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, With cmd.get_povray() (i.e. cmd.get_povray()[1]) you'll get all vertex-coordinates describing the surface, but I wouldn't know how you could use it to map something on there neatly. Cheers, Tsjerk On Wed, 22 Jun 2005 08:55:05 +0200 madsen wrote: Dear Robert, Tsjerk, Jean-Phil

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 m

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 wrote: I am sorry for being so needy ..Is there a way to quickly write thi

Re: [PyMOL] selecting residues

Try: create 4a, byres (mol around 4 . ) Tsjerk On Wed, 8 Jun 2005 20:50:11 -0700 Eric Hu 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 not select the whole

Re: [PyMOL] coloring bonds

Hi Brandon, What you want is not possible. But, if you make a pdb file containing the atoms involved in flexible bonding and a pdb with the atoms involved in rigid bonding, you can get the image you want. load Protein, protein.pdb load Flex, flexible.pdb load Rigid, rigid.pdb hide everythin

Re: [PyMOL] cgo cylinders with flat ends? More details

0.0, 0.0, 1.0, # RGB Color 1 0.0, 0.0, 1.0, # RGB Color 2 ] ) # then we load it into PyMOL cmd.load_cgo(obj,'cgo013') # move the read clipping plane back a bit to that that is it brighter cmd.clip('far',-5) On Tue, 10 May 2005, T.A.

[PyMOL] Building residues

Hi Warren, I noticed that if I build residues at the N-terminus of a protein, the protein is reoriented to give a best fit to the new residue. I think it's more natural to have the newly added residues reoriented to fit the original protein, as happens when adding to the C-terminus. To add r

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 200

[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" 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, or to t

[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 th

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 ho