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

[Catherine Jenifer Rajam Rajendran]

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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