[Chimera-users] [External] Re: Align two structures

Tue Apr 5 15:24:21 PDT 2022

Hi Elaine,

Yes, I was generating the new PDB files using "write relative #0 #1
filename". The lines of information I mentioned earlier are from the pdb
files generated before and after the "match" command was implemented.

Let me explain my data. My input files are an original structure pdb file
and 90⁰ rotated structure. Looking at the ReplyLog I could see that if I
perform overall alignment using "match #1 #0", it's perfectly aligned.
Is there a way to perform each chain alignment between structures in one
command? I want to align something like "match #1:.D,.A,.B,.C
#0:.A,.B,.C,.D" where first #1 D is matched with #0 A, then #1 A with #0 B
and so on. But, this command doesn't quite generate the expected alignment. I
also tried "match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D". This
seems to perform the alignment I prefer.

Do you think this match command performs chain alignment in sequence or is
there a better way to do it?

Thanks,
Catherine

On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Catherine,
> I don't understand the lines of information that you sent, or what you
> mean by "doesn't perform the alignment."   If there is an error, it should
> say what the problem is, like malformed atom specification or unequal
> numbers of atoms specified.  Or if there was a superposition attempt but
> you don't like the result, then look in the Reply Log (in Favorites menu)
> to see how many pairs of atoms were matched and the RMSD.
>
> I also don't understand "it gives me a new pdb file with new coordinates."
> To get a new pdb file with new coordinates you would have to explicitly
> save a PDB file and choose the option to save the moved model "relative to"
> the reference model used in the match.
>
> Also just because some specific atom is not matched well doesn't mean that
> there wasn't a fit to the whole set of atoms that you specified in the
> command.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via
> Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hi Elaine,
> >
> > Thank you for the response. I'm working on similar structures with the
> same number of atoms. I have mentioned below the coordinates of the same
> atoms in two chains in a pdb. You could see that if I match a specific
> chain, it gives me a new pdb file with new coordinates. But when I try to
> match all the atoms or specific atom types. It doesn't perform the
> alignment. Am I missing something? And about matchmatcher; I prefer to have
> options to align all atoms or CA atoms or CB atoms.
> >
> > Structure 1:
> > ATOM     19  N   ASN A   2      12.612  28.406  -9.353
> > ATOM    968  N   ASN B   2      -6.828  36.102  -9.743
> >
> > Structure 2:
> > ATOM      1  N   ASN A   2      -7.732  35.011  -9.283
> > ATOM    873  N   ASN B   2      -0.035  54.442  -9.992
> >
> > match #1:.A at CA #0:.B at CA
> > ATOM      1  N   ASN A   2      -7.691  35.166  -9.397
> > ATOM    873  N   ASN B   2       0.155  54.542  -9.986
> >
> > match #1 #0
> > ATOM      1  N   ASN A   2      12.612  28.406  -9.353
> > ATOM    873  N   ASN B   2      -6.828  36.102  -9.743
> >
> > match #1:*@CA #0:*@CA
> > ATOM      1  N   ASN A   2      12.612  28.406  -9.353
> > ATOM    873  N   ASN B   2      -6.828  36.102  -9.743
> >
> > Thanks,
> > Catherine
> >
> > On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > This message was sent from a non-IU address. Please exercise caution
> when clicking links or opening attachments from external sources.
> > -------
> >
> > Hi Catherine,
> > If you just give the model number it specifies the all the atoms in the
> model,for example:
> > match #1 #0
> >
> > However, in most cases this will not work because the two models don't
> have exactly the same numbers of atoms in exactly the same order for proper
> pairing.
> >
> > Instead you probably want to use the matchmaker command, which will try
> to figure out the residue pairing for you automatically.  It just uses the
> alpha-carbons (1 atom per residue).  Example:
> >
> > matchmaker #0 #1
> >
> > ...there are lots of possible options of this command, see
> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
> >
> > See aso the discussion of different ways to superimpose structures, and
> links therein:
> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via
> Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > >
> > > Hi,
> > >
> > > I'm trying to use the "match" command to align two protein pdb
> structures. Instead of specifying which chains or atoms or residues to
> align, Is there a way to align the whole structure from the command line?
> > >
> > > Thanks,
> > > Catherine
> >
> >
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