Hi, I want to use model_map.inp to perform a very simple Fo map calculation (experimental Fo and sigma, phase calculated from the provided pdb, exclude...
1928
Ed Pozharski
pozharski
Apr 30, 2010 2:08 pm
Try this "grep checkversion minimize.inp" and post the result. If it says "checkversion 1.1" then you have to find this line in your input file and edit it so...
1927
kieft
Apr 30, 2010 6:33 am
Hi all, I am running CNS version 1.21. The issue I am having is with minimize.inp. I edited a NEW version of the input file that I got from...
1926
Ed Pozharski
pozharski
Apr 29, 2010 3:41 pm
... No, pvdw means "packing van der Waals", so it refers to the interaction with symmetry mates. -- "I'd sacrifice myself, but I'm too good at whistling." ...
1925
Jirundon Yuvaniyama
scjyv@...
Apr 29, 2010 3:27 pm
Dear Ed, Thank you very much for your prompt suggestion. I saw the FAQ for option 1, but I might not put my question specific enough. I was thinking of using: ...
1924
Ed Pozharski
pozharski
Apr 29, 2010 2:05 pm
Tough one, but there are several options I can see. 1. What is pushing them apart is vdw. You can selectively turn that off by using igroup statements (see...
1923
Jirundon Yuvaniyama
scjyv@...
Apr 29, 2010 11:47 am
Dear Sirs, Question 1: I have two Cys residues from symmetry-related molecules forming a disulfide bond. How would I make a patch so that CNS takes into ...
1922
Ed Pozharski
pozharski
Apr 28, 2010 8:10 pm
You see, this is a different story. Your original question was something most people would simply ignore, as it is answered in the tutorial. Check the segids....
1921
Ed Pozharski
pozharski
Apr 28, 2010 1:36 pm
((residue 10:15 and segid A) or (residue 12:17 and segid B)) This is rather primitive and you should take a look at this first ...
1920
amitk.iit07
Apr 28, 2010 12:41 pm
How one will select and write into cns input file For example: I would like to select following residues for omission to calculate SA-omit map: "residue 10 to...
1919
Ed Pozharski
pozharski
Apr 27, 2010 4:38 pm
Or you can use the attached bash-version of the cns_solve_env (make sure you edit it to specify correct value of CNS_SOLVE). As others mentioned, Ubuntu does...
1918
Rajagopalan, Senapathy
srajagopalan@...
Apr 27, 2010 6:16 am
Hi Everyone, I am in the process of refining my protein's xtal structure and noticed that my Rfree increases 27.63->27.85 when I increase the number of...
1917
Moody, Peter C.E. (Dr.)
pcem1@...
Apr 26, 2010 9:21 am
I think that Ubuntu 9.x does not include csh as default, you will have to install it first (it caught me out too!) Peter Peter Moody 1/56 Henry Wellcome...
1916
Justin Lecher
j.lecher@...
Apr 26, 2010 9:08 am
... there are different types of shells in UNIX-(like) systems. The one you need is (t)csh. So before you source the cns installation just type "csh". then it...
1915
Yuri Zherdev
byyaatch@...
Apr 25, 2010 6:44 pm
Greetings, I'm a new to Linux and CNS, so please be patient. I'm trying to install cns_solve_1.21 on Ubuntu 9.10 running on SunVirtualBox 3.1.6 r59338 running...
1914
Justin Lecher
j.lecher@...
Apr 13, 2010 1:14 pm
... That's clear, but more interesting is that cns calculates a model where the atoms are spread far apart: ATOM 14 CB ALA 2 -8.305 -14.055...
1913
Christian Biertuempfel
cbiertue
Apr 13, 2010 1:11 pm
Hmm, if I run alternate twice I get 3 conformers for all residues which were used for the double conformations - not only for the ones selected in the second...
1912
Sanishvili, Ruslan
rsanishvili@...
Apr 7, 2010 2:42 pm
Dear Colleagues, This is a third and final call for applications for the third annual CCP4 school: "From data collection to structure refinement and beyond" ...
1911
Axel Brunger
brunger@...
Apr 6, 2010 9:35 pm
This happens when the coordinate x,y,z exceed the limits of the allocated field, i.e.,x, y, or z > 9999.999. I suggest you translate your molecule(s) closer to...
1910
Justin Lecher
j.lecher@...
Apr 6, 2010 7:44 pm
Dear all, I am running a aria/cns run and getting weird coordinate ouputs: REMARK DATE:06-Apr-2010 17:00:01 created by user: justin REMARK VERSION:1.21 ...
1909
Christian Biertuempfel
cbiertue
Apr 5, 2010 5:38 am
Dear Ed, Thank you very much for your help. Your script did the trick. I have tried to modify alternate.inp to specify different numbers of alternate ...
1908
Ed Pozharski
pozharski
Apr 1, 2010 2:08 pm
OK, it was worth a shot. Looking at the alternate.inp script, it first assigns new segid (AC1) to all the atoms you want and the adds alternate conformations....
1907
Ed Pozharski
pozharski
Mar 31, 2010 5:13 pm
Try running alternate.inp twice - first time for double conformers, second for triple conformers using double conformer mtf/pdb as input. ... -- Edwin...
1906
Christian Biertuempfel
cbiertue
Mar 31, 2010 4:32 pm
Dear all, Is there a way to assign different numbers of alternate conformations for refinement in cns? For example, residue 53 has two alternate conformations...
1905
Sanishvili, Ruslan
rsanishvili@...
Mar 17, 2010 10:17 pm
This is just a reminder that the deadline for applications for the CCP4 school: From data collection to structure refinement and beyond, is April 9. A full...
1904
Ed Pozharski
pozharski
Mar 17, 2010 6:49 pm
I guess you have answered the question already. It must be the difference between CNS and X-plor. Check CNS website if vector is anywhere in the syntax...
1903
Alan
alansilvae
Mar 16, 2010 6:29 pm
Hi, Can someone explain me why I have this error although it's doing what requested for CNS 1.21: CNSsolve> vector do (x=x+5*rand()) (all) %CNSsolve-ERR:...
1902
Joe Krahn
joekrahn
Mar 7, 2010 6:10 pm
I am working on a Cygwin Makefile for CNS. Cygwin is a POSIX emulation layer for Windows, with all of the basic tools available in Gnu/Linux. (See...
1901
Joe Krahn
joekrahn
Mar 7, 2010 6:02 pm
CNS only allows the syntax: if ( <value> <op> <value> ) then It does not evaluate the condition as an expression. There are no logical operators to join...
1900
Joe Krahn
joekrahn
Mar 7, 2010 5:52 pm
CNS currently does not allow restraints with non-matching residue names. It is easy to modify the source code to turn these from errors into just warnings, but...
