Re: [ccp4bb] Coot question
Hi Nicolas, several possibilities are available for you: - use rigid_bod_refine_zone (http://www.biop.ox.ac.uk/coot/doc/coot/rigid_002dbody_002drefine_002dzone.html#rigid_002dbody_002drefine_002dzone) - use rigid_body_refine_by_atom_selection (see e.g. https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=COOT;7913467f.1011) - use rigid_body_refine_by_residue_ranges (http://www.biop.ox.ac.uk/coot/doc/coot/coot_002dutils.html) - (*) Hope this helps, B (*) Come and see Paul down the corridor (or today even me as I am visiting ;-) ). Dear all, My question concerns the Extension- modelling- Rigid body fit residue ranges function in Coot. Although it works well through the interface, I cannot have it to work in a python script, does somebody know the correct syntax? Thanks in advance, Nicolas - No virus found in this message. Checked by AVG - www.avg.com Version: 2013.0.3267 / Virus Database: 3160/6194 - Release Date: 03/21/13
[ccp4bb] Coot question
Dear all, My question concerns the Extension- modelling- Rigid body fit residue ranges function in Coot. Although it works well through the interface, I cannot have it to work in a python script, does somebody know the correct syntax? Thanks in advance, Nicolas
[ccp4bb] Coot question
Greetings all I am trying to change the color scheme Coot uses when opening PDB files. When I open two seperate PDB files in the same session I would like to change the colors such that there is a clear and distinct difference between the two chains (coot does not always do this), ie red and green instead of Coot offering me green and light green. I am comparing two different maps which are quite similar so the distinction is needed. Any ideas? James
Re: [ccp4bb] Coot question
You can change the color of any map or molecule to any color you wish by using the Map Colour and Bond Colour menus. After you have opened a map or molecular model simply go to the Edit menu at the top of the window; Map Colour will be the top option and Bond Colour will be the third from the top. Cheers, Jim On Tue, Jul 14, 2009 at 12:50 PM, James Tucker Swindell II jtswi...@secsg.uga.edu wrote: Greetings all I am trying to change the color scheme Coot uses when opening PDB files. When I open two seperate PDB files in the same session I would like to change the colors such that there is a clear and distinct difference between the two chains (coot does not always do this), ie red and green instead of Coot offering me green and light green. I am comparing two different maps which are quite similar so the distinction is needed. Any ideas? James -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 jfair...@utk.edu james.fair...@case.edu
[ccp4bb] coot question for any/all?
Hello, So sorry to post this here but I'm at wits end and am just hoping that somebody here has had a similar problem (and subsequent fix). Here goes. I have 7 systems, close to identical, all running FC7. For all, I used the autobuild script on the ccp4 website to generate the entire ccp4 package (including coot0.3.1). As I don't want to deal with network problems, I install the programs on every computer following the same build methods. I know I could do this differently, but for now I don't want to change methods. Now, everything appears to be running normally with no issues. However, I just recently tried building a model from scratch, using the baton-mode and then CAatoms - mainchain button. One one computer, this works great, and I can build, combine fragments, renumber, blah blah blah and get a structure. For the other 6 machines, I can do the baton mode (and it seems to work), but when I hit the CA - mainchain button, nothing happens (it just spins for a few seconds then appears to work but there are no new atoms on the screen). I tried downloading the newest ccp4 with no luck, and also the newest coot (from the coot website). They seem to run fine, but again get stalled when I try to do what I state above. It just doesn't work (though coot appears to be working normally - I can display molecules/maps and move things around and such). The problem is, I don't even know where to start here. I would gladly replace/uninstall/reinstall, but what is it that is broken and needs fixing? Like I said, I tried several different reinstalls today with no luck at all (even the new coot gave the same problem). I went to the coot faq and did the soft-link of the reference-libraries (which is an old fix but you never know) and it had no effect. I will say the one machine that is working is my one at home, and so I can't simply share that directory via nfs and see if it works on the other machines (not trivial). All were built the same way, but obviously I missed a file/link or something that is not allowing this important part of the program to work. Any helpful tips? Thanks so much. Dave Roberts [EMAIL PROTECTED]
Re: [ccp4bb] coot question for any/all?
David, check if your personal environment (login scripts, paths, etc...) is the same on your home machine and the other machines. Looks as if there might be a difference. What does the coot console say, any error messages or hints? HTH Carsten -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of David Roberts Sent: Wednesday, March 05, 2008 2:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] coot question for any/all? Hello, So sorry to post this here but I'm at wits end and am just hoping that somebody here has had a similar problem (and subsequent fix). Here goes. I have 7 systems, close to identical, all running FC7. For all, I used the autobuild script on the ccp4 website to generate the entire ccp4 package (including coot0.3.1). As I don't want to deal with network problems, I install the programs on every computer following the same build methods. I know I could do this differently, but for now I don't want to change methods. Now, everything appears to be running normally with no issues. However, I just recently tried building a model from scratch, using the baton-mode and then CAatoms - mainchain button. One one computer, this works great, and I can build, combine fragments, renumber, blah blah blah and get a structure. For the other 6 machines, I can do the baton mode (and it seems to work), but when I hit the CA - mainchain button, nothing happens (it just spins for a few seconds then appears to work but there are no new atoms on the screen). I tried downloading the newest ccp4 with no luck, and also the newest coot (from the coot website). They seem to run fine, but again get stalled when I try to do what I state above. It just doesn't work (though coot appears to be working normally - I can display molecules/maps and move things around and such). The problem is, I don't even know where to start here. I would gladly replace/uninstall/reinstall, but what is it that is broken and needs fixing? Like I said, I tried several different reinstalls today with no luck at all (even the new coot gave the same problem). I went to the coot faq and did the soft-link of the reference-libraries (which is an old fix but you never know) and it had no effect. I will say the one machine that is working is my one at home, and so I can't simply share that directory via nfs and see if it works on the other machines (not trivial). All were built the same way, but obviously I missed a file/link or something that is not allowing this important part of the program to work. Any helpful tips? Thanks so much. Dave Roberts [EMAIL PROTECTED]
[ccp4bb] COOT question
Dear all, I have a quick question about COOT: Can the program write out maps (e.g. those generated by the 'NCS maps' averaging function) ? Thanks and best wishes, Chris Christoph Meier UCB-Celltech 216 Bath Road Slough SL1 4EN United Kingdom Tel: +44-1753-534655 Extension 2232 Fax: +44-1753-447603 Email: [EMAIL PROTECTED] - Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail. -
