Hi Warren, Thanks for the email. I want to superimpose two structures (pdb codes 1HPV, 1HSG) using residues 1-9, 86-99 @ca in both chain A and chain B (total of 46 atoms). How do I do this? So long, Madhavi
-----Original Message----- From: Warren DeLano [mailto:war...@delanoscientific.com] Sent: Friday, June 25, 2004 4:21 PM To: Nalam, Madhavi; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] superposition of structures Nalam, Yes, the pair_fit command is probably the easiest way to specify a few CA atoms over which to fit... For example: load prot1.pdb load prot2.pdb pair_fit prot1///11-26/CA, prot2///34-49/CA would superimpose prot1 on prot2 using C-alphas from residues 11-26 in prot1 and 34-49 in prot2. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Nalam, Madhavi > Sent: Friday, June 25, 2004 10:55 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] superposition of structures > > Hello, > I would like to superimpose two structures using c-alpha > atoms of few residues (not all c-alpha atoms). Can I do this in PyMOL? > Thanks, > Madhavi > > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > pymol-users-requ...@lists.sourceforge.net > Sent: Friday, June 25, 2004 2:29 AM > To: pymol-users@lists.sourceforge.net > Subject: PyMOL-users digest, Vol 1 #630 - 5 msgs > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ad...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more > specific than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. RE: Orient molecule (Warren DeLano) > 2. cartoon and alternates (Robert Schwarzenbacher) > 3. RE: cartoon and alternates (Warren DeLano) > 4. Question about rotation (Qun Wan) > 5. Questions about rotation view (Qun Wan) > > --__--__-- > > Message: 1 > From: "Warren DeLano" <war...@delanoscientific.com> > To: "'Steve Bowlus'" <chezbow...@goldrush.com>, > <chemis...@ccl.net> > Cc: <pymol-users@lists.sourceforge.net> > Date: Wed, 23 Jun 2004 22:59:43 -0700 > Subject: [PyMOL] RE: Orient molecule > > Steve, > > This is something PyMOL can do with a little help from Python... > > # PyMOL script: view2coord.pml > > # get the current camera matrix > v=cmd.get_view() > > # translate atoms to the current origin of rotation > alter_state 1, all, \ > (x,y,z) = (x-v[12],y-v[13],z-v[14]) > > # apply the rotation (matrix multiplication) alter_state 1, all, \ > (x,y,z) = (x*v[0]+y*v[3]+z*v[6], \ > x*v[1]+y*v[4]+z*v[7], x*v[2]+y*v[5]+z*v[8]) > > # end script > > After loading a molecule and choosing a view (either with the > mouse, or using commands like "orient", "turn", "move", > "center", etc.), you then simply run the script and save the > new coordinates: > > load original_mol.pdb > orient > center 10/ca > @view2coord.pml > save transformed_mol.pdb > quit > > Oh, and yes, PyMOL is still free unless you choose to pay for it. > > Cheers, > Warren > > -- > mailto:war...@delsci.com > Warren L. DeLano, Ph.D. > Principal Scientist > DeLano Scientific LLC > Voice (650)-346-1154 > Fax (650)-593-4020 > > > > -----Original Message----- > > From: Computational Chemistry List > > [mailto:chemistry-requ...@ccl.net] On Behalf Of Steve Bowlus > > Sent: Wednesday, June 23, 2004 8:42 PM > > To: chemis...@ccl.net > > Subject: CCL:Orient molecule > > > > I am frantically searching for a simple piece of code that > will allow > > me to: > > > > Read a standard file (mol, pdb, Sybyl ...) select an atom to put at > > the Cartesian origin select an atom to put on the X axis select an > > atom to put in the XY plane Do a rigid rotation Do sequential rigid > > rotations about Cartesian axes Freeze the molecule in the new > > orientation Output the NEW, transformed coordinates. > > > > This is equivalent to the Sybyl "orient" command, plus rigid > > rotations, plus "Freeze molecule". But I have not found a free (or > > even cheap) package that will freeze a molecule in the new > coordinates > > before output. > > > > Thanks in advance for any pointers, > > Steve > > > > > > -= This is automatically added to each message by the > mailing script > > =- To send e-mail to subscribers of CCL put the string > > CCL: on your Subject: line and send your message to: > > chemis...@ccl.net > > > > Send your subscription/unsubscription requests to: > > chemistry-requ...@ccl.net > > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > > > If your mail is bouncing from CCL.NET domain send it to the > > maintainer: > > Jan Labanowski, jlaba...@nd.edu (read about it on CCL Home Page) > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > -+-+-+-+-+ > > > > > > > > > > > > > > > > > --__--__-- > > Message: 2 > From: Robert Schwarzenbacher <robe...@sdsc.edu> > Date: Wed, 23 Jun 2004 23:46:50 -0700 > To: Warren DeLano <war...@delanoscientific.com> > Cc: pymol-users@lists.sourceforge.net > Subject: [PyMOL] cartoon and alternates > > hi there, > > I get broken cartoons with alternate conformations. Is there > a quick way to solve this problem? > > thanks, > > robert > > --- > Robert Schwarzenbacher, PhD > The Joint Center for Structural Genomics > phone: 858 822 3637 > > > --__--__-- > > Message: 3 > From: "Warren DeLano" <war...@delanoscientific.com> > To: <pymol-users@lists.sourceforge.net> > Subject: RE: [PyMOL] cartoon and alternates > Date: Thu, 24 Jun 2004 08:27:49 -0700 > > Robert, > > This sounds like a potential bug. You might be able to work around it > by > removing all but one alternate conformation... > > remove not alt ''+A > rebuild > > But I'd like to take a look at the file to understand why PyMOL is > having > trouble. Could you send me a copy (directly, not via the > mailing list) > or > let me know what PDB code to look for? > > Cheers, > Warren > > -- > mailto:war...@delsci.com > Warren L. DeLano, Ph.D. > Principal Scientist > DeLano Scientific LLC > Voice (650)-346-1154 > Fax (650)-593-4020 > > > -----Original Message----- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > > Robert Schwarzenbacher > > Sent: Wednesday, June 23, 2004 11:47 PM > > To: Warren DeLano > > Cc: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] cartoon and alternates > > > > hi there, > > > > I get broken cartoons with alternate conformations. Is there > > a quick way to solve this problem? > > > > thanks, > > > > robert > > > > --- > > Robert Schwarzenbacher, PhD > > The Joint Center for Structural Genomics > > phone: 858 822 3637 > > > > > > ------------------------------------------------------- > > This SF.Net email sponsored by Black Hat Briefings & Training. > > Attend Black Hat Briefings & Training, Las Vegas July 24-29 - > > digital self defense, top technical experts, no vendor pitches, > > unmatched networking opportunities. Visit www.blackhat.com > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > --__--__-- > > Message: 4 > Date: Thu, 24 Jun 2004 12:08:14 -0400 > From: Qun Wan <qun....@uvm.edu> > To: <pymol-users@lists.sourceforge.net> > Subject: [PyMOL] Question about rotation > > 1.When I want to get the exact rotation of my current view, I did as > the following instruction, but Pymol programe says: invalid syntax. I > do not know why that happens. Could you figure it out for me? > > Getting the right view in the script: > > When creating the script, it is nice to have the view come up in the > right orientation. To do this, you need to get the coordinates. > First, position the molecule the way you would like it to appear, > this can include zooming and rotating the molecule. Once it is in the > correct position, click on the "Get View" button In the PyMOL window > (the one that doesn't show the molecule), a set_view command will be > created for you and you simply cut (from either the PyMol window or > the Terminal window) and paste this text into your script. > > 2. If I want to get a particular rotation, what can I do? For > example, if I want to rotation the the current view by 50 degree in > the x-axis, what is the syntax? > > > > --__--__-- > > Message: 5 > Date: Thu, 24 Jun 2004 13:54:29 -0400 > From: Qun Wan <qun....@uvm.edu> > To: <pymol-users@lists.sourceforge.net> > Subject: [PyMOL] Questions about rotation view > > 1.When I want to get the exact rotation of my current view, I did as > the following instruction, but Pymol programe says: invalid syntax. I > do not know why that happens. Could you figure it out for me? > > Getting the right view in the script: > > When creating the script, it is nice to have the view come up in the > right orientation. To do this, you need to get the coordinates. > First, position the molecule the way you would like it to appear, > this can include zooming and rotating the molecule. Once it is in the > correct position, click on the "Get View" button In the PyMOL window > (the one that doesn't show the molecule), a set_view command will be > created for you and you simply cut (from either the PyMol window or > the Terminal window) and paste this text into your script. > > 2. If I want to get a particular rotation, what can I do? For > example, if I want to rotation the the current view by 50 degree in > the x-axis, what is the syntax? > > > > > > --__--__-- > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest > > > ------------------------------------------------------- > This SF.Net email sponsored by Black Hat Briefings & Training. > Attend Black Hat Briefings & Training, Las Vegas July 24-29 - > digital self defense, top technical experts, no vendor pitches, > unmatched networking opportunities. Visit www.blackhat.com > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
