Madhavi, I think the following will work:
load 1HPV.pdb, 1hpv load 1HSG.pdb, 1hsv pair_fit 1hpv//A+B/1-9+86-99/CA, 1hsg//A+B/1-9+86-99/CA 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 1:48 PM > To: Warren DeLano; pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] superposition of structures > > 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 > > > > > > > ------------------------------------------------------- > 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 >
