mol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Pymol insertion code
> Date: Thu, 20 Mar 2014 17:26:21 +
>
> Sorry - one quick correction to my previous email:
>
> On Mar 20, 2014, at 10:50 AM, Sampson, Jared wrote:
>
> > If you don’t need the cartoon representation t
Sorry - one quick correction to my previous email:
On Mar 20, 2014, at 10:50 AM, Sampson, Jared wrote:
> If you don’t need the cartoon representation to be continuous (e.g. if you’re
> zooming in on a different section of the protein you can replace the 3rd line
> with:
>
> alter prodomain, c
Hi Nick -
This PDB employs non-standard usage of the PDB insertion code column.
Typically, it is used to insert one or more residues between adjacent numbers
in a canonically numbered structure, e.g. residue 42A (along with 42B, 42C, … ,
42P, etc.) is between residues 42 and 43.
As for whethe
Hi,
I'm new to Pymol and am looking at the structure of pepsinogen (PDB: 3psg).
This protein contains a 44 residue prodomain, which the pdb file says is
assigned an insertion code 'P' and labelled 1 - 44. This prodomain is cleaved
to yield pepsin (5pep), whose sequence is labelled 1 - 326. I gat
Hi,
Wouldn't you get about the same if you did:
import string
proper = set([ i.resi for i in cmd.get_model('all').atom if not
i.resi[-1] in string.ascii_letters ])
I admit, there is a pattern with my previous posts :p And I know, the
import statement can be added as __import__('string').ascii_le
Hi Nat,
I don't think PyMOL natively handles something that slick. I would
then start scripting:
fetch 3edx, async=0
# start a Python block
python
# import stored
from pymol import stored
# create a set to hold residue identifiers
stored.resiList = set()
# this set will contain those resi
On Tue, Feb 15, 2011 at 2:07 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Interesting question. PyMOL's wildcards can help here:
>
> select allButInsertionsA, not (i. *A)
>
> This will look for all residue NUMBERS that end in "A" and select
> everything but that.
>
Thanks, that
Hi Nat,
Interesting question. PyMOL's wildcards can help here:
select allButInsertionsA, not (i. *A)
This will look for all residue NUMBERS that end in "A" and select
everything but that.
Cheers,
-- Jason
On Tue, Feb 15, 2011 at 4:10 PM, Nat Echols wrote:
> Is there a way to select specific
Is there a way to select specific insertion codes - or rather, their
absence? I'm automatically building up selections like "chain A and ((resi
1:5) or (resi 10) or (resi 13))", and I want to ignore insertions, which
tend to duplicate residue numbers. "help selection" didn't turn up
anything, and
