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@CA #0:.B@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@cgl.ucsf.edu> wrote:

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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@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