pymol-users
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From: Gilmar Salgado <gilmar@em...> - 2003-05-13 18:02:14
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Hi all, I'm new with Pymol and I would like your help in the following problem: I have a receptor image that I want to emphasize the ligand in its interior. Its a nonpeptidic ligand that I would like to increase the radius of the sticks model. I also would like to draw a plane connecting 4 atoms in one specific region of the ligand. I would appreciate your suggestions. Thanks: Gilmar Gilmar Salgado Old Chem. Bld #114 Univ. of Arizona 520-6212537 |
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From: Nat Echols <nat@bi...> - 2003-05-13 19:44:06
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> I'm new with Pymol and I would like your help in the following problem: > I have a receptor image that I want to emphasize the ligand in its interior. I'm a big fan of transparent surfaces for this, e.g.: http://bioinfo.mbb.yale.edu/people/nat/mbp.mpg > Its a nonpeptidic ligand that I would like to increase the radius of the > sticks model. set stick_radius = 0.3 or something like that - I think the default is 0.25 or something like that. > I also would like to draw a plane connecting 4 atoms in one specific region > of the ligand. Use a CGO: http://pymol.sourceforge.net/html/S0500cgo.html What you'd really need is probably a triangle strip - the two triangles being the two haves of the quadrilateral object with the 4 atoms as vertices. ---------------------------------------------------------------------------- Nathaniel Echols Programmer nat@... Gerstein Lab 203-589-6765 Yale University ---------------------------------------------------------------------------- |
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From: Robert Campbell <rlc1@po...> - 2003-05-13 20:01:00
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* Nat Echols <nat@...> [2003-05-13 15:38] wrote: > > I'm new with Pymol and I would like your help in the following problem: > > I have a receptor image that I want to emphasize the ligand in its interior. > > I'm a big fan of transparent surfaces for this, e.g.: > http://bioinfo.mbb.yale.edu/people/nat/mbp.mpg > > > Its a nonpeptidic ligand that I would like to increase the radius of the > > sticks model. > > set stick_radius = 0.3 > or something like that - I think the default is 0.25 or something like > that. And if you want to draw sticks for both the protein and ligand at different radii, you can do: set stick_radius, 0.2, protein set stick_radius, 0.5, ligand assuming that "protein" and "ligand" are different objects. If they come from one PDB file, then you can read the PDB file in and then create a separate object for the ligand with something like: create ligand, (selection) in which you replace "selection" with something that will select only your ligand. Hope this helps, Robert -- Robert L. Campbell, Ph.D. <rlc1@...> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-633-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 |
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From: yibin xu <yibin.xu@jc...> - 2003-05-20 07:19:14
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Dear All, I want to show sticks for only side-chains (CA and beyond CA) of selected residues in the cartoon mode. Is there an easy way to do that ( my way is to use SELECT followed by showing sc but mc atoms are still displayed)? Thank you very much in advance. Regards yibin |
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From: Warren L. DeLano <warren@de...> - 2003-05-20 09:41:47
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Yibin, show sticks, (not name c,n,o) show cartoon set cartoon_smooth_loops, 0 and perhaps set cartoon_flat_sheets, 0 Cheers, Warren -- mailto:warren@... Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -----Original Message----- From: pymol-users-admin@... [mailto:pymol-users-admin@...] On Behalf Of yibin xu Sent: Monday, May 19, 2003 11:08 PM To: 'PyMOL list' Subject: [PyMOL] how to show sticks for the side-chains of selected residues Dear All, I want to show sticks for only side-chains (CA and beyond CA) of selected residues in the cartoon mode. Is there an easy way to do that ( my way is to use SELECT followed by showing sc but mc atoms are still displayed)? Thank you very much in advance. Regards yibin ------------------------------------------------------- This SF.net email is sponsored by: ObjectStore. If flattening out C++ or Java code to make your application fit in a relational database is painful, don't do it! Check out ObjectStore. Now part of Progress Software. http://www.objectstore.net/sourceforge _______________________________________________ PyMOL-users mailing list PyMOL-users@... https://lists.sourceforge.net/lists/listinfo/pymol-users |