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
