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
