Thank you once again. I have been trying to change the color of the cell. cell = [] cell.append(CYLINDER) cell = cell + vert_000 + vert_100 + [radius] + [0,0,0] + [1,0,0] cell.append(CYLINDER) cell = cell + vert_000 + vert_010 + [radius] + [0,0,0] + [0,1,0] cell.append(CYLINDER)
if I put cell.append(CYLINDER, [COLOR, 0, 0, 1]), pymol complains "TypeError: append() takes exactly one argument". If I add a line "cell.extend([COLOR, 0.0, 0.0, 1.0])" after the above cell.append(CYLINDER), nothing displays. There is also very little description of cgo on "http://pymol.sourceforge.net/newman/user/S0500cgo.html"; How to change the color of the cell ? What is append(), and extend() ? Is there a document that describes complete functionalities of CGO ? Basically, I would like learn how CGO, python, and openGL are connected within pymol. Please let me know. Thank you again, Vivek Ranjan On Tue, Jul 13, 2010 at 12:13 PM, Robert Campbell <robert.campb...@queensu.ca> wrote: > Hello Vivek, > > On Tue, 13 Jul 2010 11:21:03 -0400 Vivek Ranjan <vran...@gmail.com> wrote: > >> Hello, >> >> First, thanks a lot for your help. Pymol with cctbx works now for me. >> I changed the script "pymol" and replaced "/usr/binpython" to "python" >> and thats it. Few more questions: >> >> (i) draw_cell.py uses lavv.pdb as an example. Where can I find this >> pdb file ? Basically, I am making my own pdb file for a crystal >> system, the file lavv.pdb can help me figure out how to put crystal >> information in my own pdb file. > > That would be "1avv" not "lavv". All PDB structure codes begin with a number. > You could use "fetch 1avv" to get it, but I guess you know that. > >> (ii) I used "draw_cell_param" command to put crystal information at >> command prompt. Then I wanted to change radius, etc. How to undo what >> has already be drawn so that I can re-sketch ? Or killing the pymol, >> starting it again, and loading everything again is the only option ? >> Similarly, is there a way to turn off labels ? > > The only way to "undo" what you have done is to delete the objects created by > draw_cell_param (or similarly with draw_cell) and rerun the draw_cell_param > function. You'll find the delete function under the "A" menu next to the > object name or simply type "delete cell*" to delete all objects whose name > begins with "cell". > > As far as the labels go, you'll note that two objects are created by the > draw_cell function. One object is the cell border and the second is the > labels. Simply click on the name of the labels and they will turn off. This > is true of any object. > >> (iii) For the same reason as stated above, I would like to know how to >> get the file for 2x19 ? When I issue the command "fetch 2x19" it draws >> a structure. Where is the pdb file for it and how to get it to my >> computer ? > > The fetch command should leave the 2x19.pdb file in the directory from which > you started PyMOL. > > Cheers, > Rob > -- > Robert L. Campbell, Ph.D. > Senior Research Associate/Adjunct Assistant Professor > Botterell Hall Rm 644 > Department of Biochemistry, Queen's University, > Kingston, ON K7L 3N6 Canada > Tel: 613-533-6821 Fax: 613-533-2497 > <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Thank you and Regards, Vivek Ranjan ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
