Re: [PyMOL] rearranging the coordinates of a PDB file

Hi Vanessa, (1) Are there commands that I can type such that I can shift the coordinate for the entire PDB file without using the mouse? Try: alter_state 1,selection,(x,y,z)=(newx,newy,newz) (2) If the mouse is the only way I can shift coordinates, then how do I use the mouse so that I

Re: [PyMOL] colouring surfaces according to molecular properties

Hi Anders, You can add a property value to the b-factor or occupancy field in the pdb file. Then you can color using the spectrum command. Just have a look at the help for that. For real fancy coloring, either in some way construct a 3D map, which you can read in in Pymol (can someone give

Re: [PyMOL] how to get pymol sec structure assignments printed out to a file

I think you can try: ffout=open('secstruc.txt','w') iterate name ca, ffout.write(repr((chain, resi, ss))) Hope it works, but otherwise Warren will correct me :) Tsjerk On Fri, 17 Jun 2005 11:12:53 -0400 hari jayaram hari...@gmail.com wrote: I am sorry for being so needy ..Is there a way to

Re: [PyMOL] selecting residues

Try: create 4a, byres (mol around 4 . ) Tsjerk On Wed, 8 Jun 2005 20:50:11 -0700 Eric Hu eric.y...@gmail.com wrote: Hi, I ran into a problem selecting nearby residues of one molecule regarding the binding partner. The byres command seems to work only with one single residue. It does

Re: [PyMOL] Own CGO or R3D - Surfaces

Hi Jason, As far as I know of, there is not. This is basically the point that you should consider taking the best of two worlds: Pymol for handling the chemics and Povray for other objects and graphics. Maybe the macro I posted yesterday will be of some value. Cheers, Tsjerk On 18 Feb

[PyMOL] Povray macro

Hi Guys, For those interested, I've made a macro for Povray which allows to transform the Pymol povray output back to model space, or to transform povray models to Pymols camera space. After #including pymolmacro.inc call PYMOL_VIEW() with the eighteen floats from cmd.get_view() to set the

[PyMOL] Povray macro (with attachment)

Okay, smart.., forgot the attachment and took a while to realize it :) On Thu, 17 Feb 2005 11:21:53 +0100 T.A.Wassenaar t.a.wassen...@rug.nl wrote: Hi Guys, For those interested, I've made a macro for Povray which allows to transform the Pymol povray output back to model space

Re: [PyMOL] change from spectrum to solid colour in animation

Hi Noboru, Basically you could use that command, though you would have to extend it such that it reads the starting color from the atoms. As I recall that is possible in pymol. Only question which remains then is whether spectrum truly colors by atom. But that one Warren knows (as he knows