[Chimera-users] [External] Re: Align two structures
Catherine Jenifer Rajam Rajendran
catrajen at iu.edu
Mon Apr 11 12:14:10 PDT 2022
Hi Elaine & Eric,
Thank you for the information about updating the match command with colon.
It worked as expected.
Thanks,
Catherine
On Thu, Apr 7, 2022 at 8:40 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> To expand on what Eric said, it will still use all those atoms, but the
> commas do not specify ordering. Thus the order of the match stayed the same
> even though you entered the comma-separated chains in a different order.
> When you use the colons instead, it does specify the order.
>
> I would also put in a plug for ChimeraX: we improved atom specification
> in ChimeraX, so that to do the matches with two different chain pairings,
> the ChimeraX commands would be:
>
> align #2/A,B,C,D at ca to #1/A,B,C,D at ca
> ...giving
> RMSD between 436 atom pairs is 0.001 angstroms
>
> align #2/D,A,B,C at ca to #1/A,B,C,D at ca
> ...giving
> RMSD between 436 atom pairs is 0.294 angstroms
>
> ...and a different match orientation, as expected. (In ChimeraX, the
> command is "align" so that it is less likely to get confused with
> "matchmaker", and the syntax is slightly different, making it clear which
> thing is being aligned to which other thing.)
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Apr 7, 2022, at 4:20 PM, Eric Pettersen via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hi Catherine,
> > I know this is pretty arcane, but when also specifying specific
> atoms you have to use colons instead of commas in your atom spec, i.e.:
> >
> > 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
> >
> > Commas can only be used to separate parts of the spec “at the same
> level”, and the @CA is going down from the residue level to the atom
> level. Sorry it’s so non-obvious.
> >
> > --Eric
> >
> > Eric Pettersen
> > UCSF Computer Graphics Lab
> >
> >
> >> On Apr 7, 2022, at 12:51 PM, Catherine Jenifer Rajam Rajendran via
> Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >>
> >> Hi Elaine,
> >>
> >> Yes, it says, it uses the specified chain atoms to align the
> structures. But, the output generated produces the same coordinates. I have
> attached my input files. If you perform the match command as below, it
> generates two files with the same coordinates.
> >>
> >> 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
> >> write relative #0 #1 all_CA.pdb
> >>
> >> match #1:.D at CA #0:.A at CA
> >> write relative #0 #1 AD_CA.pdb
> >>
> >> Can you please clarify why the output generated has the same values? Am
> I missing something?
> >>
> >> Thanks,
> >> Catherine
> >>
> >> On Wed, Apr 6, 2022 at 5:04 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >> The reported numbers of atoms used in the matches suggests that all the
> chains specified in the command are being included. There isn't anything
> else I can say about it from the information given.
> >> Best,
> >> Elaine
> >>
> >> > On Apr 6, 2022, at 1:54 PM, Catherine Jenifer Rajam Rajendran via
> Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >> >
> >> > 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
> >> > > >
> >> > > >
> >> > > > _______________________________________________
> >> > > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> >> > > > Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
> >> > >
> >> > > _______________________________________________
> >> > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> >> > > Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
> >> >
> >> > _______________________________________________
> >> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> >> > Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
> >>
> >>
> <1nc7_90_Rotated.pdb><1nc7_original_processed.pdb>_______________________________________________
> >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> >> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimera-users/attachments/20220411/5e703818/attachment.html>
More information about the Chimera-users
mailing list