Re: [ccp4bb] image compression

Dear Frank, Re "pushing terabytes around cyberspace". Well, actually, the synchrotron facilities hosting the datasets locally that were measured there is a major step forward for diffraction data preservation, especially for MX but also true for SAXS, XAFS etc, as is being pushed forward by Alun A

[ccp4bb] Description of a newly solved structure

Hello everyone, I have submitted one cysteine protease structure in PDB and now i have to describe the structure completely for my PhD thesis. I know some web servers who are good to provide knowledge about protein but i would like to ask expert persons of this field as i am quite new in descri

Re: [ccp4bb] how to add Cadmium ion to structure and do the refinement

Hi, Thanks for your advice! My problem has been solved, coot has cadmium ion (which I didn't know at first), and the reason that it didn't work at first is I put Cd instead of CD (should be *upper case*) under the "place atom at pointer" menu, so the refmac and coot don't recognize it. Now I learne

Re: [ccp4bb] image compression

(Old thread, just cleaning up, sorry...) I thought James' algorithm didn't do anything to the spots, just to the stuff in between. So one obvious way to handle this is for the data processing programs to be looking between the integrated spots as well, whether they're missing anything; the

Re: [ccp4bb] jumping ligand

Does it happens when you use automatic NCS restraints? On 30 Nov 2011, at 18:40, Ed Pozharski wrote: > Did anyone ever seen a ligand molecule (or water, maybe) moved into a > symmetry-related position upon refinement in refmac? If that is a > feature (e.g. to make sure that non-protein stuff is

[ccp4bb] jumping ligand

Did anyone ever seen a ligand molecule (or water, maybe) moved into a symmetry-related position upon refinement in refmac? If that is a feature (e.g. to make sure that non-protein stuff is coordinated to the spot of the closest contact), how can I disable it? Cheers, Ed. -- Oh, suddenly throwi

Re: [ccp4bb] sugar and coot

The issue I would raise here is not just for coot, but also for PDB format itself. Last time I asked on ACA2011, Dr. Berman said polysacchride residues in PDB is still not yet uniformly represented. The issue I have is to polysacchride chains refinement in general, but here more specific about bra

Re: [ccp4bb] Superpositions: Deviation by Residue

Dear Crystallographers, is there a ccp4 program--or otherwise--which can compute ca-ca distances of corresponding residues between two superposed structures? You mean to produce something like this? http://xray.bmc.uu.se/usf/pics/distplot_1chr.gif That can be done with LSQMAN - http://xray.b

[ccp4bb] CCP4 user wiki: change of account creation policy, and usage statistics

Dear users of the CCP4 wiki (), the bad news is: due to the number of spammers that surmount the Captchas, we will change the account creation policy: new contributors are welcome, but they will have to send a personal emai

Re: [ccp4bb] Superpositions: Deviation by Residue

On 11/28/2011 10:22 PM, Jacob Keller wrote: Dear Crystallographers, is there a ccp4 program--or otherwise--which can compute ca-ca distances of corresponding residues between two superposed structures? Jacob Dont you get that from SSM and lsqkab (you have to turn on - list atom distances or s

Re: [ccp4bb] how to add Cadmium ion to structure and do the refinement

Hasanyone answered this? Possibilities 1) COOt by default may have written your CD to another coordinate file - usually called PointerAtoms.pdb 2) You got the atom into the pdb you want to refine but it is wrongly labelled. You need ATOM471 N ASP A 81 23.896 6.780 5.956 1.