Wonderful. I'm close to completing what I need, thanks a lot.
I have one other question here. Say I have a peptide:
N-Ala-Ala-Glu-COO (I'm just pointing out the terminal amide and carbonyl
groups). Then I protonate it with h_add
H2N-Ala-Ala-Glu-(C=O)H. Now I carry out a mutation on the last
Hi Martin,
atoms within less than VdW distance. Is there an easy, very low-level, PyMOL
way of fixing this? Can the sculpting wizard be used for this?
Yes, after you place the sidechain and have the new structure (via the
apply function) you can then apply sculpting. It would look
something
Martin,
I am wondering, are there any scripts/ plugins for PyMOL out there that
facilitate the generation of a large amount of rotamers for different
mutants? I might take the effort and start building this into a plugin.
I'm not aware of any. Some of our other seasoned PyMOLers might,
On Mon, Sep 13, 2010 at 12:30 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
# get it's one-letter residue id
print string.split(cmd.get_fastastr(mySelection),'\n')[1]
# get it's three-letter residue id
print three_letter[string.split(cmd.get_fastastr(mySelection),'\n')[1]]
I just
These are all great ideas--I'm glad I asked.
I updated the wiki page (http://www.pymolwiki.org/index.php/Aa_codes)
to reflect this discussion.
Cheers,
-- Jason
On Mon, Sep 13, 2010 at 4:17 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Jason e.a.,
I usually do the hashing like:
aa1 =
Hi all
I want to do some scripted mutations on a range of residues. Say I want
to mutate residue 189 to every rotamer of [Asp, His, Glu, Thr, Lys]
available in the PyMOL internal rotamer library. I'm seeing that PyMOL
issues cmd.get_wizard().do_state(i) to select rotamer 'i' for a
mutation.
