting the following error when running the generate.inp script on any of our Linux boxes. All are either RHE4 or Fedora5. This is the...
1492
Eddy Arnold
life_sciences
Oct 11, 2006 1:44 pm
POSITION FOR MANAGER OF X-RAY FACILITY A full-time position is available for an experienced macromolecular crystallographer to support operation and...
1491
xiaohuxj83
Oct 4, 2006 7:20 pm
Does anyone know how to build a crystal cell model based on published X-ray data, such as space group, by spdbv viewer? Basically I want to see how individual...
1490
Douglas L. Theobald
dtheobald@...
Sep 26, 2006 5:15 pm
Announcing a fundamentally new way to superimpose structures: Maximum likelihood instead of least squares. http://www.theseus3d.org/ The Program: THESEUS is a...
1489
JingHua LU
lujinghua_2000
Sep 26, 2006 12:42 am
Hi, Sasha and Changdong and CNSbbers: Thank you guys very much for your kind help. Just like What Sasha told, new residues have to be inserted to the CNS...
1488
JingHua LU
lujinghua_2000
Sep 21, 2006 11:48 am
Hi, cnsbber: Recently I found that there was a big bulge on the head of Tyr residue in my structure. But this bulge was too colse to the hydroxyl to build a...
1487
icky_math
Sep 21, 2006 11:43 am
Here is a quick hack that worked for me when I encountered the same problem. Look in the subdirectory "bin" in the main CNS directory (the one where you...
1486
icky_math
Sep 21, 2006 11:43 am
Are the atom types in the .mtf files sometimes different than the types specified in the topology parameter files? I've tried CNS on a number of proteins from...
1485
Brian Smith
brian_o_smith
Sep 20, 2006 1:38 pm
Hi, I am trying to extend MN's xplor2diana3.inp from ARIA 1.2 to do the full IUPAC atom name conversion i.e. change HN to H. I have hit a syntax problem - I...
1484
W.M. B.
butianyuri@...
Sep 20, 2006 9:34 am
Hi, ALL Im trying to install CNS 1.1 in Dell Precision 690n (Xeon dual core) RH EW4 Linux. I got the error below ... the architecture of the machine is unknown...
1483
W.M. B.
butianyuri@...
Sep 13, 2006 1:33 pm
Hi, ALL Im trying to install CNS 1.1 in Dell Precision 690n (Xeon dual core) RH EW4 Linux. I got the error below ... the architecture of the machine is unknown...
1482
Lari Lehtio
lari.lehtio@...
Sep 7, 2006 3:58 pm
If you collect data below the edge and you get a signal, I would assume it's not coming from Mg, but perhaps low occupancy Fe, Mn, Co or Cr. In this case you...
1481
Sanishvili, Ruslan
rsanishvili@...
Sep 7, 2006 2:17 pm
I don't know if it will be helpful at this point but in principle you could collect the anomalous data below the Zn edge and see if you got any anomalous peaks...
1480
kmjxxx
Sep 7, 2006 1:57 pm
We are attempting to estimate the relative occupancy of Zn++ at a site in our protein; we think that the site is occupied by both Zn++ and Mg++. The plan is...
1479
xiaohuxj83
Sep 7, 2006 6:17 am
Hi all, I am a new user of CNS. Is there any tutorial or manual which describe how to manually generate distance constraints input file? I need to get a rough...
1478
Kevin Jude
kmjxxx
Sep 7, 2006 1:16 am
We are attempting to estimate the relative occupancy of Zn++ at a site in our protein; we think that the site is occupied by both Zn++ and Mg++. The plan is...
1477
anything you want it ...
TOleafgirl
Sep 4, 2006 3:45 am
Hi Everyone, I would like to calculate the volume of water separating/around the different asymmetric units in my unit cell. For example, there are some...
