Vivek, append and extend are Python functions. "cell = []" asks Python to create you a Python list and name it "cell." For more information on list functions see the Python docs (http://docs.python.org/library/stdtypes.html#mutable-sequence-types) about mutable sequence types.
Cheers, -- Jason On Tue, Jul 13, 2010 at 1:18 PM, Vivek Ranjan <vran...@gmail.com> wrote: > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? 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