<div dir="ltr">Hi Elaine,<div><br></div><div><font face="arial, sans-serif">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. </font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Let me explain my data. My input files are an original structure pdb file and 90<span style="color:black;font-weight:bold">⁰ </span>rotated structure. Looking at the ReplyLog I could see that if I perform overall alignment using "match #1 #0", it's perfectly aligned. </font></div><div><span style="font-family:arial,sans-serif">Is there a way to perform each chain alignment between structures in one command? </span><font face="arial, sans-serif">I want to align something like "<span style="color:inherit;font-style:inherit;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit">match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" where </span></font><span style="font-style:inherit;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit;color:inherit;font-family:arial,sans-serif">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. </span><span style="font-style:inherit;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit;color:inherit;font-family:arial,sans-serif">I also tried "</span>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. </div><div><br></div><div>Do you think this match command performs chain alignment in sequence or is there a better way to do it?</div><div><span style="font-family:arial,sans-serif;color:inherit;font-style:inherit;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit"><br></span></div><div><span style="color:inherit;font-family:arial,sans-serif;font-style:inherit;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit">Thanks,</span><br></div><div><span style="font-family:arial,sans-serif;color:inherit;font-style:inherit;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit">Catherine</span></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Catherine,<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
Best,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi Elaine,<br>
> <br>
> 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. <br>
> <br>
> Structure 1:<br>
> ATOM 19 N ASN A 2 12.612 28.406 -9.353<br>
> ATOM 968 N ASN B 2 -6.828 36.102 -9.743<br>
> <br>
> Structure 2:<br>
> ATOM 1 N ASN A 2 -7.732 35.011 -9.283<br>
> ATOM 873 N ASN B 2 -0.035 54.442 -9.992<br>
> <br>
> match #1:.A@CA #0:.B@CA<br>
> ATOM 1 N ASN A 2 -7.691 35.166 -9.397<br>
> ATOM 873 N ASN B 2 0.155 54.542 -9.986<br>
> <br>
> match #1 #0<br>
> ATOM 1 N ASN A 2 12.612 28.406 -9.353<br>
> ATOM 873 N ASN B 2 -6.828 36.102 -9.743<br>
> <br>
> match #1:*@CA #0:*@CA<br>
> ATOM 1 N ASN A 2 12.612 28.406 -9.353<br>
> ATOM 873 N ASN B 2 -6.828 36.102 -9.743<br>
> <br>
> Thanks,<br>
> Catherine<br>
> <br>
> On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br>
> This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.<br>
> -------<br>
> <br>
> Hi Catherine,<br>
> If you just give the model number it specifies the all the atoms in the model,for example: <br>
> match #1 #0<br>
> <br>
> 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.<br>
> <br>
> 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:<br>
> <br>
> matchmaker #0 #1<br>
> <br>
> ...there are lots of possible options of this command, see<br>
> <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html</a>><br>
> <br>
> See aso the discussion of different ways to superimpose structures, and links therein:<br>
> <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html</a>><br>
> <br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <br>
> > On Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> > <br>
> > Hi,<br>
> > <br>
> > 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?<br>
> > <br>
> > Thanks,<br>
> > Catherine<br>
> <br>
> <br>
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</blockquote></div>