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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Re: [PyMOL] Super and Align missing residues

[Thomas Holder]

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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Re: [PyMOL] Super and Align missing residues

[Thomas Holder]

Hi Nathan,

Sounds like you are doing everything correct. Would it be possible to send me 
the input files?

Thanks,
  Thomas

> On Jun 26, 2018, at 10:58 AM, Nathan Clement  wrote:
> 
> 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

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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