[PyMOL] another question about ca trace model.
Hi, there: I am trying to make a movie following the intruction at http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html From Lsqman, I got a serial of PDB files morphing between two conformations. These PDB files contain only alpha carbon and non-hydrogen side-chain atoms. Then I used DSSP to include the secondary structure information ito the PDB files. In the pymol, after set cartoon_trace, 1 the helix and loop showed up nicely. But all the strands are missing. I tried several setting about cartoon but just can't get them out. Do you have any idea how to solve this problem. Thank you. Tiger _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
Re: [PyMOL] another question about ca trace model.
Tiger, Unfortunately I don't have much experience with this procedure. But one thing came to mind, you can manually assign secondary structure within DEEPVIEW/SWISS PDB Viewer [EDIT]. Not sure how many pdb files you have generated for the morph, but if nothing else works, you could try manually assigning secondary structures and see how that works out. Yep, a huge pain in the buttocks I know, but it should work, in theory. Best of Luck. Cheers, Nick - Original Message - From: Geng Tian gengt...@hotmail.com To: pymol-users@lists.sourceforge.net Sent: Tuesday, April 18, 2006 6:24 AM Subject: [PyMOL] another question about ca trace model. Hi, there: I am trying to make a movie following the intruction at http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html From Lsqman, I got a serial of PDB files morphing between two conformations. These PDB files contain only alpha carbon and non-hydrogen side-chain atoms. Then I used DSSP to include the secondary structure information ito the PDB files. In the pymol, after set cartoon_trace, 1 the helix and loop showed up nicely. But all the strands are missing. I tried several setting about cartoon but just can't get them out. Do you have any idea how to solve this problem. Thank you. Tiger _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] mutations
Hi all I'm a newbie to Pymol and so far have been very impressed. However I have tried to mutate some residues in my structure and have hit a brick wall. Has anyone done this with pymol and let me know how to do it? Regards Orla Dr.Orla O'Sullivan Research Officer Biotechnology Moorepark Food Research Centre Teagasc Moorepark Fermoy, Co. Cork Ireland Tel: +353 - (0)25 - 42344
[PyMOL] (small) Pymol feature request--filter for edit settings window
While we're discussing ways to make our favorite program a little better, I had an idea I thought I'd throw out there... While making some figures the other day, I found myself scrolling endlessly through the edit settings menu (under Setting -- Edit All) a number of times, mostly to locate a relatively small number of settings related to ray tracing. This got me thinking about a way to improve access to the many wonderful features that have been added to PyMOL. The solution I came up with is a filter line which could be placed directly above the window listing all the settings. Users could then type a word, say ray or cartoon, and only the settings containing this word would be shown. The best example of a program containing this feature is the about:config window in Firefox. When you open a browser and type about:config instead of an address, a window containing hundreds of settings appears. At the top is a filter bar which you can use to pare down the number of settings listed below. I think this would be a great addition to PyMOL and would help users familiarize themselves with the many new settings which have been (and will be) implemented. :) Perhaps others have even better solutions to this problem. The use of a filter is just the first idea which came to my mind. I think it would be relatively easy to implement, although my python programming skills are somewhat limited. Thanks, Michelle Gill
Re: [PyMOL] mutations
Orla, This is simply, for the most part. Here is what I do. Load your *.pdb file. Then under WIZARD in the menu bar, select MUTAGENESIS. Then pretty much, follow directions. In the PyMOL VIEWER window, it will ask you to ' pick a residue.' Once you pick a residue, select the type of residue you want to mutate to by left clicking on [No Mutation] button and holding down (under Mutagenesis). This brings up a list of residues that you can then select from. Once you select the residue you want, hit APPLY, then DONE. If everything was done correctly, you should see your mutated residue. There are probably other ways to do this, but I hope this helps. If you would like screenshots of the steps, just let me know. Cheers, Nick - Original Message - From: Orla O'Sullivan To: pymol-users@lists.sourceforge.net Sent: Tuesday, April 18, 2006 11:31 AM Subject: [PyMOL] mutations Hi all I'm a newbie to Pymol and so far have been very impressed. However I have tried to mutate some residues in my structure and have hit a brick wall. Has anyone done this with pymol and let me know how to do it? Regards Orla Dr.Orla O'Sullivan Research Officer Biotechnology Moorepark Food Research Centre Teagasc Moorepark Fermoy, Co. Cork Ireland Tel: +353 - (0)25 - 42344
[PyMOL] anybody have experience with the get_area command?
Does it work? We're running version 0.99rc6 on both windoze and linux (RHEL,WS4) and the get_area command returns nothing (no error, no value). I've tried this with a number of situations, including loading a single object with a single protein chain and issuing get_area all, get_area n+c, get_area /obj01 et cetera following the examples listed in Warren's former e-mail and subsequently replicated on the Wiki. get_area ? lists the syntax as get_area [ selection [, state [, load_b [, quiet , but help get_area does not help Thanks for any suggestions, Tom This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. Exelixis, Inc. reserves the right, to the extent and under circumstances permitted by applicable law, to retain, monitor and intercept e-mail messages to and from its systems.
[PyMOL] isomesh for electrostatic potential
Dear PyMoler, In the pymol apbs tool, there is an option to show the negative/positive isosurface (not the molecular surface) upon loading an electrostatic map. My question is if there is a way to show the electrostatic potential surface as mesh instead of solid surface, also if it is possible to show the potential as a series of contours. Thank you. Chun
Re: [PyMOL] isomesh for electrostatic potential
On Tue, 18 Apr 2006, Chun Tang wrote: Dear PyMoler, In the pymol apbs tool, there is an option to show the negative/positive isosurface (not the molecular surface) upon loading an electrostatic map. My question is if there is a way to show the electrostatic potential surface as mesh instead of solid surface, also if it is possible to show the potential as a series of contours. Thank you. Chun The plugin doesn't allow you to show a mesh, but it would be a good idea to build that in. You can do it from the command line with the isomesh command. If you're using the plugin to do everything, you can do something like this: isomesh iso_pos_mesh, apbs_map, 0.5 color blue, iso_pos_mesh If you're not using the plugin, change 'apbs_map' to whatever your map is called. the idea of showing a series of contours is probably a good one. I'm not sure how to make a nice GUI interface for it, though. I recently switched to a Mac. It was broken for quite a while, but I think I finally got things working properly this weekend. I'll try to put out a new version of the plugin soon. At the moment, here's what I'm planning to add: - the ability to use pdb2pqr to generate pqr files - the ability to display the APBS version - the ability to display isomeshes in addition to isosurfaces any other big suggestions? -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mler...@umich --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] another question about ca trace model.
Hi, Noinaj: Thanks for your suggestion. I feel it is not the assignment problem. I tried using cartoon tube to show the 2nd structure and the strand part can showed up. Then I painted the molecule according to the secondary structure by using util.cbss(morphy_01,red,yellow,green) and the strand is color as yellow correctly in the cartoon tube mode. Then I tried another thing, I copy-pasted the second structure information from the ca trace pdb to my formal all stoms pdb, the strand showed up correctly. This means these information are correct. So I guess under the default cartoon automatic mode, pymol can't draw arrow for the strand residues which do not have the coordinates of N, C, O written in the PDB file. This might be a default setting of pymol I can't find to turn off or just an internal problem for cartoon automatic mode. Thank you again. Tiger From: Noinaj noi...@uky.edu To: Geng Tian gengt...@hotmail.com,pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] another question about ca trace model. Date: Tue, 18 Apr 2006 11:06:49 -0400 Tiger, Unfortunately I don't have much experience with this procedure. But one thing came to mind, you can manually assign secondary structure within DEEPVIEW/SWISS PDB Viewer [EDIT]. Not sure how many pdb files you have generated for the morph, but if nothing else works, you could try manually assigning secondary structures and see how that works out. Yep, a huge pain in the buttocks I know, but it should work, in theory. Best of Luck. Cheers, Nick - Original Message - From: Geng Tian gengt...@hotmail.com To: pymol-users@lists.sourceforge.net Sent: Tuesday, April 18, 2006 6:24 AM Subject: [PyMOL] another question about ca trace model. Hi, there: I am trying to make a movie following the intruction at http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html From Lsqman, I got a serial of PDB files morphing between two conformations. These PDB files contain only alpha carbon and non-hydrogen side-chain atoms. Then I used DSSP to include the secondary structure information ito the PDB files. In the pymol, after set cartoon_trace, 1 the helix and loop showed up nicely. But all the strands are missing. I tried several setting about cartoon but just can't get them out. Do you have any idea how to solve this problem. Thank you. Tiger _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users _ On the road to retirement? Check out MSN Life Events for advice on how to get there! http://lifeevents.msn.com/category.aspx?cid=Retirement
[PyMOL] RE: filter for edit settings window
Hi Michelle, In case no one's mentioned it yet, Zac Panepucci has contributed a grepset.py script which, after being run, allows you to type grepset x to see all settings (and their values) associated with whatever x is. It's not directly integrated into the pymol distribution but pretty tidily achieves what you describe. More info and the script itself is on the wiki: http://www.pymolwiki.org/index.php/Grepset Cheers, Seth (on behalf of Zac and his useful scripts)
[PyMOL] povray image mapping and default pigments
This is for the povray gurus out there...
Occasionally I muck around with the time-consuming practice of trying to map
pictures onto molecular surfaces with povray.
I had this working to some extent, but something has changed (I think with
the povray file format produced by pymol make_pov where now there are
fancy texture_list texture and pigment statements, rather than simple
pigment ones.)
In the past, I set it up so that the povray file has a header (cameras,
lights, etc.) separate from the molecular scene description. Then I would
usually edit the header to apply some #default texture or pigment to use the
povray parlance. So the approach I used to use was to strip out all the
pigment {} statements from the molecular scene descriptor povray input with
a perl script, and then use the #default pigment {image_map{
mypicturehere.gif }} syntax in the header to map the image on to the
surface...the practical uses of having a picture of someone, say,
snowboarding down a mountain mapped onto the surface of some kinase are just
endless. But that aside, the problem now is that these newer texture_list
statements aren't so amenable to this global pigment removal thing, and I
haven't quite figured out how best to get around this. (Couldn't remove them
entirely and putting in the image_map pigment thing didn't seem to work,
although maybe I just didn't get the right combination of open and closed
brackets {?}}})
Anyone have any experiences along these lines? As near as I can tell, there
was some switch in smooth triangle definitions with Povray 3.5 which was
capitalized on by some pymol 0.98 edition. Perhaps I have to go back to an
old archived version of pymol? Or, more sensibly, perhaps I should recognize
that pictures of easter bunnies or whatever don't belong on some
wood-textured rendition of a half-submerged albumin, glowing softly in the
warm light(s) of a double sunset over an infinite lake lapping at the shores
of a checkered beach. But for some reason journal editors seem to enjoy
this.
Thanks,
Seth
