Hi everyone, I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix" tl;dr. Trying to align ring atoms of a ligand instead of protein chain Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010@uga.edu Mobile: (470) 641-3884
Hi Alex, The Matchmaker tool and "matchmaker" command are for sequence-alignable biopolymer chains (peptides, RNA, DNA) and use only one mainchain atom per residue. When you enter "match" it is just recognized as a truncation of "matchmaker" so you get the same thing. The command in ChimeraX to match any atoms of your choice in any kinds of molecules is "align" ... for example: align #1:203@C19,C20,C21,C16,C17,O18 to #2:125@C2,C3,C4,C5,C6,O6 (or the other way around, if you wanted #2 to move) See the help for various command options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> Maybe you were looking at the help pages for Chimera, which is different than ChimeraX. Only Chimera has a separate "match" command, which we renamed as "align" in ChimeraX because truncated commands are accepted. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2024, at 2:20 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix"
tl;dr. Trying to align ring atoms of a ligand instead of protein chain
Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker
Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX
Can I piggyback on this question to ask if there is a recommended way of doing the atom pairing for commonly seen ligands? For example, there does not appear to be a standardized atom ordering for ATP. Recently I was examining some ATP binding sites across different structures and I wanted to align on the ATP molecule, but it was a colossal pain because the ATP atoms were not in the same order. As far as I could tell the only way was for me to manually go through the ATP atoms (or some subset of them) and one by one identify the corresponding atom IDs in the two structures so I could pass that to the align command. Does anyone have a script/recommended strategy for this use case? Thanks, Daniel
On May 22, 2024, at 2:45 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Alex, The Matchmaker tool and "matchmaker" command are for sequence-alignable biopolymer chains (peptides, RNA, DNA) and use only one mainchain atom per residue. When you enter "match" it is just recognized as a truncation of "matchmaker" so you get the same thing.
The command in ChimeraX to match any atoms of your choice in any kinds of molecules is "align" ... for example:
align #1:203@C19,C20,C21,C16,C17,O18 to #2:125@C2,C3,C4,C5,C6,O6
(or the other way around, if you wanted #2 to move)
See the help for various command options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
Maybe you were looking at the help pages for Chimera, which is different than ChimeraX. Only Chimera has a separate "match" command, which we renamed as "align" in ChimeraX because truncated commands are accepted.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2024, at 2:20 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix"
tl;dr. Trying to align ring atoms of a ligand instead of protein chain
Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker
Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hello Daniel, If the structures are from the Protein DataBank, my understanding is that there is a standard residue name (ATP in this case), and for that residue aka chemical component, a standard set of atom names and maybe even a standard order in which they appear in the file. If that were the case, you'd only need to give the residue numbers in the "align" command, or even just :ATP if each structure only has one ATP. The "align" command does have options to require same chain ID, or same residue number, or to use the atom names regardless of the order in which they appear. Still, depending on how your input files are constructed and to which conventions they adhere, using one or more of these options may or may not make your life easier. See the "align" help page for the keyword options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> I hope this helps, Elaine
On May 22, 2024, at 4:21 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
Can I piggyback on this question to ask if there is a recommended way of doing the atom pairing for commonly seen ligands?
For example, there does not appear to be a standardized atom ordering for ATP. Recently I was examining some ATP binding sites across different structures and I wanted to align on the ATP molecule, but it was a colossal pain because the ATP atoms were not in the same order. As far as I could tell the only way was for me to manually go through the ATP atoms (or some subset of them) and one by one identify the corresponding atom IDs in the two structures so I could pass that to the align command.
Does anyone have a script/recommended strategy for this use case?
Thanks, Daniel
On May 22, 2024, at 2:45 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Alex, The Matchmaker tool and "matchmaker" command are for sequence-alignable biopolymer chains (peptides, RNA, DNA) and use only one mainchain atom per residue. When you enter "match" it is just recognized as a truncation of "matchmaker" so you get the same thing.
The command in ChimeraX to match any atoms of your choice in any kinds of molecules is "align" ... for example:
align #1:203@C19,C20,C21,C16,C17,O18 to #2:125@C2,C3,C4,C5,C6,O6
(or the other way around, if you wanted #2 to move)
See the help for various command options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
Maybe you were looking at the help pages for Chimera, which is different than ChimeraX. Only Chimera has a separate "match" command, which we renamed as "align" in ChimeraX because truncated commands are accepted.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2024, at 2:20 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix"
tl;dr. Trying to align ring atoms of a ligand instead of protein chain
Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker
Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Daniel, Seems like if your ATP ligands use the same atom names the you just use ChimeraX command align #2:ATP to #1:ATP matchAtomNames true In my look at a few PDB mmCIF files (8g1j, 6r81) they put the ATP atoms in the same order so the "matchAtomNames true" does not appear to be necessary for PDB entries. Tom
On May 22, 2024, at 4:42 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Daniel, If the structures are from the Protein DataBank, my understanding is that there is a standard residue name (ATP in this case), and for that residue aka chemical component, a standard set of atom names and maybe even a standard order in which they appear in the file. If that were the case, you'd only need to give the residue numbers in the "align" command, or even just :ATP if each structure only has one ATP.
The "align" command does have options to require same chain ID, or same residue number, or to use the atom names regardless of the order in which they appear. Still, depending on how your input files are constructed and to which conventions they adhere, using one or more of these options may or may not make your life easier.
See the "align" help page for the keyword options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
I hope this helps, Elaine
On May 22, 2024, at 4:21 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
Can I piggyback on this question to ask if there is a recommended way of doing the atom pairing for commonly seen ligands?
For example, there does not appear to be a standardized atom ordering for ATP. Recently I was examining some ATP binding sites across different structures and I wanted to align on the ATP molecule, but it was a colossal pain because the ATP atoms were not in the same order. As far as I could tell the only way was for me to manually go through the ATP atoms (or some subset of them) and one by one identify the corresponding atom IDs in the two structures so I could pass that to the align command.
Does anyone have a script/recommended strategy for this use case?
Thanks, Daniel
On May 22, 2024, at 2:45 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Alex, The Matchmaker tool and "matchmaker" command are for sequence-alignable biopolymer chains (peptides, RNA, DNA) and use only one mainchain atom per residue. When you enter "match" it is just recognized as a truncation of "matchmaker" so you get the same thing.
The command in ChimeraX to match any atoms of your choice in any kinds of molecules is "align" ... for example:
align #1:203@C19,C20,C21,C16,C17,O18 to #2:125@C2,C3,C4,C5,C6,O6
(or the other way around, if you wanted #2 to move)
See the help for various command options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
Maybe you were looking at the help pages for Chimera, which is different than ChimeraX. Only Chimera has a separate "match" command, which we renamed as "align" in ChimeraX because truncated commands are accepted.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2024, at 2:20 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix"
tl;dr. Trying to align ring atoms of a ligand instead of protein chain
Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker
Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you both. It seems as if some structures have ATP hydrogens and others don’t, but this was very helpful. I’ve tried this align command with a few structures and it seems to work. Does matchAtomNames true attempt to create a new pairwise mapping between group A atoms and group B atoms where the names are the same? Or is the mapping always based on atom order, and matchAtomNames true merely filters out pairs whose names don’t match? Thanks, Daniel
On May 22, 2024, at 4:47 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Daniel,
Seems like if your ATP ligands use the same atom names the you just use ChimeraX command
align #2:ATP to #1:ATP matchAtomNames true
In my look at a few PDB mmCIF files (8g1j, 6r81) they put the ATP atoms in the same order so the "matchAtomNames true" does not appear to be necessary for PDB entries.
Tom
On May 22, 2024, at 4:42 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Daniel, If the structures are from the Protein DataBank, my understanding is that there is a standard residue name (ATP in this case), and for that residue aka chemical component, a standard set of atom names and maybe even a standard order in which they appear in the file. If that were the case, you'd only need to give the residue numbers in the "align" command, or even just :ATP if each structure only has one ATP.
The "align" command does have options to require same chain ID, or same residue number, or to use the atom names regardless of the order in which they appear. Still, depending on how your input files are constructed and to which conventions they adhere, using one or more of these options may or may not make your life easier.
See the "align" help page for the keyword options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
I hope this helps, Elaine
On May 22, 2024, at 4:21 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
Can I piggyback on this question to ask if there is a recommended way of doing the atom pairing for commonly seen ligands?
For example, there does not appear to be a standardized atom ordering for ATP. Recently I was examining some ATP binding sites across different structures and I wanted to align on the ATP molecule, but it was a colossal pain because the ATP atoms were not in the same order. As far as I could tell the only way was for me to manually go through the ATP atoms (or some subset of them) and one by one identify the corresponding atom IDs in the two structures so I could pass that to the align command.
Does anyone have a script/recommended strategy for this use case?
Thanks, Daniel
On May 22, 2024, at 2:45 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Alex, The Matchmaker tool and "matchmaker" command are for sequence-alignable biopolymer chains (peptides, RNA, DNA) and use only one mainchain atom per residue. When you enter "match" it is just recognized as a truncation of "matchmaker" so you get the same thing.
The command in ChimeraX to match any atoms of your choice in any kinds of molecules is "align" ... for example:
align #1:203@C19,C20,C21,C16,C17,O18 to #2:125@C2,C3,C4,C5,C6,O6
(or the other way around, if you wanted #2 to move)
See the help for various command options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
Maybe you were looking at the help pages for Chimera, which is different than ChimeraX. Only Chimera has a separate "match" command, which we renamed as "align" in ChimeraX because truncated commands are accepted.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2024, at 2:20 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix"
tl;dr. Trying to align ring atoms of a ligand instead of protein chain
Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker
Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Daniel, If you use "matchAtomNames true" it ignores the given atom order. I also was wondering about this and it wasn't clear from the align command documentation so I looked at the source code. Atoms in one set that don't have an atom in the other set of the same name are not used in the comparison. So if one ATP has hydrogens but the other does not, then it will just align on all the non-hydrogen atoms that both ATPs have in common. Tom
On May 22, 2024, at 5:01 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
Thank you both. It seems as if some structures have ATP hydrogens and others don’t, but this was very helpful. I’ve tried this align command with a few structures and it seems to work.
Does matchAtomNames true attempt to create a new pairwise mapping between group A atoms and group B atoms where the names are the same? Or is the mapping always based on atom order, and matchAtomNames true merely filters out pairs whose names don’t match?
Thanks, Daniel
On May 22, 2024, at 4:47 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Daniel,
Seems like if your ATP ligands use the same atom names the you just use ChimeraX command
align #2:ATP to #1:ATP matchAtomNames true
In my look at a few PDB mmCIF files (8g1j, 6r81) they put the ATP atoms in the same order so the "matchAtomNames true" does not appear to be necessary for PDB entries.
Tom
On May 22, 2024, at 4:42 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Daniel, If the structures are from the Protein DataBank, my understanding is that there is a standard residue name (ATP in this case), and for that residue aka chemical component, a standard set of atom names and maybe even a standard order in which they appear in the file. If that were the case, you'd only need to give the residue numbers in the "align" command, or even just :ATP if each structure only has one ATP.
The "align" command does have options to require same chain ID, or same residue number, or to use the atom names regardless of the order in which they appear. Still, depending on how your input files are constructed and to which conventions they adhere, using one or more of these options may or may not make your life easier.
See the "align" help page for the keyword options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
I hope this helps, Elaine
On May 22, 2024, at 4:21 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
Can I piggyback on this question to ask if there is a recommended way of doing the atom pairing for commonly seen ligands?
For example, there does not appear to be a standardized atom ordering for ATP. Recently I was examining some ATP binding sites across different structures and I wanted to align on the ATP molecule, but it was a colossal pain because the ATP atoms were not in the same order. As far as I could tell the only way was for me to manually go through the ATP atoms (or some subset of them) and one by one identify the corresponding atom IDs in the two structures so I could pass that to the align command.
Does anyone have a script/recommended strategy for this use case?
Thanks, Daniel
On May 22, 2024, at 2:45 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Alex, The Matchmaker tool and "matchmaker" command are for sequence-alignable biopolymer chains (peptides, RNA, DNA) and use only one mainchain atom per residue. When you enter "match" it is just recognized as a truncation of "matchmaker" so you get the same thing.
The command in ChimeraX to match any atoms of your choice in any kinds of molecules is "align" ... for example:
align #1:203@C19,C20,C21,C16,C17,O18 to #2:125@C2,C3,C4,C5,C6,O6
(or the other way around, if you wanted #2 to move)
See the help for various command options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
Maybe you were looking at the help pages for Chimera, which is different than ChimeraX. Only Chimera has a separate "match" command, which we renamed as "align" in ChimeraX because truncated commands are accepted.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2024, at 2:20 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix"
tl;dr. Trying to align ring atoms of a ligand instead of protein chain
Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker
Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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My reply below said "regardless of the order" but I agree it needs to be stated in the documentation, so I will add it! I have also tested that it is not dependent on order of the remaining atoms even after stripping the non-matching ones (the hydrogens in Tom's example). The remaining atoms can also be in a different order. Elaine
On May 22, 2024, at 5:05 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Daniel,
If you use "matchAtomNames true" it ignores the given atom order. I also was wondering about this and it wasn't clear from the align command documentation so I looked at the source code. Atoms in one set that don't have an atom in the other set of the same name are not used in the comparison. So if one ATP has hydrogens but the other does not, then it will just align on all the non-hydrogen atoms that both ATPs have in common.
Tom
On May 22, 2024, at 5:01 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
Thank you both. It seems as if some structures have ATP hydrogens and others don’t, but this was very helpful. I’ve tried this align command with a few structures and it seems to work.
Does matchAtomNames true attempt to create a new pairwise mapping between group A atoms and group B atoms where the names are the same? Or is the mapping always based on atom order, and matchAtomNames true merely filters out pairs whose names don’t match?
Thanks, Daniel
On May 22, 2024, at 4:47 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Daniel,
Seems like if your ATP ligands use the same atom names the you just use ChimeraX command
align #2:ATP to #1:ATP matchAtomNames true
In my look at a few PDB mmCIF files (8g1j, 6r81) they put the ATP atoms in the same order so the "matchAtomNames true" does not appear to be necessary for PDB entries.
Tom
On May 22, 2024, at 4:42 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Daniel, If the structures are from the Protein DataBank, my understanding is that there is a standard residue name (ATP in this case), and for that residue aka chemical component, a standard set of atom names and maybe even a standard order in which they appear in the file. If that were the case, you'd only need to give the residue numbers in the "align" command, or even just :ATP if each structure only has one ATP.
The "align" command does have options to require same chain ID, or same residue number, or to use the atom names regardless of the order in which they appear. Still, depending on how your input files are constructed and to which conventions they adhere, using one or more of these options may or may not make your life easier.
See the "align" help page for the keyword options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
I hope this helps, Elaine
On May 22, 2024, at 4:21 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
Can I piggyback on this question to ask if there is a recommended way of doing the atom pairing for commonly seen ligands?
For example, there does not appear to be a standardized atom ordering for ATP. Recently I was examining some ATP binding sites across different structures and I wanted to align on the ATP molecule, but it was a colossal pain because the ATP atoms were not in the same order. As far as I could tell the only way was for me to manually go through the ATP atoms (or some subset of them) and one by one identify the corresponding atom IDs in the two structures so I could pass that to the align command.
Does anyone have a script/recommended strategy for this use case?
Thanks, Daniel
On May 22, 2024, at 2:45 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Alex, The Matchmaker tool and "matchmaker" command are for sequence-alignable biopolymer chains (peptides, RNA, DNA) and use only one mainchain atom per residue. When you enter "match" it is just recognized as a truncation of "matchmaker" so you get the same thing.
The command in ChimeraX to match any atoms of your choice in any kinds of molecules is "align" ... for example:
align #1:203@C19,C20,C21,C16,C17,O18 to #2:125@C2,C3,C4,C5,C6,O6
(or the other way around, if you wanted #2 to move)
See the help for various command options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
Maybe you were looking at the help pages for Chimera, which is different than ChimeraX. Only Chimera has a separate "match" command, which we renamed as "align" in ChimeraX because truncated commands are accepted.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
> On May 22, 2024, at 2:20 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hi everyone, > > I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix" > > tl;dr. Trying to align ring atoms of a ligand instead of protein chain > > Chimerax > mask 1 = #1:203@C19,C20,C21,C16,C17,O18 > mask 2 = #2:125@C2,C3,C4,C5,C6,O6 > matchmaker: No matrix compatible with both reference structure and all match structures > match: Same as above. In reply log, match is extended to matchmaker > > Chimera > mask 1 = #0:203@C19,C20,C21,C16,C17,O18 > mask 2 = #1:125@C2,C3,C4,C5,C6,O6 > matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix > match: Gives me RMSD > ** I need this atom match functionality in ChimeraX >
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You did say that and I just missed it. Thank you for confirming and for updating the docs!
On May 22, 2024, at 5:14 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
My reply below said "regardless of the order" but I agree it needs to be stated in the documentation, so I will add it!
I have also tested that it is not dependent on order of the remaining atoms even after stripping the non-matching ones (the hydrogens in Tom's example). The remaining atoms can also be in a different order.
Elaine
On May 22, 2024, at 5:05 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Daniel,
If you use "matchAtomNames true" it ignores the given atom order. I also was wondering about this and it wasn't clear from the align command documentation so I looked at the source code. Atoms in one set that don't have an atom in the other set of the same name are not used in the comparison. So if one ATP has hydrogens but the other does not, then it will just align on all the non-hydrogen atoms that both ATPs have in common.
Tom
On May 22, 2024, at 5:01 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
Thank you both. It seems as if some structures have ATP hydrogens and others don’t, but this was very helpful. I’ve tried this align command with a few structures and it seems to work.
Does matchAtomNames true attempt to create a new pairwise mapping between group A atoms and group B atoms where the names are the same? Or is the mapping always based on atom order, and matchAtomNames true merely filters out pairs whose names don’t match?
Thanks, Daniel
On May 22, 2024, at 4:47 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Daniel,
Seems like if your ATP ligands use the same atom names the you just use ChimeraX command
align #2:ATP to #1:ATP matchAtomNames true
In my look at a few PDB mmCIF files (8g1j, 6r81) they put the ATP atoms in the same order so the "matchAtomNames true" does not appear to be necessary for PDB entries.
Tom
On May 22, 2024, at 4:42 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Daniel, If the structures are from the Protein DataBank, my understanding is that there is a standard residue name (ATP in this case), and for that residue aka chemical component, a standard set of atom names and maybe even a standard order in which they appear in the file. If that were the case, you'd only need to give the residue numbers in the "align" command, or even just :ATP if each structure only has one ATP.
The "align" command does have options to require same chain ID, or same residue number, or to use the atom names regardless of the order in which they appear. Still, depending on how your input files are constructed and to which conventions they adhere, using one or more of these options may or may not make your life easier.
See the "align" help page for the keyword options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
I hope this helps, Elaine
On May 22, 2024, at 4:21 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
Can I piggyback on this question to ask if there is a recommended way of doing the atom pairing for commonly seen ligands?
For example, there does not appear to be a standardized atom ordering for ATP. Recently I was examining some ATP binding sites across different structures and I wanted to align on the ATP molecule, but it was a colossal pain because the ATP atoms were not in the same order. As far as I could tell the only way was for me to manually go through the ATP atoms (or some subset of them) and one by one identify the corresponding atom IDs in the two structures so I could pass that to the align command.
Does anyone have a script/recommended strategy for this use case?
Thanks, Daniel
> On May 22, 2024, at 2:45 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hi Alex, > The Matchmaker tool and "matchmaker" command are for sequence-alignable biopolymer chains (peptides, RNA, DNA) and use only one mainchain atom per residue. When you enter "match" it is just recognized as a truncation of "matchmaker" so you get the same thing. > > The command in ChimeraX to match any atoms of your choice in any kinds of molecules is "align" ... for example: > > align #1:203@C19,C20,C21,C16,C17,O18 to #2:125@C2,C3,C4,C5,C6,O6 > > (or the other way around, if you wanted #2 to move) > > See the help for various command options: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> > > Maybe you were looking at the help pages for Chimera, which is different than ChimeraX. Only Chimera has a separate "match" command, which we renamed as "align" in ChimeraX because truncated commands are accepted. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Resource for Biocomputing, Visualization, and Informatics > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On May 22, 2024, at 2:20 PM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: >> >> Hi everyone, >> >> I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix" >> >> tl;dr. Trying to align ring atoms of a ligand instead of protein chain >> >> Chimerax >> mask 1 = #1:203@C19,C20,C21,C16,C17,O18 >> mask 2 = #2:125@C2,C3,C4,C5,C6,O6 >> matchmaker: No matrix compatible with both reference structure and all match structures >> match: Same as above. In reply log, match is extended to matchmaker >> >> Chimera >> mask 1 = #0:203@C19,C20,C21,C16,C17,O18 >> mask 2 = #1:125@C2,C3,C4,C5,C6,O6 >> matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix >> match: Gives me RMSD >> ** I need this atom match functionality in ChimeraX >> > > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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participants (4)
-
Alexander Hung Lee -
Daniel David Richman -
Elaine Meng -
Tom Goddard