hi everybody, i have some exprience in calculating monomer structure structure by using ARIA/CNS, but i don't have any idea about calculating homo-dimer...
1058
cnsbb@...
Aug 3, 2004 3:06 pm
Here is some info on a new project that may be interesting to some of your users. ... http://progports.sourceforge.net ... ProgPorts provides a robust method...
1059
Brian Smith
brian_o_smith
Aug 3, 2004 4:36 pm
... There are a few basic steps to getting homo-oligomer structure calculations to work from NMR restraints. On the CNS side, for a dimer you need to: Modify...
1060
Paul Paukstelis
paul@...
Aug 3, 2004 11:27 pm
I am currently trying to write out non-bonded distances between specific atoms in between cycles of rigid body refinement. I am calling a separate file that...
1061
Paul Paukstelis
paul@...
Aug 3, 2004 11:53 pm
As always, I figured it out right after I post. The distance function uses the cutnb which can't be overidden by the cutoff parameter directly. Looks like I...
1062
cstojkoski
Aug 4, 2004 6:37 am
Hi list, I have a large number of protein homology models derived from MODELLER. I would like to refine these models externally and would appreciate input from...
1063
jean jakoncic
wmeining
Aug 4, 2004 6:39 am
I'm using a computer wich has : Mandrake 10.0 64 bit the computer has a dual AMD opteron 248 3Gb memory I'd really like to install CNS on this machine is there...
1064
jean_jakoncic
Aug 4, 2004 8:10 pm
Hi I collected data on a crystal containing HolmiumChloride (HO+3, in ion topo from cns) i m close to complete the refinement here the question: duting the...
1065
cnsbbs
Aug 5, 2004 3:10 am
I used detect_twinning.inp to test my data. The result given below makes me comfused. Anybody can tell me what this result mean? Thanks in advance. ... ...
1068
bs01ndf
Aug 6, 2004 5:31 am
Hello, This is my first time posting a message on the cnsbb, i really hope someone can help me! I am attempting simulated annealing, and have gone through the...
1069
Calvin Yip
calvin@...
Aug 6, 2004 4:11 pm
Hi all, I have obtained a very nice map from a Hg-SAD experiment (resolution of 1.8A) and built pretty much most of structure (4 molecules in the AU) using...
1070
parasu_priya
Aug 6, 2004 7:41 pm
Hi, Im new to cns / xplor. First question: What is the difference between cns and XPLOR? (Sorry if it sounds dumb)...
1071
Eddy Arnold
life_sciences
Aug 6, 2004 9:02 pm
Dear Andy, You might want to take a look at the actual coordinates for the atoms listed..are they all at 0, 0, 0 or some other recognizable place? In general...
1072
goragot
Aug 7, 2004 7:26 am
Hi, I have experienced some strange things when I refined two protein-DNA complex structures with group B-factor refinement (limit between 2-150 A2). The first...
1073
Andy Dore
bs01ndf
Aug 9, 2004 9:59 am
Hi everyone, Thanks for the responses to my last email on the cnsbb. It was really good to get such an informative response ... I didn't realise resources like...
1074
Gerard DVD Kleywegt
gerard@...
Aug 9, 2004 12:59 pm
do you have reason to believe that you know the cell lengths with an accuracy of 0.001 A ??? (or even 0.01 A ?) if not, do the sensible thing and let precision...
1075
Gerard DVD Kleywegt
gerard@...
Aug 9, 2004 1:15 pm
... both are in the right ball-park at least ... but what happened to Rfree ? ... this often happens because there are no restraints on the differences between...
1076
Gerard DVD Kleywegt
gerard@...
Aug 9, 2004 1:16 pm
... most likely these are fourier artefacts. if your data extended to very high resolution they would disappear --dvd ...
1077
Gerard DVD Kleywegt
gerard@...
Aug 9, 2004 1:23 pm
perhaps the orientation/position of the molecules in the two crystals is different enough to bring it outside the radius of convergence of rigid-body...
1078
Rongjin Guan
ziweiguan@...
Aug 9, 2004 4:48 pm
Dear all, How many protein-ligand complex were obtained by soaking ligand into protein crystals so far? How to search PDB for this information? which one is...
1079
Calvin Yip
calvin@...
Aug 9, 2004 7:06 pm
Hi, Thanks to all those who responded to my question. I can finally refine against my native dataset after reindexing it. Calvin...
1080
Karen Champagne
kchampag2000
Aug 11, 2004 4:43 pm
Hi Everyone, I am trying to use ncs restraints to refine a molecule with four-fold symmetry in the asymmetric unit. There are 2 different monomers, four of...
1081
Bryan W. Lepore
salmonrushdee
Aug 11, 2004 5:04 pm
... my understanding is that it is imperative that the protomer residue compositions are identical when using restraints. i haven't tried selecting out...
1082
Mark A. White
white@...
Aug 11, 2004 5:09 pm
Karen, Check the syntax of your logic statements. This is the correct syntax for your NCS group selection group.1 =( (segid A) and (resid 27:30 or resid 35:45...
1083
Bryan W. Lepore
salmonrushdee
Aug 12, 2004 12:23 am
i have around 27000 atoms in my model and get this at the generate stage: %GENRES error encountered: exceeded MAXA parameter --> recompile program cns.inc...
1084
Gerard DVD Kleywegt
gerard@...
Aug 12, 2004 11:13 am
besides the syntax error which has already been pointed out, you may also want to experiment with ncs restraint weights that are *smaller* than 300 kcal/... ...
1085
S Bhattacharya
suparna99
Aug 13, 2004 9:40 pm
Hi Guys, I need some suggestion regarding water picking in crystal structure. I am working with a crystal structure of 2.2 A resolution and 99% completeness....
1086
Eddy Arnold
life_sciences
Aug 13, 2004 10:15 pm
Hello Suparna, Routines like Water_Pick in CNS facilitate the location of peaks in the difference map, and identification of these as possible sites for the ...
1087
rimmer
rim3r
Aug 17, 2004 5:44 pm
Does anyone have an example generate.inp with corresponding topology and parameter files for a protein with a covalently bound ligand? Thanks...
1088
Alan Purvis
purvis_alan
Aug 18, 2004 8:14 am
It took me two months to figure that one out, so I wrote it on my webpage: http://www.rdg.ac.uk/~sas01app/page32.html Good luck Alan >From: rimmer...
