[chimerax-users] [EXTERNAL] Re: Match/Matchmaker multiple segments of two protein sequences

[Elaine Meng]

Awww, you're welcome!  :-)

Elaine


> On Jul 21, 2022, at 12:32 PM, Gong, Zhen via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
>  
> Wow, your response is sooooooo thorough and helpful, which is exactly what I was looking for and even extended beyond that. Thank you sooooooo much for your thoughtful help! You have saved my day!!!
>  
> Best regards,
> Zhen
>  
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Date: Thursday, July 21, 2022 at 15:15
> To: Gong, Zhen <zg2234 at cumc.columbia.edu>
> Cc: Gong, Zhen via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
> Subject: [EXTERNAL] Re: [chimerax-users] Match/Matchmaker multiple segments of two protein sequences
> 
> Hi Zhen,
> If you already have the lists of the exact residue numbers you want to pair, then you can just use the "align" command.  The "matchmaker" command is to make it easy for you when you don't feel like figuring out the residue-number pairing (and the sequences are similar enough to align).
> 
> E.g. something like command:
> 
> align #1:3-13,23-70,72-81,86-101 at ca to #2:7-17,18-65,67-76,77-92 at ca cutoffDistance 3  
> 
> You have to give equal numbers of atoms, of course.  So I had to change "18-66" in your example to "18-65" to work with the structures I had open, and also add "@ca" to specify only using the CA atom of each residue (since different residue types would have different numbers of atoms).
> 
> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Falign.html&data=05%7C01%7Czg2234%40cumc.columbia.edu%7C1f1199f04f894919e31508da6b4d5001%7Cb0002a9b0017404d97dc3d3bab09be81%7C1%7C0%7C637940277051928371%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=b7%2BmnANKHVHEJgiq6VxvK3bwgQVmNEPB6ZUNnqB6UHc%3D&reserved=0>
> 
> If you were using "matchmaker" however, there are lots of options to adjust how the sequence alignment is calculated, e.g. using heaver weight of secondary structure vs. residue type and/or using a more evolutionarily distant scoring matrix.  See matchmaker alignment scoring options:
> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmatchmaker.html%23scoring&data=05%7C01%7Czg2234%40cumc.columbia.edu%7C1f1199f04f894919e31508da6b4d5001%7Cb0002a9b0017404d97dc3d3bab09be81%7C1%7C0%7C637940277051928371%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7HUNI%2FR25YqGBKt3uxvap%2BMf3JTnuhU%2B0d22PGVrMu4%3D&reserved=0>
> 
> The alignment scoring options can also be adjusted in the Matchmaker GUI:
> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmatchmaker.html%23alignment&data=05%7C01%7Czg2234%40cumc.columbia.edu%7C1f1199f04f894919e31508da6b4d5001%7Cb0002a9b0017404d97dc3d3bab09be81%7C1%7C0%7C637940277051928371%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FmufuBUyyH852XOjX1DRtYwKdwx1Nn5WpnNWRFwejjY%3D&reserved=0>
> 
> In Chimera (but not ChimeraX currently) you can open your own sequence alignment from a file and then use it to superimpose the structures.  Chimera Multalign Viewer and how to superimpose structures after opening the alignment file:
> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fmultalignviewer%2Fframemav.html&data=05%7C01%7Czg2234%40cumc.columbia.edu%7C1f1199f04f894919e31508da6b4d5001%7Cb0002a9b0017404d97dc3d3bab09be81%7C1%7C0%7C637940277051928371%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tWPRdBd0r5mMmFTtdxp7go%2FUuIwKQtYRlNczXMx5kwg%3D&reserved=0>
> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fmultalignviewer%2Fmultalignviewer.html%23superposition&data=05%7C01%7Czg2234%40cumc.columbia.edu%7C1f1199f04f894919e31508da6b4d5001%7Cb0002a9b0017404d97dc3d3bab09be81%7C1%7C0%7C637940277051928371%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8YmSYFDz%2BtbUhDVUEFJ8P1j7HYe1c2qXJE3PTDvjo4k%3D&reserved=0>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Jul 21, 2022, at 10:39 AM, Gong, Zhen via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Dear Chimerax developers and users, 
> >  
> > I am wondering if chimerax is able to do match/matchmaker multiple segments of two protein sequences, something like:
> > match #1:3-13, 23-70, 72-81, 86-101 to #2:7-17, 18-66, 67-76, 77-92 cutoffDistance 3  showAlignment true
> > Maybe it can but I did not put the command in correct format. Please help.
> >  
> > A related question would be that the default alignment algorithm in chimerax (Needleman-Wunsch or Smith-Waterman) did not do a good job when the two proteins share high structural similarities with low sequence identity. I would like to do the manual sequence alignment, save the alignment as .aln file and use that for matchmaker, iterate with cutoff and get final rmsd of aligned atoms. Is it possible to execute such procedures in chimerax?
> >  
> > Many thanks in advance for any helpful suggestion and discussion!
> >  
> > Best regards,
> > Zhen
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users