Tsjerk, Hope you are doing fine. I was toying with your graph.py script. I am trying to mod it to generate solid cube.( display triangles instead of lines) Could you toss an example how to add triangle inside your graph.py? I could not find details in the docs. It appears pymol needs normals for all vertex. This kind of strange as opposed to one for each triangle. Thanks for you help!
--Amit -----Original Message----- From: Tsjerk Wassenaar [mailto:t.a.wassen...@chem.rug.nl] Sent: Tuesday, May 25, 2004 1:04 AM To: a...@sdsc.edu Subject: Re: [PyMOL] 3d plotting in pymol Hi Amit, Well, that was my mistake.., I took adding the cmd.extend() a bit too light-hearted, but I forgot to then parse the (string) elements on the command line. So, for the size and radius these are trivial, but the list arguments are a bit more extensive to parse in five minutes of debugging ;) I have to do that later. You can for now try to use it as a function graph(selection,shape,....etc) That should work. I deliberately tried to progam it in such a way that it would be easy to add new shapes and in a later stage also adapt coloring and such. I can imagine it would be nice to be able to color according to coordinate, b-factor, whatever. But I hope this will do for now :) Good luck, Tsjerk Amit Chourasia wrote: >Tsjerk, >This is what I tried > >1) load a small pdb files (10 atoms) >2) run graph.py >3) graph all, star, 1, 0.10,[1,0,0], >[0,0,1],[[1,0,0],[0,1,0],[0,0,1]], >"graph" > >This is what I am getting >************************************* >Traceback (most recent call last): > File "C:\Program Files\PyMOL/modules\pymol\parser.py", line 139, in parse > result=apply(kw[nest][0],args[nest],kw_args[nest]) > File "C:/Documents and Settings/amit/Desktop/graph.py", line 230, in >graph > >obj.extend(shapefunctions[shape](sel.atom[i].coord,size,r,rgb1,rgb2,mtx >)) > File "C:/Documents and Settings/amit/Desktop/graph.py", line 58, in star > i[0] = mvmult(mtx,i[0]) > File "C:/Documents and Settings/amit/Desktop/graph.py", line 7, in mvmult > return [ a[0][0]*b[0]+a[0][1]*b[1]+a[0][2]*b[2], >TypeError: can't multiply sequence to non-int >************************************* > >Is this something to do with the end of line? Need to use special >character for line continuation when line is broken into several lines? > >Please let me know > >Thanks >--Amit > > > > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :) Molecular Dynamics Group -- :) Dept. of Biophysical Chemistry -- :) University of Groningen -- :) Nijenborgh 4 -- :) 9747 AG Groningen -- :) The Netherlands -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Hi! I'm a .signature virus! -- :) Copy me into your ~/.signature to help me spread! -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
