Thank you, it was really what I asked!
Em seg, 5 de ago de 2019 15:50, Christian "Cole" French <
christian.fre...@schrodinger.com> escreveu:
> select_with_filter allows you to make a selection as you would with the
> select command, so it supports all selection algebra including byres,
>
select_with_filter allows you to make a selection as you would with the
select command, so it supports all selection algebra including byres,
chain, organic, etc. Here's a modified example from the wiki:
# Select all residues within 5 Ang. of any organic small molecules whose
x-coordinate is at
Yes, one more question.
How to use all other "functions", like byres, "chain A" or "organic"?
Em seg, 5 de ago de 2019 12:36, Christian "Cole" French <
christian.fre...@schrodinger.com> escreveu:
> I see now. I updated the code at the link in my previous email to provide
> behavior which should
I see now. I updated the code at the link in my previous email to provide
behavior which should allow you to do what you want. Here are your examples
written using the command:
select_with_filter sele, flag 8, lambda s: len(cmd.get_chains(s)) < 2
select_with_filter sele, flag 8, lambda s:
I expressed myself wrong, I'm looking something like:
select peplength < 15 and chain A
Where peplength is an user defined function like:
def peplength(atom):
return compute_peplength(atom)
I'm looking for the availability of user defined functions on selection
expressions. How to?
Em
Edit: remove the cmd. part when running select_with_filter. (Since it's a
custom command, it doesn't belong to the cmd module.)
On Fri, Aug 2, 2019 at 2:41 PM Christian "Cole" French <
christian.fre...@schrodinger.com> wrote:
> Hi Pedro Lacerda,
>
> Here is a link to a script I wrote which adds
Hi Pedro Lacerda,
Here is a link to a script I wrote which adds a command which does what you
ask: https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865.
To use it, download the file to the directory where you run PyMOL from,
then open PyMOL and run run select_with_filter.py.
For
Katherine,
not sure if that is what you are looking for but you can select for non-polymer
residues with:
select lig, prot and organic
That will select any non polymer (protein and R(D)NA) residues present in the
pdb. You then would need to break the selection further into the individual
Hi Carsten,
Thanks for the help. I've tried variants of that selection and it works
great if there is only one ligand. Unfortunately it breaks down when there
are multiple ligands and they don't all fit the criteria. I'm surveying
almost half the PDB so these are all different proteins with
Hi Katherine,
PyMOL can do what you want. I've done this exact task before.
Here's the idea. If you have a PDB with multiple ligands and you use,
select allLigands, organic and myProtein
you create the selection allLigands which contains all the ligand
atoms in myProtein. What you need to do
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