Align command; designating the positions to align
Hi,
I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details:
Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336
When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms.
Here is what I thought would work:
align #1:11-323 to_atoms #2:24-336
Here is the error message:
Unequal number of atoms to pair, 2483 to 2371
I am still trying to understand the nomenclature for understanding residues and atoms.
Thanks for any help you can provide.
Phil McClean
Hi Phil, Your syntax is fine if you really meant to specify all atoms of the residues. Most likely reasons for the error are:
(1) the residue types are not identical, so they contain different numbers of atoms (e.g. tryptophan has many more atoms than alanine) (2) one structure or the other is missing some residues from the coordinates (e.g. a flexible loop was not resolved from density) (3) one structure or the other has multiple chains so you are getting residues with those numbers from more than one chain (e.g. chain A has residues 11-323 but so does chain B)
Another possible problem is that there is no underscore in the "toAtoms" option keyword. You can truncate it to "to" if you like.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html
Assuming it is the first one, the solution is to specify matching only backbone atoms, or only alpha-carbons. Whichever you would like the RMSD to reflect. You would use an @ symbol to specify atom names. So it may be something like
align #1:11-323@n,ca,c,o to #2:24-336@n,ca,c,o
...for all backbone atoms, or for alpha-carbons only:
align #1:11-323@ca to #2:24-336@ca
https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.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 Jul 18, 2022, at 2:22 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details:
Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336
When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms.
Here is what I thought would work:
align #1:11-323 to_atoms #2:24-336
Here is the error message:
Unequal number of atoms to pair, 2483 to 2371
I am still trying to understand the nomenclature for understanding residues and atoms.
Thanks for any help you can provide.
Phil McClean
Hi Phil,
Another solution would be to use MatchMakerhttps://www.rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html instead. Instead of the command you tried, use: mmaker #1:11-323 to #2:24-336 In my experience, MatchMaker is quite powerful.
Best, Harper ________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Monday, July 18, 2022 5:33 PM To: McClean, Phillip phillip.mcclean@ndsu.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Align command; designating the positions to align
Hi Phil, Your syntax is fine if you really meant to specify all atoms of the residues. Most likely reasons for the error are:
(1) the residue types are not identical, so they contain different numbers of atoms (e.g. tryptophan has many more atoms than alanine) (2) one structure or the other is missing some residues from the coordinates (e.g. a flexible loop was not resolved from density) (3) one structure or the other has multiple chains so you are getting residues with those numbers from more than one chain (e.g. chain A has residues 11-323 but so does chain B)
Another possible problem is that there is no underscore in the "toAtoms" option keyword. You can truncate it to "to" if you like.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
Assuming it is the first one, the solution is to specify matching only backbone atoms, or only alpha-carbons. Whichever you would like the RMSD to reflect. You would use an @ symbol to specify atom names. So it may be something like
align #1:11-323@n,ca,c,o to #2:24-336@n,ca,c,o
...for all backbone atoms, or for alpha-carbons only:
align #1:11-323@ca to #2:24-336@ca
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
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 18, 2022, at 2:22 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details:
Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336
When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms.
Here is what I thought would work:
align #1:11-323 to_atoms #2:24-336
Here is the error message:
Unequal number of atoms to pair, 2483 to 2371
I am still trying to understand the nomenclature for understanding residues and atoms.
Thanks for any help you can provide.
Phil McClean
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
God point. Also, if you use matchmaker, it will do a sequence alignment and figure out which numbers go with which (so you don't have to give residue ranges at all, unless you want to restrict it). Matchmaker will only use the alpha-carbons, though. Align will give you more precise control over exactly which residues are used and allow you to use all backbone atoms if you want.
There is both a Matchmaker GUI (tool) and a command. https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
Elaine
On Jul 18, 2022, at 2:38 PM, Smith, Harper E. smith.12510@buckeyemail.osu.edu wrote:
Hi Phil,
Another solution would be to use MatchMaker instead. Instead of the command you tried, use: mmaker #1:11-323 to #2:24-336 In my experience, MatchMaker is quite powerful.
Best, Harper From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Monday, July 18, 2022 5:33 PM To: McClean, Phillip phillip.mcclean@ndsu.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Align command; designating the positions to align
Hi Phil, Your syntax is fine if you really meant to specify all atoms of the residues. Most likely reasons for the error are:
(1) the residue types are not identical, so they contain different numbers of atoms (e.g. tryptophan has many more atoms than alanine) (2) one structure or the other is missing some residues from the coordinates (e.g. a flexible loop was not resolved from density) (3) one structure or the other has multiple chains so you are getting residues with those numbers from more than one chain (e.g. chain A has residues 11-323 but so does chain B)
Another possible problem is that there is no underscore in the "toAtoms" option keyword. You can truncate it to "to" if you like.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
Assuming it is the first one, the solution is to specify matching only backbone atoms, or only alpha-carbons. Whichever you would like the RMSD to reflect. You would use an @ symbol to specify atom names. So it may be something like
align #1:11-323@n,ca,c,o to #2:24-336@n,ca,c,o
...for all backbone atoms, or for alpha-carbons only:
align #1:11-323@ca to #2:24-336@ca
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
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 18, 2022, at 2:22 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details:
Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336
When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms.
Here is what I thought would work:
align #1:11-323 to_atoms #2:24-336
Here is the error message:
Unequal number of atoms to pair, 2483 to 2371
I am still trying to understand the nomenclature for understanding residues and atoms.
Thanks for any help you can provide.
Phil McClean
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
LOL, make that "Good point"!! Darn multitasking. :-)
Elaine
On Jul 18, 2022, at 2:42 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
God point. Also, if you use matchmaker, it will do a sequence alignment and figure out which numbers go with which (so you don't have to give residue ranges at all, unless you want to restrict it). Matchmaker will only use the alpha-carbons, though. Align will give you more precise control over exactly which residues are used and allow you to use all backbone atoms if you want.
There is both a Matchmaker GUI (tool) and a command. https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
Elaine
On Jul 18, 2022, at 2:38 PM, Smith, Harper E. smith.12510@buckeyemail.osu.edu wrote:
Hi Phil,
Another solution would be to use MatchMaker instead. Instead of the command you tried, use: mmaker #1:11-323 to #2:24-336 In my experience, MatchMaker is quite powerful.
Best, Harper From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Monday, July 18, 2022 5:33 PM To: McClean, Phillip phillip.mcclean@ndsu.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Align command; designating the positions to align
Hi Phil, Your syntax is fine if you really meant to specify all atoms of the residues. Most likely reasons for the error are:
(1) the residue types are not identical, so they contain different numbers of atoms (e.g. tryptophan has many more atoms than alanine) (2) one structure or the other is missing some residues from the coordinates (e.g. a flexible loop was not resolved from density) (3) one structure or the other has multiple chains so you are getting residues with those numbers from more than one chain (e.g. chain A has residues 11-323 but so does chain B)
Another possible problem is that there is no underscore in the "toAtoms" option keyword. You can truncate it to "to" if you like.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
Assuming it is the first one, the solution is to specify matching only backbone atoms, or only alpha-carbons. Whichever you would like the RMSD to reflect. You would use an @ symbol to specify atom names. So it may be something like
align #1:11-323@n,ca,c,o to #2:24-336@n,ca,c,o
...for all backbone atoms, or for alpha-carbons only:
align #1:11-323@ca to #2:24-336@ca
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
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 18, 2022, at 2:22 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details:
Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336
When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms.
Here is what I thought would work:
align #1:11-323 to_atoms #2:24-336
Here is the error message:
Unequal number of atoms to pair, 2483 to 2371
I am still trying to understand the nomenclature for understanding residues and atoms.
Thanks for any help you can provide.
Phil McClean
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Harper, that code worked.
With regards to the align command, I just check and every pair of amino acids is identical and the number of atoms is identical. I still can't figure how to get the rmsd value for all of the atoms found with each pair.
Phil ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, July 18, 2022 4:42 PM To: Smith, Harper E. smith.12510@buckeyemail.osu.edu; McClean, Phillip phillip.mcclean@ndsu.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Align command; designating the positions to align
God point. Also, if you use matchmaker, it will do a sequence alignment and figure out which numbers go with which (so you don't have to give residue ranges at all, unless you want to restrict it). Matchmaker will only use the alpha-carbons, though. Align will give you more precise control over exactly which residues are used and allow you to use all backbone atoms if you want.
There is both a Matchmaker GUI (tool) and a command. https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
Elaine
On Jul 18, 2022, at 2:38 PM, Smith, Harper E. smith.12510@buckeyemail.osu.edu wrote:
Hi Phil,
Another solution would be to use MatchMaker instead. Instead of the command you tried, use: mmaker #1:11-323 to #2:24-336 In my experience, MatchMaker is quite powerful.
Best, Harper From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Monday, July 18, 2022 5:33 PM To: McClean, Phillip phillip.mcclean@ndsu.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Align command; designating the positions to align
Hi Phil, Your syntax is fine if you really meant to specify all atoms of the residues. Most likely reasons for the error are:
(1) the residue types are not identical, so they contain different numbers of atoms (e.g. tryptophan has many more atoms than alanine) (2) one structure or the other is missing some residues from the coordinates (e.g. a flexible loop was not resolved from density) (3) one structure or the other has multiple chains so you are getting residues with those numbers from more than one chain (e.g. chain A has residues 11-323 but so does chain B)
Another possible problem is that there is no underscore in the "toAtoms" option keyword. You can truncate it to "to" if you like.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
Assuming it is the first one, the solution is to specify matching only backbone atoms, or only alpha-carbons. Whichever you would like the RMSD to reflect. You would use an @ symbol to specify atom names. So it may be something like
align #1:11-323@n,ca,c,o to #2:24-336@n,ca,c,o
...for all backbone atoms, or for alpha-carbons only:
align #1:11-323@ca to #2:24-336@ca
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
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 18, 2022, at 2:22 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details:
Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336
When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms.
Here is what I thought would work:
align #1:11-323 to_atoms #2:24-336
Here is the error message:
Unequal number of atoms to pair, 2483 to 2371
I am still trying to understand the nomenclature for understanding residues and atoms.
Thanks for any help you can provide.
Phil McClean
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
Hi Phil, Maybe some sidechains are truncated, but I can't tell the reason for the difference in numbers of atoms without having the exact files to try myself. You can send them to just me (or tell me PDB IDs if they are in the PDB) instead of mailing to the whole list if you want. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2022, at 2:46 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks Harper, that code worked.
With regards to the align command, I just check and every pair of amino acids is identical and the number of atoms is identical. I still can't figure how to get the rmsd value for all of the atoms found with each pair.
Phil From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, July 18, 2022 4:42 PM To: Smith, Harper E. smith.12510@buckeyemail.osu.edu; McClean, Phillip phillip.mcclean@ndsu.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Align command; designating the positions to align
God point. Also, if you use matchmaker, it will do a sequence alignment and figure out which numbers go with which (so you don't have to give residue ranges at all, unless you want to restrict it). Matchmaker will only use the alpha-carbons, though. Align will give you more precise control over exactly which residues are used and allow you to use all backbone atoms if you want.
There is both a Matchmaker GUI (tool) and a command. https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
Elaine
On Jul 18, 2022, at 2:38 PM, Smith, Harper E. smith.12510@buckeyemail.osu.edu wrote:
Hi Phil,
Another solution would be to use MatchMaker instead. Instead of the command you tried, use: mmaker #1:11-323 to #2:24-336 In my experience, MatchMaker is quite powerful.
Best, Harper From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Monday, July 18, 2022 5:33 PM To: McClean, Phillip phillip.mcclean@ndsu.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Align command; designating the positions to align
Hi Phil, Your syntax is fine if you really meant to specify all atoms of the residues. Most likely reasons for the error are:
(1) the residue types are not identical, so they contain different numbers of atoms (e.g. tryptophan has many more atoms than alanine) (2) one structure or the other is missing some residues from the coordinates (e.g. a flexible loop was not resolved from density) (3) one structure or the other has multiple chains so you are getting residues with those numbers from more than one chain (e.g. chain A has residues 11-323 but so does chain B)
Another possible problem is that there is no underscore in the "toAtoms" option keyword. You can truncate it to "to" if you like.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
Assuming it is the first one, the solution is to specify matching only backbone atoms, or only alpha-carbons. Whichever you would like the RMSD to reflect. You would use an @ symbol to specify atom names. So it may be something like
align #1:11-323@n,ca,c,o to #2:24-336@n,ca,c,o
...for all backbone atoms, or for alpha-carbons only:
align #1:11-323@ca to #2:24-336@ca
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
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 18, 2022, at 2:22 PM, McClean, Phillip via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details:
Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336
When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms.
Here is what I thought would work:
align #1:11-323 to_atoms #2:24-336
Here is the error message:
Unequal number of atoms to pair, 2483 to 2371
I am still trying to understand the nomenclature for understanding residues and atoms.
Thanks for any help you can provide.
Phil McClean
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
McClean, Phillip -
Smith, Harper E.