[PyMOL] colors and font size while ray tracing
Hello: I am trying to generate stereo figures for my manuscript. When I try to ray trace at higher resolution, the font size (I use label_font_id=4) is becoming very small. If I use any fonts from the settings tab, the font size doesn't change with ray tracing. If I am correct, many journals prefer Helvitica/Arial fonts for the publication quality figures. So my question is are the fonts found in the settings preferred by the journals? If not, can anyone please tell me what can be done to keep the font size from decreasing during ray tracing? Also, I have vdW spheres shown as dots in the figure. The color of the dots for the vdW spheres is very light after I ray trace the figure. Last week when I ray traced the figure from the same PyMOL session, the colors are much darker!! As far as I know, I haven't changed anything in the session file. So can anyone please tell me how to increase the darkness of the vdW spheres? I use PyMOL version 1.3.x on Windows. Thanks in advance, Madhavi -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ 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] mutagenesis
Hello: I am trying to mutate ALA to VAL in PyMOL. I would like to see possible rotamers for Val. Is it possible to do this in PyMOL? I am using mutagenesis option in PyMOL. Once I select the Val residue, it asks to select a conformational state. I assume this is for various rotamers. But how do I choose a conformational state? Thanks in advance, Madhavi
[PyMOL] vdw radii
Hi, In PyMOL, do the dots and spheres represent the vdW radii of the atoms? If so, how can I find the default values for each element? If not, what is the command to show the vdW spheres? Thanks in advance, Madhavi
[PyMOL] moving around the files
Hello: I would like to make one figure consisting of two inhibitors from two different files. Is there a way that I can move inhibitor from one file w.r.t. the inhibitor from the second file? Thanks in advance, Madhavi -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of pymol-users-requ...@lists.sourceforge.net Sent: Wednesday, November 29, 2006 2:41 PM To: pymol-users@lists.sourceforge.net Subject: PyMOL-users Digest, Vol 6, Issue 24 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-ow...@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: morphing between complexes (Nat Echols) 2. electrostatic potential structure (shivesh kumar) 3. Re: electrostatic potential structure (Martin H?fling) 4. Re: APBS and Pymol (Andreas Henschel) -- Message: 1 Date: Tue, 28 Nov 2006 14:04:59 -0800 (PST) From: Nat Echols Subject: Re: [PyMOL] morphing between complexes To: pymol Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > unfortunately I've already tried that server and I've seen that also in > that case, the ligand is stripped out.I obtain movies with only the > protein movements. I don't know if i have problems with my pdbs: > I have 245 residues + 1 ligand (246). it has the ATOM and not the HETATM > indication, could be this a problem? The server itself doesn't deal with heteroatoms, mostly because it makes dealing with the PDB even more of a nightmare than usual. The underlying CNS input file will handle any ligand you want as long as you have the correct topology and parameter files (e.g. from Gerard Kleywegt's HIC-UP server). I don't know of any program that will morph between *different* ligands, though. You can cheat by using a dummy ligand that has the conserved core, and adding in the rest manually once you have the interpolation. For instance, to show ATP hydrolysis, you use ADP in both PDB files, and later re-insert the original ATP in place of the ADP in the first frame(s). PyMOL makes this very easy. -Nat -- Message: 2 Date: Wed, 29 Nov 2006 06:31:25 -0800 (PST) From: shivesh kumar Subject: [PyMOL] electrostatic potential structure To: pymol-users@lists.sourceforge.net Message-ID: <20061129143125.79852.qm...@web53602.mail.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Dear all, How can I get the electrostatic potential structure of my protein molecule.Thanx in advance. S shivesh - Want to start your own business? Learn how on Yahoo! Small Business. -- next part -- An HTML attachment was scrubbed... URL: http://sourceforge.net/mailarchive/forum.php?forum=pymol-users/attachmen ts/20061129/9e9aecab/attachment.html -- Message: 3 Date: Wed, 29 Nov 2006 15:58:09 +0100 From: Martin H?fling Subject: Re: [PyMOL] electrostatic potential structure To: pymol-users@lists.sourceforge.net Message-ID: <200611291558.09623.martin.hoefl...@gmx.de> Content-Type: text/plain; charset="iso-8859-1" Am Mittwoch, 29. November 2006 15:31 schrieb shivesh kumar: > Dear all, > How can I get the electrostatic potential structure of my protein > molecule.Thanx in advance. S what do you mean by "electrostatic potential structure"? The potential can be calculated with apbs (by hand or via plugin). This produces a map file which when loaded can be visualized as fieldlines or as equipotential surfaces. I think coloring of the ses of a protein is also possible. Cheers Martin -- Message: 4 Date: Wed, 29 Nov 2006 20:40:31 +0100 From: Andreas Henschel Subject: Re: [PyMOL] APBS and Pymol To: Anastassis Perrakis Cc: ba...@biochem.wustl.edu, pymol-users@lists.sourceforge.net Message-ID: <456de22f.3070...@biotec.tu-dresden.de> Content-Type: text/plain; charset="iso-8859-1" Hi Anastassis, I got the same error with a few pdb files. The problem is the following. The B-factor in the pymol-generated pdb file is somtimes set to values larger than 100 (119.63 in your case) thus occupying all its columns of the lovely PDB-format and not leaving any space to the preceding occupancy column (1.00 in your case). The script psize.py however parses these lines by splitting on white-spaces and crashes when converting the merged field ... The remedy is to modify psize.py like this: around line 108, replace words = stri
[PyMOL] hydrogen bonds
Hello, How do I draw a hydrogen bond between two atoms in PyMol? Thanks in advance, Madhavi
[PyMOL] how do I color specific residues
Hello, I am trying to learn PyMOL and doesn't know any programming. I am working with a file from pdb (1HPV). I would like to color specific residues. Basically I have trouble picking residues (there are two chains and a ligand in the asymmetric unit). How do I choose a specific residue/atom? Please help me. Thanks in advance, Madhavi
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" > To: "'Steve Bowlus'" , > > Cc: > 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 "
[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" To: "'Steve Bowlus'" , Cc: 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 Date: Wed, 23 Jun 2004 23:46:50 -0700 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 --__--__-- Message: 3 From: "Warren DeLano" To: 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
