RE: [PyMOL] Selective Z-clipping
Hi Kelley, I just worked out a procedure to do this with VMD/Raster3D (oops, this is the PyMol list ...). Anyhow, it boils down to that you can apply selective bounding or clipping planes in Raster3D. In the case of a clipped surface you want to use a bounding plane, which slices through an object and produces a sealed cut (bounding plane) or really play with the lights to get rid of all the interior surfaces exposed by a non-sealing cut with a clipping plane. I played around a little bit with Povray to achieve the same effect. I figured out to use an intersection with CGOs but somehow I could not get it to work with a surface definition. May be somebody else knows how to do this. I'd be interested in it to. Here is what I did. Split your scene into their components and write out the raster3d input files. Remove all headers from the r3d files and save one header into a control script (master.r3d) If you use vmd (oops again...) you have to get rid of the object 17 in the surface definition, otherwise you will not be able change colors, transparency etc. Use remove_17.pl for this. The animate_bounding.pl script allows you to move the bounding plane in a given range to find the right orientation. The only way to do this is by trial and error. A good starting point is a plane defined by the normal vector 0,0,1 (x,y plane at origin of scene). good luck. Carsten animate_bounding.pl Description: Binary data master.r3d Description: Binary data remove_17.pl Description: Binary data
[PyMOL] settings of ribbons and cartoons
Where can I find a list of what I can set with regard to ribbons and cartoons. Currently the cartoons command just shows a thin round tube and the ribbons command shows just a thin line. I'd ideally like to have cartoonishly round ribbons with some of the residues on them drawn in sticks. I'm a new pymole user and am finding it frustrating to work with because it isn't that well documented ... Am I just not looking in the correct places for documentation? I have the pdf at http://pymol.scourceforge.net/userman.pdf, but it isn't specific enough. Please help the hopelessly confussed. Kristl
Re: [PyMOL] settings of ribbons and cartoons
Have you set your sheet and helix part in your pdb? For my personal case, things you experienced happened when this part wasn't built. I guess that PyMOL cannot find the secondary structures as softwares like Rasmol can. Try to determine your secondary structures with DSSP for example and to paste it in your pdb file before loading it in PyMOL, your cartoonish rendering should be great :) Cheers Virgile ADAM
Re: [PyMOL] settings of ribbons and cartoons
Hi Kristl The problem is that the secondary structure of your protein hasn't been defined in the PDB file. This is why the cartoon looks ike a tube. What you need to do is type util.ss into the command line and this will calculate some sort of secondary structure for you although it's not that accurate. Alternatively click on the little diamond next to your protein name in the in the OpenGL window and then click on 'assign ss'. As for your best bet on finding out how to do things this is probably it. Jules On Mon, 25 Nov 2002, Kristl Adams wrote: Where can I find a list of what I can set with regard to ribbons and cartoons. Currently the cartoons command just shows a thin round tube and the ribbons command shows just a thin line. I'd ideally like to have cartoonishly round ribbons with some of the residues on them drawn in sticks. I'm a new pymole user and am finding it frustrating to work with because it isn't that well documented ... Am I just not looking in the correct places for documentation? I have the pdf at http://pymol.scourceforge.net/userman.pdf, but it isn't specific enough. Please help the hopelessly confussed. Kristl --- This SF.net email is sponsored by: Get the new Palm Tungsten T handheld. Power Color in a compact size! http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0002en ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] selecting specific hetatm's
Hello, while this is a simple question, I can't seem to find the answer anywhere. How do I select a specific hetatm: The pdb file says: HETBCL C 1 51 HETBCL C 2 66 HETBCL C 3 66 HETBCL C 4 66 HETBPH C 5 51 HETBPH C 6 65 HETFE2 C 7 1 HETU10 C 8 38 HETU10 C 9 44 HETLDA C 10 16 HETLDA C 11 16 HETLDA C 12 16 HETLDA C 13 16 HETBCL D 1 51 HETBCL D 2 66 HETBCL D 3 66 HETBCL D 4 66 HETBPH D 5 52 HETBPH D 6 65 HETFE2 D 7 1 HETU10 D 8 32 HETU10 D 9 18 And I want to select these individually. I can show all by saying show sticks, (het). I realize this is partially my lack of understanding of how a pdb file is put together, if there is a tutorial on that that someone could refer me to that would be great as well. Thanks, Carly
[PyMOL] Re: PyMOL-users digest, Vol 1 #218 - 1 msg
Hi Carsten, I appreciate your reply and I would assume that it makes impressive graphics, but it sounds WAY beyond my meager abilities (I am struggling with the Mac OS X version of Pymol after all and haven't ventured into the realm of raster3D yet). I assume that since there has been a resounding lack of response within the Pymol masses that it either can't be done or hasn't been done. Just in case somebody missed the prior posting I would like to be able to perform a selective Z-clipping in order to cross-section an active site pocket with a bound ligand. The challenge comes in trying to Z-clip the protein structure (shown as a surface display) while retaining the entire ligand (no Z-clip on the ligand). Prior attempts have either Z-clipped everything (create protein as an object, create ligand as an object, then Z-clip) or Z-clipped nothing (create protein as an object, execute the Z-clip, then create ligand as an object and display it). Somehow the creation of the ligand as an object and displaying it over-rides the prior Z-clip and both objects are displayed in their entirety. Any suggestion within the Pymol world? Thanks, Kelley On 11/25/02 3:06 PM, pymol-users-requ...@lists.sourceforge.net pymol-users-requ...@lists.sourceforge.net wrote: --__--__-- Message: 1 From: Schubert, Carsten carsten.schub...@3dp.com To: 'Kelley Moremen' more...@arches.uga.edu, pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Selective Z-clipping Date: Mon, 25 Nov 2002 09:07:13 -0500 Hi Kelley, I just worked out a procedure to do this with VMD/Raster3D (oops, this is the PyMol list ...). Anyhow, it boils down to that you can apply selective bounding or clipping planes in Raster3D. In the case of a clipped surface you want to use a bounding plane, which slices through an object and produces a sealed cut (bounding plane) or really play with the lights to get rid of all the interior surfaces exposed by a non-sealing cut with a clipping plane. I played around a little bit with Povray to achieve the same effect. I figured out to use an intersection with CGOs but somehow I could not get it to work with a surface definition. May be somebody else knows how to do this. I'd be interested in it to. Here is what I did. Split your scene into their components and write out the raster3d input files. Remove all headers from the r3d files and save one header into a control script (master.r3d) If you use vmd (oops again...) you have to get rid of the object 17 in the surface definition, otherwise you will not be able change colors, transparency etc. Use remove_17.pl for this. The animate_bounding.pl script allows you to move the bounding plane in a given range to find the right orientation. The only way to do this is by trial and error. A good starting point is a plane defined by the normal vector 0,0,1 (x,y plane at origin of scene). good luck. Carsten Dr. Kelley Moremen Associate Professor Complex Carbohydrate Research Center Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602-7229 Office (706) 542-1705Fax: (706) 542-1759 Email: more...@arches.uga.edu (send email with large attachments to: more...@bmb.uga.edu) Website: http://bmbiris.bmb.uga.edu/moremen/lab/
