Re: [PyMOL] Series of general questions
Tony, I'll answer the easy questions, and leave the tough ones to the real gurus... 1) I would like to show certain residues and have no problem getting the ones I want selected and displayed as sticks or whatever. The problem is color. When I change the color of the selection, it changes the color of the associated section of the ribbon. I would like to leave the ribbon, say green, and show the residues in yellow. The easiest way is to use two objects. Say you already have your protein object (my_protein) and the selection of required objects (my_sel): hide everything create copy, my_protein show ribbon, my_protein color green, ribbon show sticks, my_sel color yellow, my_sel 2) When selecting specific sidechains, it is often preferable to choose only the sidechain atoms instead of the sidechain+backbone. In the good ol' molscript days you would say select and not c or n or o but if you do that in pymol it thinks you mean all carbon, nitrogen, and oxygen atoms instead of their id in the PDB file. I'm sure this is worked out but I don't see it in the example scripts I've found on line. PyMOL distinguished between element types and PDB atom names. For example, select all_oxygen, (e;o) select backbone_oxygen, (n;o) So to select sidechain atoms of an existing selection my_sel: select sidechain_of_my_sel, (my_sel !n;n,c,o) Gareth -- --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548 http://www.ebi.ac.uk/~gareth
Re: [PyMOL] Series of general questions
Tony, Gareth, when I display sidechains only, I want to see the proline nitrogen. After I've loaded all objects, I select all mainchain atoms (except proline nitrogen) and display sidechains like this: select mainchain, n;C,O,N and not pro/n show sticks, object and not mainchain The advantage is that the mainchain selection works for all objects that have been read into pymol before selection, like so: show sticks, object2 and not mainchain show sticks, object3 and not mainchain etc Andreas 2) When selecting specific sidechains, it is often preferable to choose only the sidechain atoms instead of the sidechain+backbone. In the good ol' molscript days you would say select and not c or n or o but if you do that in pymol it thinks you mean all carbon, nitrogen, and oxygen atoms instead of their id in the PDB file. I'm sure this is worked out but I don't see it in the example scripts I've found on line. PyMOL distinguished between element types and PDB atom names. For example, select all_oxygen, (e;o) select backbone_oxygen, (n;o) So to select sidechain atoms of an existing selection my_sel: select sidechain_of_my_sel, (my_sel !n;n,c,o) Gareth -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529 http://www.biochem.utah.edu/~andreas
RE: [PyMOL] Series of general questions
1) I would like to show certain residues and have no problem getting the ones I want selected and displayed as sticks or whatever. The problem is color. When I change the color of the selection, it changes the color of the associated section of the ribbon. I would like to leave the ribbon, say green, and show the residues in yellow. Is there a way to uncouple the color assignment of the ribbon and the residue. For set ribbon_color, green Same goes for cartoon_color, sphere_color, surface_color, dot_color, and mesh_color. Note that these are for global, full-object, or full-state uniform color. If you need finer-grained color control, then you have to create separate objects as Garrett suggested. 3) Is there a way to change the particular rendering of the beta-strands at a paritcular residue. If you use 'flat Yes -- new in version 0.95: flag no_smooth, selection, set rebuild For example, if residue 200 is shown both in sticks and in a flat sheet, you can force that sheet to pass through the resi 200 CA position as follows: show sticks, resi 200 and (pro/n | !*/n+c+o+h) show cartoon flag no_smooth, resi 200, set rebuild The alternative, which I personally find distasteful, is to drag the CA atom position into the plane of the sheet using the mouse in editing mode (ctrl-shift-left-click-and-drag) in order to create an unreasonably long CA-CA bond. This is best done with a separate copy of the object so that the cartoon itself doesn't move. 4) This is the hard but cool one. Is there a way to make a particular atom or object the light source for an image. You can imagine if you turned off all other lighting and put your omnidirectional light on your cooridnated metal atom it could look pretty cool (or just have a dim headlight seeting). Does anyone know how to arbitrarily set the lighting in this fashion? PyMOL can't do this -- you'd need to export to POV-Ray...but PyMOL's current export code is quite dated. Cheers, Warren
