[PyMOL] RE: Writing info to files

[Warren L. D. <wa...@de...>]

> Currently, i=20
> work on a complexe proteinic which includes two proteins.
> I calculate distances (in a cut-off of 10 Angstr=F6m in order=20
> to obtain atoms=20
> which are within the interface of both molecules) between=20
> these proteins. Now, i would like to know what atoms belong=20
> to my selection and write them=20
> in a file. Could you help me please ?

iterate selection, python-code

For example:

load $PYMOL_DATA/demo/pept.pdb
output=3D open("output.txt",'w')
iterate (name ca), output.write("%s %s %s %s\n"%(resn,chain,resi,name))
output.close()

Would create "output.txt" containing:

ASP E 1 CA
CYS E 2 CA
ALA E 3 CA
TRP E 4 CA
HIS E 5 CA
LEU E 6 CA
GLY E 7 CA
GLU E 8 CA
LEU E 9 CA
VAL E 10 CA
TRP E 11 CA
CYS E 12 CA
THR E 13 CA

Notice how you can freely intersperse Python and PyMOL commands in PyMOL
command scripts in order to accomplish tasks such as this.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020