[PyMOL] Super and Align missing residues

[Nathan Clement]

Hi,

I'm trying to compute the interface RMSD (iRMSD) between two protein pairs
that are highly similar (might have a few missing residues, but are
otherwise identical). Right now, my code does something like the following
for protein pairs "gold" and "test" (receptor has chains A+B and ligand has
chains C):

PyMOL>select contact_rec, (gold & chain A+B) & all within 10 of (gold &
chain C) & n. ca
PyMOL>select contact_lig, (gold & chain C) & all within 10 of (gold & chain
A+B) & n. ca
PyMOL>align gold & contact_rec + contact_lig, test, cycles=0
 Match: read scoring matrix.
 Match: assigning 82 x 445 pairwise scores.
 MatchAlign: aligning residues (82 vs 445)...
 MatchAlign: score 257.500
 ExecutiveAlign: 67 atoms aligned.
 Executive: RMS =   14.161 (67 to 67 atoms)

This seems to suggest that, even with cycles=0, 82-67=15 atoms were not
included in the alignment. When I look at the alignment (object=aln), it
appears that most of the "missing" residues from this alignment have the
same residue name, are matches in the sequence alignment, and are in a
nearby location.

Is it possible to force align to give the full RMSD calculation? super has
the same issue, and I'm concerned that using something like rms or fit
won't work because the "gold" and "test" have different residue numbering
(and might be missing residues so it's not always possible to give them an
equivalent numbering).

Does anybody have any suggestions?

Thanks in advance,

Nathan
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Re: [PyMOL] Preventing Output of pair_fit

[Nathan Clement]

Awesome. This is exactly what I was looking for.

Nathan

On Mon, Jul 23, 2018 at 11:16 AM Jarrett Johnson <
jarrett.john...@schrodinger.com> wrote:

> Hello Nathan,
>
> While we prepare to rollout the "quiet" argument for pair_fit, in the
> meantime try:
>
> cmd.feedback("disable", "executive", "results")
>
> Jarrett J.
>
> On Sun, Jul 22, 2018 at 6:47 PM, Jarrett Johnson <
> jarrett.john...@schrodinger.com> wrote:
>
>> Hello Nathan,
>>
>> We actually just implemented a 'quiet' argument for the pair_fit command
>> on Friday. This should be live in an upcoming update.
>>
>> Jarrett J.
>>
>> On Sun, Jul 22, 2018 at 6:32 PM,  wrote:
>>
>>> Hi,
>>>
>>> Consider the following (simplified) Pymol script, test.py:
>>>
>>> -
>>> import sys
>>> cmd.load(sys.argv[1], 'prot1')
>>> cmd.load(sys.argv[2], 'prot2')
>>> rms = cmd.pair_fit('prot1 & n. ca','prot2 & n. ca')
>>> print 'This should print', rms
>>>
>>> -
>>>
>>> I would like the only output for this program to be created by the line,
>>> 'This should print.' However, here is what I actually get, with a few
>>> different options:
>>>
>>> $ pymol -qc test.py -- protein.pdb protein.pdb
>>>  ExecutiveRMS: RMS =0.000 (96 to 96 atoms)
>>> This should print 0.0
>>> $ pymol -Qc test.py -- protein.pdb protein.pdb
>>> $
>>>
>>> (The first prints output from ExecutiveRMS, and the second prints nothing
>>> at all.)
>>> Is there any way to prevent the ExecutiveRMS output? Either
>>> programmatically or on the command line?
>>>
>>> Thanks much,
>>>
>>> Nathan
>>>
>>>
>>>
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>>
>>
>>
>> --
>> Jarrett Johnson,
>> Schrödinger
>>
>
>
>
> --
> Jarrett Johnson,
> Schrödinger
>
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Re: [PyMOL] Super and Align missing residues

[Nathan Clement]

For anyone who has found this thread, I've taken some time and put together
an alignment + RMSD script for Pymol (using BioPython). You can find it on
GitHub, here 
.
It's a bit overkill, and only handles single chain proteins, but it's quite
robust if it fits your needs.

On Wed, Jul 4, 2018 at 3:05 PM Thomas Holder 
wrote:

> Hi Nathan,
>
> I have some insights for this issue. Basically the long gaps between the
> selected parts become too expensive in the alignment scoring. Changing e.g.
> the gap extension penalty leads to the expected result:
>
> # default is extend=-0.7, lowering to -0.6
> super gold & contact_all, test, cycles=0, object=super, extend=-0.6
>
> I think PyMOL's handling of selection gaps during the alignment could be
> improved, they should be handled different from regular alignment gaps.
>
> Cheers,
>   Thomas
>
> > On Jun 28, 2018, at 2:14 PM, Thomas Holder <
> thomas.hol...@schrodinger.com> wrote:
> >
> > Hi Nathan,
> >
> > Thank you very much for the files and instructions. I can reproduce the
> problem. I haven't seen this before and don't know yet what's going wrong,
> we will investigate.
> >
> > Cheers,
> >  Thomas
> >
> >> On Jun 28, 2018, at 10:50 AM, nclem...@cs.utexas.edu wrote:
> >>
> >> The alignment in this example is nearly perfect. Even the residues left
> >> out of the fitting have perfect matches at the sequence level (as can be
> >> seen by saving the super object and turning on the sequence alignment
> and
> >> contact_all).
> >>
> >> PyMOL>load 1AY7_u.pdb, test
> >> CmdLoad: "1AY7_u.pdb" loaded as "test".
> >> PyMOL>load 1AY7_b.pdb, gold
> >> CmdLoad: "1AY7_b.pdb" loaded as "gold".
> >> PyMOL>select contact_rec, gold & chain R & (all within 10 of gold &
> chain
> >> L) & n. ca
> >> Selector: selection "contact_rec" defined with 33 atoms.
> >> PyMOL>select contact_lig, gold & chain L & (all within 10 of gold &
> chain
> >> R) & n. ca
> >> Selector: selection "contact_lig" defined with 33 atoms.
> >> PyMOL>select contact_all, contact_rec + contact_lig
> >> Selector: selection "contact_all" defined with 66 atoms.
> >> PyMOL>super gold & contact_all, test, cycles=0
> >> MatchAlign: aligning residues (66 vs 185)...
> >> MatchAlign: score 143.882
> >> ExecutiveAlign: 58 atoms aligned.
> >> Executive: RMS =0.524 (58 to 58 atoms)
> >>
> >> <1AY7_u.pdb><1AY7_b.pdb>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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