[PyMOL] Distance measurment
Hi all I have to measure a distance between one atom in one molecule (object) and second atom in many molecules (objects) - to do so interactively there is no problem: distance MODEL1//A/211/CA , ManyMODELS_*///100/CA. How can I write a script that will help to get the list of the distances. Any hints will be appreciated Thank You Rotem Sertchook --- Rotem Sertchook, Ph.D. Bioinformatics Unit, Biological Services Weizmann Institute of Science, Rehovot 76100, Israel. -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] PyMOLWiki MovieSchool
PyMOLers, There's a new tutorial on the PyMOLWiki for making movies with the newer PyMOL versions 1.2+. It's detailed, covers concepts, and has scripts that you can directly copy/paste into PyMOL. So, if you have time and want to learn about making movies in PyMOL, check out the PyMOLWiki's MovieSchool: http://pymolwiki.org/index.php/MovieSchool Hope this helps someone, -- Jason -- Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL-users Digest, Vol 38, Issue 9
> Message: 6 > Date: Sat, 11 Jul 2009 23:34:01 -0700 > From: Donnie Berkholz > Subject: [PyMOL] Comparing B-factors of aligned residues > To: pymol-users@lists.sourceforge.net > Message-ID: <20090712063401.ga10...@comet> > Content-Type: text/plain; charset=us-ascii > > Hi all, > > I'm trying to compare the B-factors in two homologous proteins I aligned > using 'super'. I can create an alignment object mapping residue pairs > together, so I think what I want to do should be possible. I'd like to > somehow use that to map the *difference* between the two CA B's onto one > of the structures, then color it by B-factor and color unaligned > residues gray. > > I can't even figure out how to get at the alignment object or what's in > it, much less how to do this. Could anyone help me? > > -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State > University Donnie, you can find something similar in the interfaceResidues script on the PyMOLWiki: http://pymolwiki.org/index.php/InterfaceResidues It shows you how to load something into the B-factors and calculate the difference using the q field. Don't forget you can do super protein1, protein2, object=foo and foo will be the alignment differences shown as CGO. If you could extract the values of the lengths of those CGO lines you'd be done. -- J -- Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Comparing B-factors of aligned residues
On 10:11 Sun 12 Jul , Jason Vertrees wrote: > Donnie Berkholz wrote: > > I'm trying to compare the B-factors in two homologous proteins I > > aligned using 'super'. I can create an alignment object mapping > > residue pairs together, so I think what I want to do should be > > possible. I'd like to somehow use that to map the *difference* > > between the two CA B's onto one of the structures, then color it by > > B-factor and color unaligned residues gray. > > > > I can't even figure out how to get at the alignment object or what's > > in it, much less how to do this. Could anyone help me? > > > Donnie, you can find something similar in the interfaceResidues script > on the PyMOLWiki: > >http://pymolwiki.org/index.php/InterfaceResidues > > > It shows you how to load something into the B-factors and calculate the > difference using the q field. Don't forget you can do > >super protein1, protein2, object=foo > > and foo will be the alignment differences shown as CGO. If you could > extract the values of the lengths of those CGO lines you'd be done. Yeah, that's a nice use of the occupancy field. The problem is that I can't even figure out which subtractions to do without some way to access the residue mapping between the two nonidentical sequences that I know is calculated during alignment. In my original email, I mentioned that I'd discovered how to create that alignment object, I just can't figure out how to iterate over the residue numbers it's connecting. I might have to do something annoying like threading one of the sequences onto the other structure so I can hack around this residue-mapping problem. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Comparing B-factors of aligned residues
Donnie, Please try: load $TUT/1hpv.pdb extract chA, chain A extract chB, chain B # assign some B values onto chA from random import random alter chACA, b=random() # show for later comparison... iterate chA///1-10/CA, chain,resi,b # generate an alignment align chACA, chBCA, object=aln # 'refresh' forces 'aln' to become available as a selection # before the next command... refresh # now we use a Python list, iterate, and alter to copy the # b factors using the alignment object 'aln' stored.b = [] iterate chA and aln, stored.b.append(b) stored.b.reverse() alter chB and aln, b = stored.b.pop() # confirm transfer iterate chB///1-10/CA, chain,resi,b Cheers, Warren From: Donnie Berkholz [mailto:dberkh...@gentoo.org] Sent: Sun 7/12/2009 1:15 PM To: Jason Vertrees Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Comparing B-factors of aligned residues On 10:11 Sun 12 Jul , Jason Vertrees wrote: > Donnie Berkholz wrote: > > I'm trying to compare the B-factors in two homologous proteins I > > aligned using 'super'. I can create an alignment object mapping > > residue pairs together, so I think what I want to do should be > > possible. I'd like to somehow use that to map the *difference* > > between the two CA B's onto one of the structures, then color it by > > B-factor and color unaligned residues gray. > > > > I can't even figure out how to get at the alignment object or what's > > in it, much less how to do this. Could anyone help me? > > > Donnie, you can find something similar in the interfaceResidues script > on the PyMOLWiki: > >http://pymolwiki.org/index.php/InterfaceResidues > > > It shows you how to load something into the B-factors and calculate the > difference using the q field. Don't forget you can do > >super protein1, protein2, object=foo > > and foo will be the alignment differences shown as CGO. If you could > extract the values of the lengths of those CGO lines you'd be done. Yeah, that's a nice use of the occupancy field. The problem is that I can't even figure out which subtractions to do without some way to access the residue mapping between the two nonidentical sequences that I know is calculated during alignment. In my original email, I mentioned that I'd discovered how to create that alignment object, I just can't figure out how to iterate over the residue numbers it's connecting. I might have to do something annoying like threading one of the sequences onto the other structure so I can hack around this residue-mapping problem. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Comparing B-factors of aligned residues
On 15:51 Sun 12 Jul , Warren DeLano wrote: > Donnie, > > Please try: > > > load $TUT/1hpv.pdb > > extract chA, chain A > > extract chB, chain B > > # assign some B values onto chA > > from random import random > > alter chACA, b=random() > > # show for later comparison... > > iterate chA///1-10/CA, chain,resi,b > > # generate an alignment > > align chACA, chBCA, object=aln > > # 'refresh' forces 'aln' to become available as a selection > # before the next command... > > refresh > > # now we use a Python list, iterate, and alter to copy the > # b factors using the alignment object 'aln' > > stored.b = [] > > iterate chA and aln, stored.b.append(b) > > stored.b.reverse() > > alter chB and aln, b = stored.b.pop() Warren, A-ma-zing. Worked perfectly! Thanks so much for your help. The only real modification I made was changing 'b = stored.b.pop()' to a '-=' or '/=' because I want to compare the two B's. For the curious, what I'm doing is mapping conservation scores into the B-factor field using ConSurf, then comparing two homologs to look at gain-of-function and loss-of-function overlaid as color on a single structure. Bright red or blue indicate the most interesting differences. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
