Hi, I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line? Thanks, Catherine
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0 However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing. Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example: matchmaker #0 #1 ...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> See aso the discussion of different ways to superimpose structures, and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
Hi Elaine, Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms. Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743 Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992 match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986 match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743 match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743 Thanks, Catherine On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
See aso the discussion of different ways to superimpose structures, and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
Hi Catherine, I don't understand the lines of information that you sent, or what you mean by "doesn't perform the alignment." If there is an error, it should say what the problem is, like malformed atom specification or unequal numbers of atoms specified. Or if there was a superposition attempt but you don't like the result, then look in the Reply Log (in Favorites menu) to see how many pairs of atoms were matched and the RMSD. I also don't understand "it gives me a new pdb file with new coordinates." To get a new pdb file with new coordinates you would have to explicitly save a PDB file and choose the option to save the moved model "relative to" the reference model used in the match. Also just because some specific atom is not matched well doesn't mean that there wasn't a fit to the whole set of atoms that you specified in the command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms.
Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743
Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992
match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986
match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
Thanks, Catherine
On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
See aso the discussion of different ways to superimpose structures, and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, Yes, I was generating the new PDB files using "write relative #0 #1 filename". The lines of information I mentioned earlier are from the pdb files generated before and after the "match" command was implemented. Let me explain my data. My input files are an original structure pdb file and 90⁰ rotated structure. Looking at the ReplyLog I could see that if I perform overall alignment using "match #1 #0", it's perfectly aligned. Is there a way to perform each chain alignment between structures in one command? I want to align something like "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" where first #1 D is matched with #0 A, then #1 A with #0 B and so on. But, this command doesn't quite generate the expected alignment. I also tried "match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D". This seems to perform the alignment I prefer. Do you think this match command performs chain alignment in sequence or is there a better way to do it? Thanks, Catherine On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Catherine, I don't understand the lines of information that you sent, or what you mean by "doesn't perform the alignment." If there is an error, it should say what the problem is, like malformed atom specification or unequal numbers of atoms specified. Or if there was a superposition attempt but you don't like the result, then look in the Reply Log (in Favorites menu) to see how many pairs of atoms were matched and the RMSD.
I also don't understand "it gives me a new pdb file with new coordinates." To get a new pdb file with new coordinates you would have to explicitly save a PDB file and choose the option to save the moved model "relative to" the reference model used in the match.
Also just because some specific atom is not matched well doesn't mean that there wasn't a fit to the whole set of atoms that you specified in the command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms.
Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743
Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992
match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986
match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
Thanks, Catherine
On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
See aso the discussion of different ways to superimpose structures, and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Catherine, This one looks correct, and as long as you have recent Chimera (within last couple of years), should match the atoms in the order that you gave for the chains: match #1:.D,.A,.B,.C #0:.A,.B,.C,.D The following one looks extremely wrong because you should have all of the atoms from one structure first and all of the atoms from the second structure last, not interleaved: match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D However, you are flying blind if you don't check how many pairs of atoms are used for the match. It is reported in the status line transiently, but it is also logged in theReply Log (menu: Favorites... Reply Log). You should look in the Reply Log for any error messages, and if the command executes, for the resulting RMSD and how many pairs of atoms were used to calculate it. If your command worked the way you wanted, it should be the same as number of atoms in each structure (which would have to be the same as each other). How many atoms are in a structure are reported in the status line at the bottom when it is opened. Or if it's already open and you don't feel like opening it again, you can select it select #0 and the current selection will be reported in the status line. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2022, at 3:24 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Yes, I was generating the new PDB files using "write relative #0 #1 filename". The lines of information I mentioned earlier are from the pdb files generated before and after the "match" command was implemented.
Let me explain my data. My input files are an original structure pdb file and 90⁰ rotated structure. Looking at the ReplyLog I could see that if I perform overall alignment using "match #1 #0", it's perfectly aligned. Is there a way to perform each chain alignment between structures in one command? I want to align something like "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" where first #1 D is matched with #0 A, then #1 A with #0 B and so on. But, this command doesn't quite generate the expected alignment. I also tried "match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D". This seems to perform the alignment I prefer.
Do you think this match command performs chain alignment in sequence or is there a better way to do it?
Thanks, Catherine
On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, I don't understand the lines of information that you sent, or what you mean by "doesn't perform the alignment." If there is an error, it should say what the problem is, like malformed atom specification or unequal numbers of atoms specified. Or if there was a superposition attempt but you don't like the result, then look in the Reply Log (in Favorites menu) to see how many pairs of atoms were matched and the RMSD.
I also don't understand "it gives me a new pdb file with new coordinates." To get a new pdb file with new coordinates you would have to explicitly save a PDB file and choose the option to save the moved model "relative to" the reference model used in the match.
Also just because some specific atom is not matched well doesn't mean that there wasn't a fit to the whole set of atoms that you specified in the command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms.
Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743
Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992
match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986
match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
Thanks, Catherine
On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
See aso the discussion of different ways to superimpose structures, and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, I upgraded to the latest version of Chimera. I think "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" alignment works as expected. Both generate different coordinates and RMSD values. match #1:.D,.A,.B,.C #0:.A,.B,.C,.D RMSD between 3484 atom pairs is 0.838 angstroms match #1:.D #0:.A RMSD between 871 atom pairs is 0.886 angstroms But, when I perform alignment for CA or CB atoms, it performs alignment just for the first chain. I'm not sure if it's a bug. match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA RMSD between 436 atom pairs is 0.295 angstroms match #1:.D@CA #0:.A@CA RMSD between 109 atom pairs is 0.295 angstroms RMSD is the same and I checked the coordinates; It generates same coordinates for both the match commands. So, I'm thinking it's performing the first chain alignment only. match #1:.D@CB,.A@CB,.B@CB,.C@CB #0:.A@CB,.B@CB,.C@CB,.D@CB RMSD between 400 atom pairs is 0.311 angstroms match #1:.D@CB #0:.A@CB RMSD between 100 atom pairs is 0.311 angstroms I forgot to mention, I did some preprocessing to make sure all chains have the same number of atoms. Thanks, Catherine On Tue, Apr 5, 2022 at 7:56 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Catherine, This one looks correct, and as long as you have recent Chimera (within last couple of years), should match the atoms in the order that you gave for the chains:
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D
The following one looks extremely wrong because you should have all of the atoms from one structure first and all of the atoms from the second structure last, not interleaved:
match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D
However, you are flying blind if you don't check how many pairs of atoms are used for the match. It is reported in the status line transiently, but it is also logged in theReply Log (menu: Favorites... Reply Log). You should look in the Reply Log for any error messages, and if the command executes, for the resulting RMSD and how many pairs of atoms were used to calculate it. If your command worked the way you wanted, it should be the same as number of atoms in each structure (which would have to be the same as each other).
How many atoms are in a structure are reported in the status line at the bottom when it is opened. Or if it's already open and you don't feel like opening it again, you can select it
select #0
and the current selection will be reported in the status line.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2022, at 3:24 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Yes, I was generating the new PDB files using "write relative #0 #1 filename". The lines of information I mentioned earlier are from the pdb files generated before and after the "match" command was implemented.
Let me explain my data. My input files are an original structure pdb file and 90⁰ rotated structure. Looking at the ReplyLog I could see that if I perform overall alignment using "match #1 #0", it's perfectly aligned. Is there a way to perform each chain alignment between structures in one command? I want to align something like "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" where first #1 D is matched with #0 A, then #1 A with #0 B and so on. But, this command doesn't quite generate the expected alignment. I also tried "match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D". This seems to perform the alignment I prefer.
Do you think this match command performs chain alignment in sequence or is there a better way to do it?
Thanks, Catherine
On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, I don't understand the lines of information that you sent, or what you mean by "doesn't perform the alignment." If there is an error, it should say what the problem is, like malformed atom specification or unequal numbers of atoms specified. Or if there was a superposition attempt but you don't like the result, then look in the Reply Log (in Favorites menu) to see how many pairs of atoms were matched and the RMSD.
I also don't understand "it gives me a new pdb file with new coordinates." To get a new pdb file with new coordinates you would have to explicitly save a PDB file and choose the option to save the moved model "relative to" the reference model used in the match.
Also just because some specific atom is not matched well doesn't mean that there wasn't a fit to the whole set of atoms that you specified in the command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms.
Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743
Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992
match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986
match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
Thanks, Catherine
On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
See aso the discussion of different ways to superimpose structures, and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
The reported numbers of atoms used in the matches suggests that all the chains specified in the command are being included. There isn't anything else I can say about it from the information given. Best, Elaine
On Apr 6, 2022, at 1:54 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I upgraded to the latest version of Chimera. I think "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" alignment works as expected. Both generate different coordinates and RMSD values.
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D RMSD between 3484 atom pairs is 0.838 angstroms
match #1:.D #0:.A RMSD between 871 atom pairs is 0.886 angstroms
But, when I perform alignment for CA or CB atoms, it performs alignment just for the first chain. I'm not sure if it's a bug.
match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA RMSD between 436 atom pairs is 0.295 angstroms match #1:.D@CA #0:.A@CA RMSD between 109 atom pairs is 0.295 angstroms
RMSD is the same and I checked the coordinates; It generates same coordinates for both the match commands. So, I'm thinking it's performing the first chain alignment only.
match #1:.D@CB,.A@CB,.B@CB,.C@CB #0:.A@CB,.B@CB,.C@CB,.D@CB RMSD between 400 atom pairs is 0.311 angstroms match #1:.D@CB #0:.A@CB RMSD between 100 atom pairs is 0.311 angstroms
I forgot to mention, I did some preprocessing to make sure all chains have the same number of atoms.
Thanks, Catherine
On Tue, Apr 5, 2022 at 7:56 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, This one looks correct, and as long as you have recent Chimera (within last couple of years), should match the atoms in the order that you gave for the chains:
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D
The following one looks extremely wrong because you should have all of the atoms from one structure first and all of the atoms from the second structure last, not interleaved:
match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D
However, you are flying blind if you don't check how many pairs of atoms are used for the match. It is reported in the status line transiently, but it is also logged in theReply Log (menu: Favorites... Reply Log). You should look in the Reply Log for any error messages, and if the command executes, for the resulting RMSD and how many pairs of atoms were used to calculate it. If your command worked the way you wanted, it should be the same as number of atoms in each structure (which would have to be the same as each other).
How many atoms are in a structure are reported in the status line at the bottom when it is opened. Or if it's already open and you don't feel like opening it again, you can select it
select #0
and the current selection will be reported in the status line.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2022, at 3:24 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Yes, I was generating the new PDB files using "write relative #0 #1 filename". The lines of information I mentioned earlier are from the pdb files generated before and after the "match" command was implemented.
Let me explain my data. My input files are an original structure pdb file and 90⁰ rotated structure. Looking at the ReplyLog I could see that if I perform overall alignment using "match #1 #0", it's perfectly aligned. Is there a way to perform each chain alignment between structures in one command? I want to align something like "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" where first #1 D is matched with #0 A, then #1 A with #0 B and so on. But, this command doesn't quite generate the expected alignment. I also tried "match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D". This seems to perform the alignment I prefer.
Do you think this match command performs chain alignment in sequence or is there a better way to do it?
Thanks, Catherine
On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, I don't understand the lines of information that you sent, or what you mean by "doesn't perform the alignment." If there is an error, it should say what the problem is, like malformed atom specification or unequal numbers of atoms specified. Or if there was a superposition attempt but you don't like the result, then look in the Reply Log (in Favorites menu) to see how many pairs of atoms were matched and the RMSD.
I also don't understand "it gives me a new pdb file with new coordinates." To get a new pdb file with new coordinates you would have to explicitly save a PDB file and choose the option to save the moved model "relative to" the reference model used in the match.
Also just because some specific atom is not matched well doesn't mean that there wasn't a fit to the whole set of atoms that you specified in the command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms.
Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743
Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992
match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986
match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
Thanks, Catherine
On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
See aso the discussion of different ways to superimpose structures, and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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Hi Elaine, Yes, it says, it uses the specified chain atoms to align the structures. But, the output generated produces the same coordinates. I have attached my input files. If you perform the match command as below, it generates two files with the same coordinates. match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA write relative #0 #1 all_CA.pdb match #1:.D@CA #0:.A@CA write relative #0 #1 AD_CA.pdb Can you please clarify why the output generated has the same values? Am I missing something? Thanks, Catherine On Wed, Apr 6, 2022 at 5:04 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
The reported numbers of atoms used in the matches suggests that all the chains specified in the command are being included. There isn't anything else I can say about it from the information given. Best, Elaine
On Apr 6, 2022, at 1:54 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I upgraded to the latest version of Chimera. I think "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" alignment works as expected. Both generate different coordinates and RMSD values.
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D RMSD between 3484 atom pairs is 0.838 angstroms
match #1:.D #0:.A RMSD between 871 atom pairs is 0.886 angstroms
But, when I perform alignment for CA or CB atoms, it performs alignment just for the first chain. I'm not sure if it's a bug.
match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA RMSD between 436 atom pairs is 0.295 angstroms match #1:.D@CA #0:.A@CA RMSD between 109 atom pairs is 0.295 angstroms
RMSD is the same and I checked the coordinates; It generates same coordinates for both the match commands. So, I'm thinking it's performing the first chain alignment only.
match #1:.D@CB,.A@CB,.B@CB,.C@CB #0:.A@CB,.B@CB,.C@CB,.D@CB RMSD between 400 atom pairs is 0.311 angstroms match #1:.D@CB #0:.A@CB RMSD between 100 atom pairs is 0.311 angstroms
I forgot to mention, I did some preprocessing to make sure all chains have the same number of atoms.
Thanks, Catherine
On Tue, Apr 5, 2022 at 7:56 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, This one looks correct, and as long as you have recent Chimera (within last couple of years), should match the atoms in the order that you gave for the chains:
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D
The following one looks extremely wrong because you should have all of the atoms from one structure first and all of the atoms from the second structure last, not interleaved:
match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D
However, you are flying blind if you don't check how many pairs of atoms are used for the match. It is reported in the status line transiently, but it is also logged in theReply Log (menu: Favorites... Reply Log). You should look in the Reply Log for any error messages, and if the command executes, for the resulting RMSD and how many pairs of atoms were used to calculate it. If your command worked the way you wanted, it should be the same as number of atoms in each structure (which would have to be the same as each other).
How many atoms are in a structure are reported in the status line at the bottom when it is opened. Or if it's already open and you don't feel like opening it again, you can select it
select #0
and the current selection will be reported in the status line.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2022, at 3:24 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Yes, I was generating the new PDB files using "write relative #0 #1 filename". The lines of information I mentioned earlier are from the pdb files generated before and after the "match" command was implemented.
Let me explain my data. My input files are an original structure pdb file and 90⁰ rotated structure. Looking at the ReplyLog I could see that if I perform overall alignment using "match #1 #0", it's perfectly aligned. Is there a way to perform each chain alignment between structures in one command? I want to align something like "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" where first #1 D is matched with #0 A, then #1 A with #0 B and so on. But, this command doesn't quite generate the expected alignment. I also tried "match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D". This seems to perform the alignment I prefer.
Do you think this match command performs chain alignment in sequence or is there a better way to do it?
Thanks, Catherine
On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, I don't understand the lines of information that you sent, or what you mean by "doesn't perform the alignment." If there is an error, it should say what the problem is, like malformed atom specification or unequal numbers of atoms specified. Or if there was a superposition attempt but you don't like the result, then look in the Reply Log (in Favorites menu) to see how many pairs of atoms were matched and the RMSD.
I also don't understand "it gives me a new pdb file with new coordinates." To get a new pdb file with new coordinates you would have to explicitly save a PDB file and choose the option to save the moved model "relative to" the reference model used in the match.
Also just because some specific atom is not matched well doesn't mean that there wasn't a fit to the whole set of atoms that you specified in the command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms.
Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743
Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992
match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986
match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
Thanks, Catherine
On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html
See aso the discussion of different ways to superimpose structures,
and links therein:
< https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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Hi Catherine, I know this is pretty arcane, but when also specifying specific atoms you have to use colons instead of commas in your atom spec, i.e.: match #1:.D@CA:.A@CA:.B@CA:.C@CA #0:.A@CA:.B@CA:.C@CA:.D@CA Commas can only be used to separate parts of the spec “at the same level”, and the @CA is going down from the residue level to the atom level. Sorry it’s so non-obvious. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 7, 2022, at 12:51 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Yes, it says, it uses the specified chain atoms to align the structures. But, the output generated produces the same coordinates. I have attached my input files. If you perform the match command as below, it generates two files with the same coordinates.
match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA write relative #0 #1 all_CA.pdb
match #1:.D@CA #0:.A@CA write relative #0 #1 AD_CA.pdb
Can you please clarify why the output generated has the same values? Am I missing something?
Thanks, Catherine
On Wed, Apr 6, 2022 at 5:04 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: The reported numbers of atoms used in the matches suggests that all the chains specified in the command are being included. There isn't anything else I can say about it from the information given. Best, Elaine
On Apr 6, 2022, at 1:54 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Hi Elaine,
I upgraded to the latest version of Chimera. I think "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" alignment works as expected. Both generate different coordinates and RMSD values.
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D RMSD between 3484 atom pairs is 0.838 angstroms
match #1:.D #0:.A RMSD between 871 atom pairs is 0.886 angstroms
But, when I perform alignment for CA or CB atoms, it performs alignment just for the first chain. I'm not sure if it's a bug.
match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA RMSD between 436 atom pairs is 0.295 angstroms match #1:.D@CA #0:.A@CA RMSD between 109 atom pairs is 0.295 angstroms
RMSD is the same and I checked the coordinates; It generates same coordinates for both the match commands. So, I'm thinking it's performing the first chain alignment only.
match #1:.D@CB,.A@CB,.B@CB,.C@CB #0:.A@CB,.B@CB,.C@CB,.D@CB RMSD between 400 atom pairs is 0.311 angstroms match #1:.D@CB #0:.A@CB RMSD between 100 atom pairs is 0.311 angstroms
I forgot to mention, I did some preprocessing to make sure all chains have the same number of atoms.
Thanks, Catherine
On Tue, Apr 5, 2022 at 7:56 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Catherine, This one looks correct, and as long as you have recent Chimera (within last couple of years), should match the atoms in the order that you gave for the chains:
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D
The following one looks extremely wrong because you should have all of the atoms from one structure first and all of the atoms from the second structure last, not interleaved:
match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D
However, you are flying blind if you don't check how many pairs of atoms are used for the match. It is reported in the status line transiently, but it is also logged in theReply Log (menu: Favorites... Reply Log). You should look in the Reply Log for any error messages, and if the command executes, for the resulting RMSD and how many pairs of atoms were used to calculate it. If your command worked the way you wanted, it should be the same as number of atoms in each structure (which would have to be the same as each other).
How many atoms are in a structure are reported in the status line at the bottom when it is opened. Or if it's already open and you don't feel like opening it again, you can select it
select #0
and the current selection will be reported in the status line.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2022, at 3:24 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Hi Elaine,
Yes, I was generating the new PDB files using "write relative #0 #1 filename". The lines of information I mentioned earlier are from the pdb files generated before and after the "match" command was implemented.
Let me explain my data. My input files are an original structure pdb file and 90⁰ rotated structure. Looking at the ReplyLog I could see that if I perform overall alignment using "match #1 #0", it's perfectly aligned. Is there a way to perform each chain alignment between structures in one command? I want to align something like "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" where first #1 D is matched with #0 A, then #1 A with #0 B and so on. But, this command doesn't quite generate the expected alignment. I also tried "match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D". This seems to perform the alignment I prefer.
Do you think this match command performs chain alignment in sequence or is there a better way to do it?
Thanks, Catherine
On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Catherine, I don't understand the lines of information that you sent, or what you mean by "doesn't perform the alignment." If there is an error, it should say what the problem is, like malformed atom specification or unequal numbers of atoms specified. Or if there was a superposition attempt but you don't like the result, then look in the Reply Log (in Favorites menu) to see how many pairs of atoms were matched and the RMSD.
I also don't understand "it gives me a new pdb file with new coordinates." To get a new pdb file with new coordinates you would have to explicitly save a PDB file and choose the option to save the moved model "relative to" the reference model used in the match.
Also just because some specific atom is not matched well doesn't mean that there wasn't a fit to the whole set of atoms that you specified in the command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Hi Elaine,
Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms.
Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743
Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992
match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986
match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
Thanks, Catherine
On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>>
See aso the discussion of different ways to superimpose structures, and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
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To expand on what Eric said, it will still use all those atoms, but the commas do not specify ordering. Thus the order of the match stayed the same even though you entered the comma-separated chains in a different order. When you use the colons instead, it does specify the order. I would also put in a plug for ChimeraX: we improved atom specification in ChimeraX, so that to do the matches with two different chain pairings, the ChimeraX commands would be: align #2/A,B,C,D@ca to #1/A,B,C,D@ca ...giving RMSD between 436 atom pairs is 0.001 angstroms align #2/D,A,B,C@ca to #1/A,B,C,D@ca ...giving RMSD between 436 atom pairs is 0.294 angstroms ...and a different match orientation, as expected. (In ChimeraX, the command is "align" so that it is less likely to get confused with "matchmaker", and the syntax is slightly different, making it clear which thing is being aligned to which other thing.) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2022, at 4:20 PM, Eric Pettersen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Catherine, I know this is pretty arcane, but when also specifying specific atoms you have to use colons instead of commas in your atom spec, i.e.:
match #1:.D@CA:.A@CA:.B@CA:.C@CA #0:.A@CA:.B@CA:.C@CA:.D@CA
Commas can only be used to separate parts of the spec “at the same level”, and the @CA is going down from the residue level to the atom level. Sorry it’s so non-obvious.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 7, 2022, at 12:51 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Yes, it says, it uses the specified chain atoms to align the structures. But, the output generated produces the same coordinates. I have attached my input files. If you perform the match command as below, it generates two files with the same coordinates.
match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA write relative #0 #1 all_CA.pdb
match #1:.D@CA #0:.A@CA write relative #0 #1 AD_CA.pdb
Can you please clarify why the output generated has the same values? Am I missing something?
Thanks, Catherine
On Wed, Apr 6, 2022 at 5:04 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: The reported numbers of atoms used in the matches suggests that all the chains specified in the command are being included. There isn't anything else I can say about it from the information given. Best, Elaine
On Apr 6, 2022, at 1:54 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I upgraded to the latest version of Chimera. I think "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" alignment works as expected. Both generate different coordinates and RMSD values.
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D RMSD between 3484 atom pairs is 0.838 angstroms
match #1:.D #0:.A RMSD between 871 atom pairs is 0.886 angstroms
But, when I perform alignment for CA or CB atoms, it performs alignment just for the first chain. I'm not sure if it's a bug.
match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA RMSD between 436 atom pairs is 0.295 angstroms match #1:.D@CA #0:.A@CA RMSD between 109 atom pairs is 0.295 angstroms
RMSD is the same and I checked the coordinates; It generates same coordinates for both the match commands. So, I'm thinking it's performing the first chain alignment only.
match #1:.D@CB,.A@CB,.B@CB,.C@CB #0:.A@CB,.B@CB,.C@CB,.D@CB RMSD between 400 atom pairs is 0.311 angstroms match #1:.D@CB #0:.A@CB RMSD between 100 atom pairs is 0.311 angstroms
I forgot to mention, I did some preprocessing to make sure all chains have the same number of atoms.
Thanks, Catherine
On Tue, Apr 5, 2022 at 7:56 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, This one looks correct, and as long as you have recent Chimera (within last couple of years), should match the atoms in the order that you gave for the chains:
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D
The following one looks extremely wrong because you should have all of the atoms from one structure first and all of the atoms from the second structure last, not interleaved:
match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D
However, you are flying blind if you don't check how many pairs of atoms are used for the match. It is reported in the status line transiently, but it is also logged in theReply Log (menu: Favorites... Reply Log). You should look in the Reply Log for any error messages, and if the command executes, for the resulting RMSD and how many pairs of atoms were used to calculate it. If your command worked the way you wanted, it should be the same as number of atoms in each structure (which would have to be the same as each other).
How many atoms are in a structure are reported in the status line at the bottom when it is opened. Or if it's already open and you don't feel like opening it again, you can select it
select #0
and the current selection will be reported in the status line.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2022, at 3:24 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Yes, I was generating the new PDB files using "write relative #0 #1 filename". The lines of information I mentioned earlier are from the pdb files generated before and after the "match" command was implemented.
Let me explain my data. My input files are an original structure pdb file and 90⁰ rotated structure. Looking at the ReplyLog I could see that if I perform overall alignment using "match #1 #0", it's perfectly aligned. Is there a way to perform each chain alignment between structures in one command? I want to align something like "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" where first #1 D is matched with #0 A, then #1 A with #0 B and so on. But, this command doesn't quite generate the expected alignment. I also tried "match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D". This seems to perform the alignment I prefer.
Do you think this match command performs chain alignment in sequence or is there a better way to do it?
Thanks, Catherine
On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, I don't understand the lines of information that you sent, or what you mean by "doesn't perform the alignment." If there is an error, it should say what the problem is, like malformed atom specification or unequal numbers of atoms specified. Or if there was a superposition attempt but you don't like the result, then look in the Reply Log (in Favorites menu) to see how many pairs of atoms were matched and the RMSD.
I also don't understand "it gives me a new pdb file with new coordinates." To get a new pdb file with new coordinates you would have to explicitly save a PDB file and choose the option to save the moved model "relative to" the reference model used in the match.
Also just because some specific atom is not matched well doesn't mean that there wasn't a fit to the whole set of atoms that you specified in the command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms.
Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743
Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992
match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986
match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
Thanks, Catherine
On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
See aso the discussion of different ways to superimpose structures, and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
Thanks, Catherine
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Hi Elaine & Eric, Thank you for the information about updating the match command with colon. It worked as expected. Thanks, Catherine On Thu, Apr 7, 2022 at 8:40 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
To expand on what Eric said, it will still use all those atoms, but the commas do not specify ordering. Thus the order of the match stayed the same even though you entered the comma-separated chains in a different order. When you use the colons instead, it does specify the order.
I would also put in a plug for ChimeraX: we improved atom specification in ChimeraX, so that to do the matches with two different chain pairings, the ChimeraX commands would be:
align #2/A,B,C,D@ca to #1/A,B,C,D@ca ...giving RMSD between 436 atom pairs is 0.001 angstroms
align #2/D,A,B,C@ca to #1/A,B,C,D@ca ...giving RMSD between 436 atom pairs is 0.294 angstroms
...and a different match orientation, as expected. (In ChimeraX, the command is "align" so that it is less likely to get confused with "matchmaker", and the syntax is slightly different, making it clear which thing is being aligned to which other thing.)
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2022, at 4:20 PM, Eric Pettersen via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi Catherine, I know this is pretty arcane, but when also specifying specific atoms you have to use colons instead of commas in your atom spec, i.e.:
match #1:.D@CA:.A@CA:.B@CA:.C@CA #0:.A@CA:.B@CA:.C@CA:.D@CA
Commas can only be used to separate parts of the spec “at the same level”, and the @CA is going down from the residue level to the atom level. Sorry it’s so non-obvious.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 7, 2022, at 12:51 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Yes, it says, it uses the specified chain atoms to align the structures. But, the output generated produces the same coordinates. I have attached my input files. If you perform the match command as below, it generates two files with the same coordinates.
match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA write relative #0 #1 all_CA.pdb
match #1:.D@CA #0:.A@CA write relative #0 #1 AD_CA.pdb
Can you please clarify why the output generated has the same values? Am I missing something?
Thanks, Catherine
On Wed, Apr 6, 2022 at 5:04 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: The reported numbers of atoms used in the matches suggests that all the chains specified in the command are being included. There isn't anything else I can say about it from the information given. Best, Elaine
On Apr 6, 2022, at 1:54 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I upgraded to the latest version of Chimera. I think "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" alignment works as expected. Both generate different coordinates and RMSD values.
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D RMSD between 3484 atom pairs is 0.838 angstroms
match #1:.D #0:.A RMSD between 871 atom pairs is 0.886 angstroms
But, when I perform alignment for CA or CB atoms, it performs alignment just for the first chain. I'm not sure if it's a bug.
match #1:.D@CA,.A@CA,.B@CA,.C@CA #0:.A@CA,.B@CA,.C@CA,.D@CA RMSD between 436 atom pairs is 0.295 angstroms match #1:.D@CA #0:.A@CA RMSD between 109 atom pairs is 0.295 angstroms
RMSD is the same and I checked the coordinates; It generates same coordinates for both the match commands. So, I'm thinking it's performing the first chain alignment only.
match #1:.D@CB,.A@CB,.B@CB,.C@CB #0:.A@CB,.B@CB,.C@CB,.D@CB RMSD between 400 atom pairs is 0.311 angstroms match #1:.D@CB #0:.A@CB RMSD between 100 atom pairs is 0.311 angstroms
I forgot to mention, I did some preprocessing to make sure all chains have the same number of atoms.
Thanks, Catherine
On Tue, Apr 5, 2022 at 7:56 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, This one looks correct, and as long as you have recent Chimera (within last couple of years), should match the atoms in the order that you gave for the chains:
match #1:.D,.A,.B,.C #0:.A,.B,.C,.D
The following one looks extremely wrong because you should have all of the atoms from one structure first and all of the atoms from the second structure last, not interleaved:
match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D
However, you are flying blind if you don't check how many pairs of atoms are used for the match. It is reported in the status line transiently, but it is also logged in theReply Log (menu: Favorites... Reply Log). You should look in the Reply Log for any error messages, and if the command executes, for the resulting RMSD and how many pairs of atoms were used to calculate it. If your command worked the way you wanted, it should be the same as number of atoms in each structure (which would have to be the same as each other).
How many atoms are in a structure are reported in the status line at the bottom when it is opened. Or if it's already open and you don't feel like opening it again, you can select it
select #0
and the current selection will be reported in the status line.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 5, 2022, at 3:24 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Yes, I was generating the new PDB files using "write relative #0 #1 filename". The lines of information I mentioned earlier are from the pdb files generated before and after the "match" command was implemented.
Let me explain my data. My input files are an original structure pdb file and 90⁰ rotated structure. Looking at the ReplyLog I could see that if I perform overall alignment using "match #1 #0", it's perfectly aligned. Is there a way to perform each chain alignment between structures in one command? I want to align something like "match #1:.D,.A,.B,.C #0:.A,.B,.C,.D" where first #1 D is matched with #0 A, then #1 A with #0 B and so on. But, this command doesn't quite generate the expected alignment. I also tried "match #1:.D #0:.A #1:.A #0:.B #1:.B #0:.C #1:.C #0:.D". This seems to perform the alignment I prefer.
Do you think this match command performs chain alignment in sequence or is there a better way to do it?
Thanks, Catherine
On Thu, Mar 31, 2022 at 7:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Catherine, I don't understand the lines of information that you sent, or what you mean by "doesn't perform the alignment." If there is an error, it should say what the problem is, like malformed atom specification or unequal numbers of atoms specified. Or if there was a superposition attempt but you don't like the result, then look in the Reply Log (in Favorites menu) to see how many pairs of atoms were matched and the RMSD.
I also don't understand "it gives me a new pdb file with new coordinates." To get a new pdb file with new coordinates you would have to explicitly save a PDB file and choose the option to save the moved model "relative to" the reference model used in the match.
Also just because some specific atom is not matched well doesn't mean that there wasn't a fit to the whole set of atoms that you specified in the command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:52 PM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for the response. I'm working on similar structures with the same number of atoms. I have mentioned below the coordinates of the same atoms in two chains in a pdb. You could see that if I match a specific chain, it gives me a new pdb file with new coordinates. But when I try to match all the atoms or specific atom types. It doesn't perform the alignment. Am I missing something? And about matchmatcher; I prefer to have options to align all atoms or CA atoms or CB atoms.
Structure 1: ATOM 19 N ASN A 2 12.612 28.406 -9.353 ATOM 968 N ASN B 2 -6.828 36.102 -9.743
Structure 2: ATOM 1 N ASN A 2 -7.732 35.011 -9.283 ATOM 873 N ASN B 2 -0.035 54.442 -9.992
match #1:.A@CA #0:.B@CA ATOM 1 N ASN A 2 -7.691 35.166 -9.397 ATOM 873 N ASN B 2 0.155 54.542 -9.986
match #1 #0 ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
match #1:*@CA #0:*@CA ATOM 1 N ASN A 2 12.612 28.406 -9.353 ATOM 873 N ASN B 2 -6.828 36.102 -9.743
Thanks, Catherine
On Thu, Mar 31, 2022 at 1:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. -------
Hi Catherine, If you just give the model number it specifies the all the atoms in the model,for example: match #1 #0
However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.
Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically. It just uses the alpha-carbons (1 atom per residue). Example:
matchmaker #0 #1
...there are lots of possible options of this command, see < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
See aso the discussion of different ways to superimpose structures, and links therein: < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: > > Hi, > > I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line? > > Thanks, > Catherine
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participants (3)
-
Catherine Jenifer Rajam Rajendran -
Elaine Meng -
Eric Pettersen