[Chimera-users] [External] Re: Align two structures
Catherine Jenifer Rajam Rajendran
catrajen at iu.edu
Wed Apr 6 13:54:45 PDT 2022
Hi Elaine,
I upgraded to the latest version of Chimera. I think "match #1:.D,.A,.B,.C
#0:.A,.B,.C,.D" alignment works as expected. Both generate different
coordinates and RMSD values.
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D
RMSD between 3484 atom pairs is 0.838 angstroms
match #1:.D #0:.A
RMSD between 871 atom pairs is 0.886 angstroms
But, when I perform alignment for CA or CB atoms, it performs alignment
just for the first chain. I'm not sure if it's a bug.
match #1:.D at CA,.A at CA,.B at CA,.C at CA #0:.A at CA,.B at CA,.C at CA,.D at CA
RMSD between 436 atom pairs is 0.295 angstroms
match #1:.D at CA #0:.A at CA
RMSD between 109 atom pairs is 0.295 angstroms
RMSD is the same and I checked the coordinates; It generates same
coordinates for both the match commands. So, I'm thinking it's performing
the first chain alignment only.
match #1:.D at CB,.A at CB,.B at CB,.C at CB #0:.A at CB,.B at CB,.C at CB,.D at CB
RMSD between 400 atom pairs is 0.311 angstroms
match #1:.D at CB #0:.A at CB
RMSD between 100 atom pairs is 0.311 angstroms
I forgot to mention, I did some preprocessing to make sure all chains have
the same number of atoms.
Thanks,
Catherine
On Tue, Apr 5, 2022 at 7:56 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Catherine,
> This one looks correct, and as long as you have recent Chimera (within
> last couple of years), should match the atoms in the order that you gave
> for the chains:
>
> match #1:.D,.A,.B,.C #0:.A,.B,.C,.D
>
> The following one looks extremely wrong because you should have all of the
> atoms from one structure first and all of the atoms from the second
> structure last, not interleaved:
>
> match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D
>
> However, you are flying blind if you don't check how many pairs of atoms
> are used for the match. It is reported in the status line transiently, but
> it is also logged in theReply Log (menu: Favorites... Reply Log). You
> should look in the Reply Log for any error messages, and if the command
> executes, for the resulting RMSD and how many pairs of atoms were used to
> calculate it. If your command worked the way you wanted, it should be the
> same as number of atoms in each structure (which would have to be the same
> as each other).
>
> How many atoms are in a structure are reported in the status line at the
> bottom when it is opened. Or if it's already open and you don't feel like
> opening it again, you can select it
>
> select #0
>
> and the current selection will be reported in the status line.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> > On Apr 5, 2022, at 3:24 PM, Catherine Jenifer Rajam Rajendran via
> Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >
> > 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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