Re: [PyMOL] Selecting a lot of residues

[Lieven Buts]

On Wednesday 03 December 2003 22:25, Gwendowlyn S. Knapp wrote:
 Maybe I didn't word my question right. I have several proteins (like
 15-20) that i need to do this for and i also have these lists. i was
 wanting to see if there was anyway to have pymol read in that list
 automatically so i didn't have to type in all the residues (ie, about 60
 on each protein).

OK , here's a third possiblity. This little Python script
--
from sys import stdin,stdout

stdout.write(select group,(protein and chain A and resi )

first = 1

for line in stdin.readlines():
if not first: stdout.write(,)
stdout.write( line[:-1] )
first = 0

stdout.write()\n)
--

when used as python make_select.py  list  list.pml will transform a list 
of residues like
5
10
50
51
52
100

into a single-line PyMol command

select group,(protein and chain A and resi 5,10,50,51,52,100)

which can be copied/pasted into PyMol, or read from the file with @list.pml.


-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel

[PyMOL] delete dashes from selection

[mwilke]

Here's my question:

I've used the PyMOL dist command to make H-bond dashes between a small 
molecule (I called it peng) and my protein.

dist hbonds, (peng and elem o+n),(not peng and elem o+n),3.2

This worked great except it made one H-bond between 2 carbonyl oxygens.  I'd 
like to delete the dashes for just this bond, but don't know how to select 
specifically it from the group selection hbonds so that I don't erase all the 
H-bonds in the group.  It would be a pain to have to specify each H-bond 
separately.  Any ideas?

- Mark