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

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 7 17:40:17 PDT 2022 

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
>> > > > 
>> > > > 
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