Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms. P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454 Best regards, Hrvoje Rimac Hrvoje Rimac, PhD. Postdoctoral Fellow Department of Medicinal Chemistry Faculty of Pharmacy and Biochemistry University of Zagreb A.Kovačića 1, 10000 Zagreb Croatia http://www.pharma.unizg.hr/
Dear Hrvoje Rimac, In Chimera you have to explicitly specify the atoms (e.g. list the atom names) in the command line for them to be paired up in the order specified. However, I understand that that can be difficult if you have a large number of atoms. In ChimeraX that would also be the "safest" but there may be some automatic sorting that improves the comparison order if you don't specify the atoms explicitly in the command. The "align" command also has options to match atom names, residue number, chain IDs, which may help. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> The ChimeraX "align" command also has a "move nothing" option that I believe will do what you want. However, I still get 0.252 (details below). If you believe that is incorrect, please use menu: Help... Report a Bug and attach a session file with the two ligands. I opened your two files, then command: align #1 toAtoms #2 move nothing RMSD between 24 atom pairs is 0.252 angstroms Also tried "matchAtomNames" option: align #1 toAtoms #2 matchAtomNames true move nothing RMSD between 24 atom pairs is 0.252 angstroms Even if I list all the atoms, I still get the same value. align #1@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl toAtoms #2@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl move nothing RMSD between 24 atom pairs is 0.252 angstroms I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2020, at 3:47 AM, Hrvoje Rimac <hrimac@pharma.hr> wrote:
Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms.
P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454
Best regards, Hrvoje Rimac
Oops, I misunderstood. You wanted the RMSD in the current position, not as if they had been fitted. In that case, sorry: ChimeraX does not yet have a command to measure that. Best, Elaine
On Jun 19, 2020, at 7:48 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Hrvoje Rimac, In Chimera you have to explicitly specify the atoms (e.g. list the atom names) in the command line for them to be paired up in the order specified. However, I understand that that can be difficult if you have a large number of atoms.
In ChimeraX that would also be the "safest" but there may be some automatic sorting that improves the comparison order if you don't specify the atoms explicitly in the command. The "align" command also has options to match atom names, residue number, chain IDs, which may help.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
The ChimeraX "align" command also has a "move nothing" option that I believe will do what you want. However, I still get 0.252 (details below). If you believe that is incorrect, please use menu: Help... Report a Bug and attach a session file with the two ligands.
I opened your two files, then command:
align #1 toAtoms #2 move nothing RMSD between 24 atom pairs is 0.252 angstroms
Also tried "matchAtomNames" option:
align #1 toAtoms #2 matchAtomNames true move nothing RMSD between 24 atom pairs is 0.252 angstroms
Even if I list all the atoms, I still get the same value.
align #1@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl toAtoms #2@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl move nothing RMSD between 24 atom pairs is 0.252 angstroms
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2020, at 3:47 AM, Hrvoje Rimac <hrimac@pharma.hr> wrote:
Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms.
P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454
Best regards, Hrvoje Rimac
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Dear Elaine, thank you for the answer. I guess the best solution is either to explicitly list the order of atoms in Chimera (not ChimeraX) or change the order in the pdb files. In this way I get what I want. I guess writing a script for that is inevitable :D P.S. I see a ticket has been raised for the rmsd equivalent in ChimeraX. Looking forward to a permanent solution. Thank you again, Hrvoje
Oops, I misunderstood. You wanted the RMSD in the current position, not as if they had been fitted. In that case, sorry: ChimeraX does not yet have a command to measure that. Best, Elaine
On Jun 19, 2020, at 7:48 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Hrvoje Rimac, In Chimera you have to explicitly specify the atoms (e.g. list the atom names) in the command line for them to be paired up in the order specified. However, I understand that that can be difficult if you have a large number of atoms.
In ChimeraX that would also be the "safest" but there may be some automatic sorting that improves the comparison order if you don't specify the atoms explicitly in the command. The "align" command also has options to match atom names, residue number, chain IDs, which may help.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
The ChimeraX "align" command also has a "move nothing" option that I believe will do what you want. However, I still get 0.252 (details below). If you believe that is incorrect, please use menu: Help... Report a Bug and attach a session file with the two ligands.
I opened your two files, then command:
align #1 toAtoms #2 move nothing RMSD between 24 atom pairs is 0.252 angstroms
Also tried "matchAtomNames" option:
align #1 toAtoms #2 matchAtomNames true move nothing RMSD between 24 atom pairs is 0.252 angstroms
Even if I list all the atoms, I still get the same value.
align #1@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl toAtoms #2@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl move nothing RMSD between 24 atom pairs is 0.252 angstroms
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2020, at 3:47 AM, Hrvoje Rimac <hrimac@pharma.hr> wrote:
Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms.
P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454
Best regards, Hrvoje Rimac
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Hrvoje Rimac, PhD. Postdoctoral Fellow Department of Medicinal Chemistry Faculty of Pharmacy and Biochemistry University of Zagreb A.Kovačića 1, 10000 Zagreb Croatia http://www.pharma.unizg.hr/
Dr. Rimac, My bundle has a command for that. I haven't put my bundle on ChimeraX's tool shed yet, so it won't be the easiest to install. Here's my bundle's GitHub: https://github.com/QChASM/SEQCROW/tree/dev The installation instructions can be found in the README lower on that GitHub page. The command is 'rmsdAlign'. It should work as `rmsdAlign #1 toModels #2 [#3...] align false sort true`. The RMSD's are printed to the log. I tried it on your structures and got an RMSD of 0.465 instead of 0.454. I'm not sure why I don't get the same RMSD as you. Best, Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, June 19, 2020 10:56 AM To: Hrvoje Rimac <hrimac@pharma.hr> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] RMSD command in ChimeraX [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Oops, I misunderstood. You wanted the RMSD in the current position, not as if they had been fitted. In that case, sorry: ChimeraX does not yet have a command to measure that. Best, Elaine
On Jun 19, 2020, at 7:48 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Hrvoje Rimac, In Chimera you have to explicitly specify the atoms (e.g. list the atom names) in the command line for them to be paired up in the order specified. However, I understand that that can be difficult if you have a large number of atoms.
In ChimeraX that would also be the "safest" but there may be some automatic sorting that improves the comparison order if you don't specify the atoms explicitly in the command. The "align" command also has options to match atom names, residue number, chain IDs, which may help.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
The ChimeraX "align" command also has a "move nothing" option that I believe will do what you want. However, I still get 0.252 (details below). If you believe that is incorrect, please use menu: Help... Report a Bug and attach a session file with the two ligands.
I opened your two files, then command:
align #1 toAtoms #2 move nothing RMSD between 24 atom pairs is 0.252 angstroms
Also tried "matchAtomNames" option:
align #1 toAtoms #2 matchAtomNames true move nothing RMSD between 24 atom pairs is 0.252 angstroms
Even if I list all the atoms, I still get the same value.
align #1@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl toAtoms #2@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl move nothing RMSD between 24 atom pairs is 0.252 angstroms
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2020, at 3:47 AM, Hrvoje Rimac <hrimac@pharma.hr> wrote:
Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms.
P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454
Best regards, Hrvoje Rimac
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Hi Tony, It’s possibly because of the atom ordering? By default, the atoms returned by an AtomsArg aren’t sorted, since sorting is an expensive operation if the number of atoms is large (e.g. you’re coloring a ribosome). To get the atoms for your rmsdAlign command to be sorted, use an OrderedAtomsArg instead. —Eric
On Jun 19, 2020, at 11:54 AM, Anthony James Schaefer <tony.schaefer@uga.edu> wrote:
Dr. Rimac,
My bundle has a command for that. I haven't put my bundle on ChimeraX's tool shed yet, so it won't be the easiest to install.
Here's my bundle's GitHub:https://github.com/QChASM/SEQCROW/tree/dev <https://github.com/QChASM/SEQCROW/tree/dev>
The installation instructions can be found in the README lower on that GitHub page.
The command is 'rmsdAlign'. It should work as `rmsdAlign #1 toModels #2 [#3...] align false sort true`. The RMSD's are printed to the log. I tried it on your structures and got an RMSD of 0.465 instead of 0.454. I'm not sure why I don't get the same RMSD as you.
Best,
Tony
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Friday, June 19, 2020 10:56 AM To: Hrvoje Rimac <hrimac@pharma.hr <mailto:hrimac@pharma.hr>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] RMSD command in ChimeraX
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Oops, I misunderstood. You wanted the RMSD in the current position, not as if they had been fitted. In that case, sorry: ChimeraX does not yet have a command to measure that. Best, Elaine
On Jun 19, 2020, at 7:48 AM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Dear Hrvoje Rimac, In Chimera you have to explicitly specify the atoms (e.g. list the atom names) in the command line for them to be paired up in the order specified. However, I understand that that can be difficult if you have a large number of atoms.
In ChimeraX that would also be the "safest" but there may be some automatic sorting that improves the comparison order if you don't specify the atoms explicitly in the command. The "align" command also has options to match atom names, residue number, chain IDs, which may help.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html <http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>>
The ChimeraX "align" command also has a "move nothing" option that I believe will do what you want. However, I still get 0.252 (details below). If you believe that is incorrect, please use menu: Help... Report a Bug and attach a session file with the two ligands.
I opened your two files, then command:
align #1 toAtoms #2 move nothing RMSD between 24 atom pairs is 0.252 angstroms
Also tried "matchAtomNames" option:
align #1 toAtoms #2 matchAtomNames true move nothing RMSD between 24 atom pairs is 0.252 angstroms
Even if I list all the atoms, I still get the same value.
align #1@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl toAtoms #2@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl move nothing RMSD between 24 atom pairs is 0.252 angstroms
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2020, at 3:47 AM, Hrvoje Rimac <hrimac@pharma.hr <mailto:hrimac@pharma.hr>> wrote:
Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms.
P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454
Best regards, Hrvoje Rimac
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_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Eric, I'm using ModelArg/ModelsArg instead of AtomsArg. I'm letting AaronTools do the sorting when `sort true` is used. I've checked, and AaronTools gets the order right (at least in this case). When `sort false` is used, I'm just using the order the atoms appear in AtomicStructure.atoms. Best, Tony ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Friday, June 19, 2020 3:00 PM To: Anthony James Schaefer <tony.schaefer@uga.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] RMSD command in ChimeraX [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Tony, It’s possibly because of the atom ordering? By default, the atoms returned by an AtomsArg aren’t sorted, since sorting is an expensive operation if the number of atoms is large (e.g. you’re coloring a ribosome). To get the atoms for your rmsdAlign command to be sorted, use an OrderedAtomsArg instead. —Eric On Jun 19, 2020, at 11:54 AM, Anthony James Schaefer <tony.schaefer@uga.edu<mailto:tony.schaefer@uga.edu>> wrote: Dr. Rimac, My bundle has a command for that. I haven't put my bundle on ChimeraX's tool shed yet, so it won't be the easiest to install. Here's my bundle's GitHub:https://github.com/QChASM/SEQCROW/tree/dev The installation instructions can be found in the README lower on that GitHub page. The command is 'rmsdAlign'. It should work as `rmsdAlign #1 toModels #2 [#3...] align false sort true`. The RMSD's are printed to the log. I tried it on your structures and got an RMSD of 0.465 instead of 0.454. I'm not sure why I don't get the same RMSD as you. Best, Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu<mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Sent: Friday, June 19, 2020 10:56 AM To: Hrvoje Rimac <hrimac@pharma.hr<mailto:hrimac@pharma.hr>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] RMSD command in ChimeraX [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Oops, I misunderstood. You wanted the RMSD in the current position, not as if they had been fitted. In that case, sorry: ChimeraX does not yet have a command to measure that. Best, Elaine
On Jun 19, 2020, at 7:48 AM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote:
Dear Hrvoje Rimac, In Chimera you have to explicitly specify the atoms (e.g. list the atom names) in the command line for them to be paired up in the order specified. However, I understand that that can be difficult if you have a large number of atoms.
In ChimeraX that would also be the "safest" but there may be some automatic sorting that improves the comparison order if you don't specify the atoms explicitly in the command. The "align" command also has options to match atom names, residue number, chain IDs, which may help.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
The ChimeraX "align" command also has a "move nothing" option that I believe will do what you want. However, I still get 0.252 (details below). If you believe that is incorrect, please use menu: Help... Report a Bug and attach a session file with the two ligands.
I opened your two files, then command:
align #1 toAtoms #2 move nothing RMSD between 24 atom pairs is 0.252 angstroms
Also tried "matchAtomNames" option:
align #1 toAtoms #2 matchAtomNames true move nothing RMSD between 24 atom pairs is 0.252 angstroms
Even if I list all the atoms, I still get the same value.
align #1@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl toAtoms #2@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl move nothing RMSD between 24 atom pairs is 0.252 angstroms
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2020, at 3:47 AM, Hrvoje Rimac <hrimac@pharma.hr<mailto:hrimac@pharma.hr>> wrote:
Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms.
P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454
Best regards, Hrvoje Rimac
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Thank you Anthony, in Chimera after sorting the atoms (and PyMOL) I also got 0.465. The value of 0.454 I got when I calculated it by hand in Excel, it could be a rounding issue (even though it is a little big for that) or I could've made a mistake somewhere, but I don't see where since the value of 4.147 is identical for both Excel and Chimera. In either case, thank you. Best regards, Hrvoje I will definitely try it.
Hi Tony, Itâs possibly because of the atom ordering? By default, the atoms returned by an AtomsArg arenât sorted, since sorting is an expensive operation if the number of atoms is large (e.g. youâre coloring a ribosome). To get the atoms for your rmsdAlign command to be sorted, use an OrderedAtomsArg instead.
âEric
On Jun 19, 2020, at 11:54 AM, Anthony James Schaefer <tony.schaefer@uga.edu> wrote:
Dr. Rimac,
My bundle has a command for that. I haven't put my bundle on ChimeraX's tool shed yet, so it won't be the easiest to install.
Here's my bundle's GitHub:https://github.com/QChASM/SEQCROW/tree/dev <https://github.com/QChASM/SEQCROW/tree/dev>
The installation instructions can be found in the README lower on that GitHub page.
The command is 'rmsdAlign'. It should work as `rmsdAlign #1 toModels #2 [#3...] align false sort true`. The RMSD's are printed to the log. I tried it on your structures and got an RMSD of 0.465 instead of 0.454. I'm not sure why I don't get the same RMSD as you.
Best,
Tony
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Friday, June 19, 2020 10:56 AM To: Hrvoje Rimac <hrimac@pharma.hr <mailto:hrimac@pharma.hr>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] RMSD command in ChimeraX
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Oops, I misunderstood. You wanted the RMSD in the current position, not as if they had been fitted. In that case, sorry: ChimeraX does not yet have a command to measure that. Best, Elaine
On Jun 19, 2020, at 7:48 AM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Dear Hrvoje Rimac, In Chimera you have to explicitly specify the atoms (e.g. list the atom names) in the command line for them to be paired up in the order specified. However, I understand that that can be difficult if you have a large number of atoms.
In ChimeraX that would also be the "safest" but there may be some automatic sorting that improves the comparison order if you don't specify the atoms explicitly in the command. The "align" command also has options to match atom names, residue number, chain IDs, which may help.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html <http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>>
The ChimeraX "align" command also has a "move nothing" option that I believe will do what you want. However, I still get 0.252 (details below). If you believe that is incorrect, please use menu: Help... Report a Bug and attach a session file with the two ligands.
I opened your two files, then command:
align #1 toAtoms #2 move nothing RMSD between 24 atom pairs is 0.252 angstroms
Also tried "matchAtomNames" option:
align #1 toAtoms #2 matchAtomNames true move nothing RMSD between 24 atom pairs is 0.252 angstroms
Even if I list all the atoms, I still get the same value.
align #1@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl toAtoms #2@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,s,n1,n2,n3,n4,n5,cl move nothing RMSD between 24 atom pairs is 0.252 angstroms
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2020, at 3:47 AM, Hrvoje Rimac <hrimac@pharma.hr <mailto:hrimac@pharma.hr>> wrote:
Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms.
P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454
Best regards, Hrvoje Rimac
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Hrvoje Rimac, PhD. Postdoctoral Fellow Department of Medicinal Chemistry Faculty of Pharmacy and Biochemistry University of Zagreb A.Kovačića 1, 10000 Zagreb Croatia http://www.pharma.unizg.hr/
participants (4)
-
Anthony James Schaefer -
Elaine Meng -
Eric Pettersen -
Hrvoje Rimac