[PyMOL] Surface coloring with ChemPy bricks?
Does surface coloring work with ChemPy bricks? I took the script in examples/devel/brick01.py and changed it to make a ChemPy brick that goes from [0,0,0]--[5,5,5] like so ... examples/devel/brick01.py ... brik.setup_from_min_max( [0.0,0.0,0.0], [5.0,5.0,5.0], [0.5,0.5,0.5]) ... examples/devel/brick01.py ... and then loaded up a pdb file with one hydrogen in that box (briktst.pdb) ATOM 1H H 1 2.000 2.50 2.00 H and then tried to color the surface with using the ChemPy brick ramp_new e_lvl, brick, [-0.5, 0.0, 0.5] set surface_color, e_lvl, briktst show surface, briktst but the surface seems to stay white no matter what I do. Any idea what I'm doing wrong? thanks, -michael Background: I wrote some code to make APBS and PyMOL play nicely with eachother. I wanted to play around with PyMOL's internals a bit, so I wrote some chunks of that in C. Now that other people are actually using that code, it turns out that making sure my source is always up to date with the CVS source (and ditto for other folk's source) is a bit of a pain. So, I tried to rewrite everything in Python and turn APBS's DX maps into ChemPy bricks. I get nice isosurfaces, etc, but I can't color the surface by electrostatic potential. :(. -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
[PyMOL] different stick_radius for different residues
Hi, I was wondering if Pymol is capable of setting different stick thickness for different residues of a molecule. I tried set stick_radius=0.25 show sticks, resi 1-2 set stick_radius=0.1 show sticks, resi 12-15 It appears that the stick_radius variable is global, and it changes the thickness of all the sticks. Thanks, Frank __ Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://webhosting.yahoo.com/ps/sb/
Re: [PyMOL] different stick_radius for different residues
Dear Frank, try: create forSticks1, resi 1-2 show sticks, forSticks1 set stick_radius, .25, forSticks1 create forSticks2, resi 12-15 show sticks, forSticks2 set stick_radius, .1, forSticks2 By using create, you create a new named object with its own settings database. The new object's settings can be set independently of other objects. Best, Morri On Tue, 3 Feb 2004, Dr. S. Frank Yan wrote: Hi, I was wondering if Pymol is capable of setting different stick thickness for different residues of a molecule. I tried set stick_radius=0.25 show sticks, resi 1-2 set stick_radius=0.1 show sticks, resi 12-15 It appears that the stick_radius variable is global, and it changes the thickness of all the sticks. Thanks, Frank __ Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://webhosting.yahoo.com/ps/sb/ --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Outline cartoon representation
Hello all, We'd like to render some cartoon representations of protein structures in a manner similar to the style of Jane Richardson. Basically white, opaque surfaces (no reflections) with black outlines at each of the edges. Here's a link to give you an idea what we're looking for (Figure 1b-c): http://www.nature.com/nsmb/journal/v7/n8/fig_tab/nsb0800_624_F1.html Any suggestions on how to do this using PyMOL? ~Todd
RE: [PyMOL] PyMOL on Powerbook G4
Keana, This is a problem with at least one mac web browser...for some reason the .gz gets removed from the file upon download, but the file is still compressed. If you replace the .gz, then the file will uncompress and open properly when you double-click on it. Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Keana Scott Sent: Tuesday, February 03, 2004 1:16 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] PyMOL on Powerbook G4 Hi all, I am trying to install pymol on powerbook G4 but is getting no mountable file system error. I see that there have been a couple of similar postings in the past but no responses. Can someone please help me? Thanks, Keana Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! http://us.rd.yahoo.com/evt=21608/*http://webhosting.yahoo.com /ps/sb/
RE: [PyMOL] Outline cartoon representation
Todd, Unfortunately that is not a problem PyMOL was designed to solve, and off the top of my head I can't think of any way to bend it around to do this -- you're talking about a different rendering scheme. I think it amounts to the following: trace every sharp edge, and outline every round surface that is tangent to the view. The former could be done with straight OpenGL, but the latter would take a custom shader program. Plus, ideally you'd want postscript or vector output for this kind of illustration -- not a PyMOL-style raster image. Perhaps Molscript has this capability? http://www.avatar.se I think that's what it was originally written to do, way back before color was invented ; ). If not, then you might try contacting David Goodsell. He's got some fantasic protein illustration software... http://www.scripps.edu/pub/goodsell/ Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Todd Geders Sent: Tuesday, February 03, 2004 8:02 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Outline cartoon representation Hello all, We'd like to render some cartoon representations of protein structures in a manner similar to the style of Jane Richardson. Basically white, opaque surfaces (no reflections) with black outlines at each of the edges. Here's a link to give you an idea what we're looking for (Figure 1b-c): http://www.nature.com/nsmb/journal/v7/n8/fig_tab/nsb0800_624_F1.html Any suggestions on how to do this using PyMOL? ~Todd --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
