RE: [PyMOL] modifying atom coordinates
Yes, but what happens when, for example, I take a lysine residue, and connect a glutamine residue? Shouldn't all the atoms have different coordinates from when they are stand alone, based on the forces from nearby atoms? Does pymol account for this as residues are added, or is there a command or wizard which accounts for nearby atomic forces that I would execute after I build my chain? To give some background to what I'm trying to do, the end goal of my project is to modify the forces involved in protien folding. I'm sorry if I'm asking questions that are documented, but I haven't seen anything that answers my question yet. Much Thanks, Edmund On Wed, 17 Sep 2003, Warren L. DeLano wrote: > Hi Edmund, > > Actually, PyMOL uses a set of stored coordinates for fragments > and residues. They can be found in $PYMOL_PATH/data/chempy/fragments. > The files have .pkl extensions, which stands for pickled chempy model. > These files can be viewed directly in PyMOL, or can be introspected by > unpickling them in a Python interpreter. > > Cheers, > Warren > > -- > mailto:war...@delanoscientific.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 Edmund Kump > > Sent: Wednesday, September 17, 2003 3:49 AM > > To: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] modifying atom coordinates > > > > Greetings, > > > > I am interested in modifying how pymol generates the coordinates of > > atoms in a peptide chain as you add residues to it. I am an > > undergraduate math student, so my knowledge in this area is in the > > range of "nothing". I would assume that this would be in the bonding > > or editor modules, but so far I haven't found what I'm looking for. In > > what Chempy or Pymol module(s) can I find the code that determines > > these coordinates? > > > > Thanks, > > Edmund Kump > > ek...@mathlab.sunysb.edu > > Applied Mathematics and Statistics > > SUNY Stony Brook > > > > > > > > --- > > This sf.net email is sponsored by:ThinkGeek > > Welcome to geek heaven. > > http://thinkgeek.com/sf > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > >
RE: [PyMOL] Can't load maps anymore!
Raji, Thanks for sending along the map. PyMOL can still read XPLOR maps just fine -- what's wrong in this situation is that the map doesn't cover the space of the molecule. To see this: load buckleddna.pdb load polya.map, polya, format=xplor zoom enable polya That last command will draw a box around the map, showing you how it doesn't cover the PDB file. Either you need a model which covers the map, or a map which covers the model. Cheers, Warren -- mailto:war...@delanoscientific.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 raji > Sent: Thursday, September 18, 2003 1:35 PM > To: PyMOL-users@lists.sourceforge.net > Subject: [PyMOL] Can't load maps anymore! > > Hi Everyone, > I am trying to load a CNS map around this object "buckleddna". The map > doesnt > load. I tried to convery it to *.xplor format using Mapman and retry. That > doesnt help either. > Any suggestions ? > > Executive: object "buckleddna" created. > PyMOL>load polya, polya, 1, xplor > ObjectMapLoadXPLORFile-Error: Unable to open file! > PyMOL>load polya.map, polya, 1, xplor > Crystal: Unit Cell 104.920 109.600 177.970 > Crystal: Alpha Beta Gamma90.000 90.000 90.000 > Crystal: RealToFrac Matrix > Crystal:0.0095 -0. -0. > Crystal:0.0.0091 -0. > Crystal:0.0.0.0056 > Crystal: FracToReal Matrix > Crystal: 104.92000.0. > Crystal:0. 109.60000. > Crystal:0.0. 177.9700 > Crystal: Unit Cell Volume 2046518. > Executive: object "polya" created. > PyMOL>isomesh map,polya,0.5, buckleddna > Isomesh: created "map", setting level to 0.500 > ObjectMesh: updating "map". > IsosurfVolume: Surface generated using 0 lines. > --- > Thanks a ton, > Raji > > Raji Edayathumangalam > Dept. of Biochemistry & Molecular Biology > Colorado State University > Fort Collins, CO 80523 USA > Tel:(970)491-4614 > Fax:(970)491-0494 > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Can't load maps anymore!
Hi Everyone, I am trying to load a CNS map around this object "buckleddna". The map doesnt load. I tried to convery it to *.xplor format using Mapman and retry. That doesnt help either. Any suggestions ? Executive: object "buckleddna" created. PyMOL>load polya, polya, 1, xplor ObjectMapLoadXPLORFile-Error: Unable to open file! PyMOL>load polya.map, polya, 1, xplor Crystal: Unit Cell 104.920 109.600 177.970 Crystal: Alpha Beta Gamma90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal:0.0095 -0. -0. Crystal:0.0.0091 -0. Crystal:0.0.0.0056 Crystal: FracToReal Matrix Crystal: 104.92000.0. Crystal:0. 109.60000. Crystal:0.0. 177.9700 Crystal: Unit Cell Volume 2046518. Executive: object "polya" created. PyMOL>isomesh map,polya,0.5, buckleddna Isomesh: created "map", setting level to 0.500 ObjectMesh: updating "map". IsosurfVolume: Surface generated using 0 lines. --- Thanks a ton, Raji Raji Edayathumangalam Dept. of Biochemistry & Molecular Biology Colorado State University Fort Collins, CO 80523 USA Tel:(970)491-4614 Fax:(970)491-0494
RE: [PyMOL] A couple of movie questions
> First up: Is there any way to tell PyMol *not* to change its view when > loading a > PDB file set auto_zoom,0 > Secondly: Below is an example of a small hack I have written when making > one > particular movie. This one overlays two molecules related by a 2-fold > axis by > doing a simple rotation. > > > def overlay_chains(write_frames=0, ray=0): > > # Now interpolate each point in the matrix > > i = 1 > > n = 45 > > while i <= n: > > # This is the only code I would imagine I should need: > > # cmd.mdo( "%d" % (i), "rotate y,2,chain_a; rotate y,-2,chain_b" ) > > # In the end I used the following cludge: > > cmd.do( "rotate y,2,chain_a" ) > > cmd.do( "rotate y,-2,chain_b" ) > > if ( ray ): > > cmd.do( "ray" ) > > if ( write_frames ): > > cmd.do( "png overlay_frames/overlay_%03d.png" % (i) ) > > i = i+1 > > cmd.extend( "overlay_chains", overlay_chains ) > > What is wrong with the cmd.mdo line above? The functionality I would > expect > would be that in each frame of the movie both chains are rotated 2 deg (in > the > relevant directions). What I get is that the change only occurs once per > loop > of the movie. That is to say that if I set up a movie using 'mset 1 -45' > the positions only get updated once per 45 frames, not once per frame > (which is > what I would have expected). Do you have 45 states, or just one? If you have just one, did you use the "mset 1 x45" statement to create 45 frames consisting of that one state? And finally, are you using mpng to write the movie? > Thridly: Is there any command to tell PyMol to play a movie ONLY ONCE. > This > would be *really* useful if it has not yet been implemented. I just added a "movie_loop" setting for you. Look for it in the next version. > Fourth (and last): Is there a difference b/w the ray-tracing used by the > standard 'ray' command and the 'mpng' command? I have noticed that if I > take a > still of a molecule, and then render the molecule rotating (for example) > all > within the one script I observe real differences b/w what should be > identical > frames. The clipping planes and the z camera distance move considerable. > I can > post code if that would help. Ray simply passes the current scene to the ray tracer. Mpng runs through the movie from the beginning and applies any mmatrix, mdo, or mappend operations you may have defined for the movie before handing each scene off to "ray". (Note that movie.rock and movie.roll use mdo) What you describe sounds more like the difference between having a perspective view in OpenGL and orthoscopic in the rendered scene, but that difference should occur with both ray and mpng. Cheers, Warren
RE: [PyMOL] negative images
Jules, I think there's a problem with the alpha channel with certain PyMOL images, which means that portions end up being transparent when they shouldn't be. A quick workaround is to put a black rectangle behind the PyMOL image, but I'd like to get a little more information about when the problem occurs so that we can generate a permanent bug-fix. 1) Does it happen with ray-traced images, OpenGL images, or both? 2) Does is only happen with transparent surfaces? 3) Does it only happen on selected platforms? And if possible, can you send me directly (not to the mailing list), a copy of the problematic PNG file. Thanks, Warren -- mailto:war...@delanoscientific.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 Jules Jacobsen > Sent: Thursday, September 18, 2003 12:37 AM > To: Pymol users list > Subject: [PyMOL] negative images > > Hello Pymol types, > > I have a quick question- has anyone had any trouble printing out images > in word using version 0.9 in word XP? > > The images look fine when viewed on the screen yet when it comes to > printing them out they appear as negatives, including the white > background which becomes black. I though this might be a ray_trace_fog > problem as my newer images were using this set to 1 but either on or > off, the same problem arises. I have other images rendered using 0.86 > and there is no problem with them. > > Has anyone else had this problem and found a fix for it? > > thanks in advance > > Jules > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] energy minimisation in python
On Thu, Sep 18, 2003 at 05:48:56PM +0100, Paulo Martel wrote: > On Thu, 2003-09-18 at 14:36, Alan Wilter Sousa da Silva wrote: > > > > And about Ghemical project? > > > > Ghemical is not a Python project, it is a GNU GPL package written in C FWIW, ghemical is written in C++. > using the Gtk toolkit, with the GtkGlarea widget providing OpenGl > accelerated graphics in a Gtk window. It provides much the same > functionality as Pymol (but can already do MD and QC calculations), so > there wouldnt be much point in trying to interface with it. Yes. Michael
Re: [PyMOL] energy minimisation in python
On Thu, 2003-09-18 at 14:36, Alan Wilter Sousa da Silva wrote: > > And about Ghemical project? > Dear Alan, Ghemical is not a Python project, it is a GNU GPL package written in C using the Gtk toolkit, with the GtkGlarea widget providing OpenGl accelerated graphics in a Gtk window. It provides much the same functionality as Pymol (but can already do MD and QC calculations), so there wouldnt be much point in trying to interface with it. I also think it is more oriented towards small molecule computational chemistry. Cheers, Paulo -- Paulo Martel Dept. de Química e Bioquímica Faculdade de Ciências e Tecnologia Universidade do Algarve Campus de Gambelas, 8000-117 FARO Tel: 289800900 Ext.7402
Re: [PyMOL] energy minimisation in python
And about Ghemical project? http://www.bioinformatics.org/ghemical/ On Wed, 17 Sep 2003 pymol-users-requ...@lists.sourceforge.net wrote: > On Wed, Sep 10, 2003 at 10:57:59AM +0300, Dr. Daniel James White PhD wrote: > > Warren , > > > > Are you aware of the python MMTK molecular dynamics package? > > AMBER force field and energy minimisation are there! > > Could this be easily interfaced with pymol? > > > > http://starship.python.net/crew/hinsen/MMTK/ > > Probably, given messages to this list like this one, for instance: > > http://sourceforge.net/mailarchive/forum.php?thread_id=1419207&forum_id=60 > Cheers, -- -- Alan Wilter Sousa da Silva -- B.Sc. - Dep. Física - UFPA M.Sc. - Dep. Física - PUC/RJ D.Sc. - IBCCF/UFRJ Bolsista Pesquisador LAC-INPE São José dos Campos (SP), Brasil www.lac.inpe.br/~alan
Re: [PyMOL] A couple of movie questions
Hi Stephen, * Stephen Graham [2003-09-18 21:02] wrote: > First up: Is there any way to tell PyMol *not* to change its view when > loading a > PDB file? For viewing in general, and for movies w/ morphs (etc.) in > particular > it would be nice to not have to re-set the view each time I load a new > co-ordinate set. Yes. that one is easy. set auto_zoom, 0 I have that set in my .pymolrc file, along with several other settings. I'm afraid that I'm even more of a movie novice and so cannot answer your other questions! Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
[PyMOL] A couple of movie questions
Hi all, I have just a couple of questions with regards to movie making in PyMol. Well, they are more niggling annoyances (holes in my knowledge?) which I can work around if needs be, but would rather not have to. First up: Is there any way to tell PyMol *not* to change its view when loading a PDB file? For viewing in general, and for movies w/ morphs (etc.) in particular it would be nice to not have to re-set the view each time I load a new co-ordinate set. Secondly: Below is an example of a small hack I have written when making one particular movie. This one overlays two molecules related by a 2-fold axis by doing a simple rotation. > def overlay_chains(write_frames=0, ray=0): > # Now interpolate each point in the matrix > i = 1 > n = 45 > while i <= n: > # This is the only code I would imagine I should need: > # cmd.mdo( "%d" % (i), "rotate y,2,chain_a; rotate y,-2,chain_b" ) > # In the end I used the following cludge: > cmd.do( "rotate y,2,chain_a" ) > cmd.do( "rotate y,-2,chain_b" ) > if ( ray ): > cmd.do( "ray" ) > if ( write_frames ): > cmd.do( "png overlay_frames/overlay_%03d.png" % (i) ) > i = i+1 > cmd.extend( "overlay_chains", overlay_chains ) What is wrong with the cmd.mdo line above? The functionality I would expect would be that in each frame of the movie both chains are rotated 2 deg (in the relevant directions). What I get is that the change only occurs once per loop of the movie. That is to say that if I set up a movie using 'mset 1 -45' the positions only get updated once per 45 frames, not once per frame (which is what I would have expected). Thridly: Is there any command to tell PyMol to play a movie ONLY ONCE. This would be *really* useful if it has not yet been implemented. Fourth (and last): Is there a difference b/w the ray-tracing used by the standard 'ray' command and the 'mpng' command? I have noticed that if I take a still of a molecule, and then render the molecule rotating (for example) all within the one script I observe real differences b/w what should be identical frames. The clipping planes and the z camera distance move considerable. I can post code if that would help. Many thanks for info on any of the above stuff, Stephen -- Stephen Graham PhD Candidate Crystallography Group School of Molecular and Microbial Biosciences Building G08 University of Sydney Ph: +61 2 9351 6012 Fax: +61 2 9351 4726 - This mail sent through IMP: www-mail.usyd.edu.au
[PyMOL] negative images
Hello Pymol types, I have a quick question- has anyone had any trouble printing out images in word using version 0.9 in word XP? The images look fine when viewed on the screen yet when it comes to printing them out they appear as negatives, including the white background which becomes black. I though this might be a ray_trace_fog problem as my newer images were using this set to 1 but either on or off, the same problem arises. I have other images rendered using 0.86 and there is no problem with them. Has anyone else had this problem and found a fix for it? thanks in advance Jules
