**Hi all, I have a set of protein structures (about 10) that I need to superimpose. I have used Matchmaker and superimposed by choosing a reference structure. I want to know how to calculate the overall RMSD of the superimposed structures? Where do I lokk out for it? I have checked the Reply log window, but it gets displayed only for some, whereas for others it does not. Please help.. Thanks, -Suda
Hi Suda, Matchmaker does pairwise superpositions to the reference, so even if you chose to match structures B,C,D to A, it will perform pairwise matches and report pairwise RMSD for A-B, A-C, and A-D. All of those should be in the Reply Log, but there is various other stuff between them such as parameters listings, so you would need to scroll up to see them. However, to get an overall RMSD of more than two structures, after you run MatchMaker you would run Match->Align to make a multiple sequence alignment (instead of the pairwise ones created by MatchMaker). Match->Align is in the menu under Tools... Structure Comparison. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html> Besides overall RMSD it will also give you other measures of structural similarity (SDM, Q-score), and in the output sequence alignment there will be an RMSD histogram above sequences showing the per-column values. HOWEVER, be aware it will take a pretty long time to run Match->Align on 10 structures, especially with iteration. I would try it without iteration first (which still might take a pretty long time, many minutes) and see if the resulting sequence alignment looks good enough. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 15, 2011, at 8:31 PM, Suda Parimala Ravindran wrote:
Hi all,
I have a set of protein structures (about 10) that I need to superimpose. I have used Matchmaker and superimposed by choosing a reference structure. I want to know how to calculate the overall RMSD of the superimposed structures? Where do I lokk out for it? I have checked the Reply log window, but it gets displayed only for some, whereas for others it does not. Please help..
Thanks,
-Suda
Hi Elaine.. Thanks a lot for your reply. I have run even the Match-> Align along with iteration. After running, the alignment window does show up, I have checked the reply log. But can't find the overall RMSD value for some runs. I have attached the entire reply log file along for which i didn't find the overall value. So can you please help me locate the overall RMSD value? I can only find the pairwise RMSD values. Also, I want to know on how to choose a reference structure. Say for example, i have 10 structures to superimpose and among them 5 belong to (eg) bacterial species (my query/study of interest) and the remaining 5 belong to varied organisms of different hierarchy. So how do i choose my reference structure among the 5 from my query. what I thought was to run the superimposition 5 times choosing each bacterial strcuture as a reference each time, calculate the overall RMSD and then choose the least RMSD one as reference? Can i proceed this way or are there any other better option to choose a reference structure? PLease help. Thanks, -Suda ** On Wed, Nov 16, 2011 at 11:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Suda, Matchmaker does pairwise superpositions to the reference, so even if you chose to match structures B,C,D to A, it will perform pairwise matches and report pairwise RMSD for A-B, A-C, and A-D. All of those should be in the Reply Log, but there is various other stuff between them such as parameters listings, so you would need to scroll up to see them.
However, to get an overall RMSD of more than two structures, after you run MatchMaker you would run Match->Align to make a multiple sequence alignment (instead of the pairwise ones created by MatchMaker). Match->Align is in the menu under Tools... Structure Comparison. < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchali...
Besides overall RMSD it will also give you other measures of structural similarity (SDM, Q-score), and in the output sequence alignment there will be an RMSD histogram above sequences showing the per-column values.
HOWEVER, be aware it will take a pretty long time to run Match->Align on 10 structures, especially with iteration. I would try it without iteration first (which still might take a pretty long time, many minutes) and see if the resulting sequence alignment looks good enough.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2011, at 8:31 PM, Suda Parimala Ravindran wrote:
Hi all,
I have a set of protein structures (about 10) that I need to superimpose. I have used Matchmaker and superimposed by choosing a reference structure. I want to know how to calculate the overall RMSD of the superimposed structures? Where do I lokk out for it? I have checked the Reply log window, but it gets displayed only for some, whereas for others it does not. Please help..
Thanks,
-Suda
Hi Suda,
From the Reply Log it looks like the Match->Align calculation did not run:
Match?Align cutoff: 5.0, in column if within cutoff of: any Cannot generate alignment with Bitis gabonica.pdb principal chain because it is not superimposed on the other structures Match?Align cutoff: 5.0, in column if within cutoff of: any Cannot generate alignment with Bitis gabonica.pdb principal chain because it is not superimposed on the other structures ... and this would suggest no sequence alignment including all 10 (or 5?) was output, or even if something was output, the calculation did not finish. I only see pairwise RMSD results from MatchMaker. I think your approach to try each possible reference is reasonable. Another possibility is to try to find one that generally has smaller pairwise RMSDs with the others, but that can be difficult, so what you were doing sounds fine. However, be careful to pick the chains in the Match->Align dialog that are superimposed. You can "clear" the Reply Log before running Match->Align so that you will not be confused by the results from MatchMaker. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 16, 2011, at 10:15 PM, Suda Parimala Ravindran wrote:
Hi Elaine..
Thanks a lot for your reply. I have run even the Match-> Align along with iteration. After running, the alignment window does show up, I have checked the reply log. But can't find the overall RMSD value for some runs. I have attached the entire reply log file along for which i didn't find the overall value. So can you please help me locate the overall RMSD value? I can only find the pairwise RMSD values.
Also, I want to know on how to choose a reference structure. Say for example, i have 10 structures to superimpose and among them 5 belong to (eg) bacterial species (my query/study of interest) and the remaining 5 belong to varied organisms of different hierarchy. So how do i choose my reference structure among the 5 from my query. what I thought was to run the superimposition 5 times choosing each bacterial strcuture as a reference each time, calculate the overall RMSD and then choose the least RMSD one as reference? Can i proceed this way or are there any other better option to choose a reference structure?
PLease help.
Thanks,
-Suda
On Wed, Nov 16, 2011 at 11:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Suda, Matchmaker does pairwise superpositions to the reference, so even if you chose to match structures B,C,D to A, it will perform pairwise matches and report pairwise RMSD for A-B, A-C, and A-D. All of those should be in the Reply Log, but there is various other stuff between them such as parameters listings, so you would need to scroll up to see them.
However, to get an overall RMSD of more than two structures, after you run MatchMaker you would run Match->Align to make a multiple sequence alignment (instead of the pairwise ones created by MatchMaker). Match->Align is in the menu under Tools... Structure Comparison. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html>
Besides overall RMSD it will also give you other measures of structural similarity (SDM, Q-score), and in the output sequence alignment there will be an RMSD histogram above sequences showing the per-column values.
HOWEVER, be aware it will take a pretty long time to run Match->Align on 10 structures, especially with iteration. I would try it without iteration first (which still might take a pretty long time, many minutes) and see if the resulting sequence alignment looks good enough.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2011, at 8:31 PM, Suda Parimala Ravindran wrote:
Hi all,
I have a set of protein structures (about 10) that I need to superimpose. I have used Matchmaker and superimposed by choosing a reference structure. I want to know how to calculate the overall RMSD of the superimposed structures? Where do I lokk out for it? I have checked the Reply log window, but it gets displayed only for some, whereas for others it does not. Please help..
Thanks,
-Suda
<Reply_log.txt>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks, Elaine! Would try up and let you know if I get onto more queries..!! :-) Best, Suda ** On Thu, Nov 17, 2011 at 8:44 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Suda, From the Reply Log it looks like the Match->Align calculation did not run:
Match?Align cutoff: 5.0, in column if within cutoff of: any Cannot generate alignment with Bitis gabonica.pdb principal chain because it is not superimposed on the other structures Match?Align cutoff: 5.0, in column if within cutoff of: any Cannot generate alignment with Bitis gabonica.pdb principal chain because it is not superimposed on the other structures
... and this would suggest no sequence alignment including all 10 (or 5?) was output, or even if something was output, the calculation did not finish. I only see pairwise RMSD results from MatchMaker.
I think your approach to try each possible reference is reasonable. Another possibility is to try to find one that generally has smaller pairwise RMSDs with the others, but that can be difficult, so what you were doing sounds fine.
However, be careful to pick the chains in the Match->Align dialog that are superimposed. You can "clear" the Reply Log before running Match->Align so that you will not be confused by the results from MatchMaker.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Nov 16, 2011, at 10:15 PM, Suda Parimala Ravindran wrote:
Hi Elaine..
Thanks a lot for your reply. I have run even the Match-> Align along
with iteration. After running, the alignment window does show up, I have checked the reply log. But can't find the overall RMSD value for some runs. I have attached the entire reply log file along for which i didn't find the overall value. So can you please help me locate the overall RMSD value? I can only find the pairwise RMSD values.
Also, I want to know on how to choose a reference structure. Say for
example, i have 10 structures to superimpose and among them 5 belong to (eg) bacterial species (my query/study of interest) and the remaining 5 belong to varied organisms of different hierarchy. So how do i choose my reference structure among the 5 from my query. what I thought was to run the superimposition 5 times choosing each bacterial strcuture as a reference each time, calculate the overall RMSD and then choose the least RMSD one as reference? Can i proceed this way or are there any other better option to choose a reference structure?
PLease help.
Thanks,
-Suda
On Wed, Nov 16, 2011 at 11:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Suda, Matchmaker does pairwise superpositions to the reference, so even if you
chose to match structures B,C,D to A, it will perform pairwise matches and report pairwise RMSD for A-B, A-C, and A-D. All of those should be in the Reply Log, but there is various other stuff between them such as parameters listings, so you would need to scroll up to see them.
However, to get an overall RMSD of more than two structures, after you
run MatchMaker you would run Match->Align to make a multiple sequence alignment (instead of the pairwise ones created by MatchMaker). Match->Align is in the menu under Tools... Structure Comparison.
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchali...
Besides overall RMSD it will also give you other measures of structural similarity (SDM, Q-score), and in the output sequence alignment there will be an RMSD histogram above sequences showing the per-column values.
HOWEVER, be aware it will take a pretty long time to run Match->Align on 10 structures, especially with iteration. I would try it without iteration first (which still might take a pretty long time, many minutes) and see if the resulting sequence alignment looks good enough.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2011, at 8:31 PM, Suda Parimala Ravindran wrote:
Hi all,
I have a set of protein structures (about 10) that I need to superimpose. I have used Matchmaker and superimposed by choosing a reference structure. I want to know how to calculate the overall RMSD of the superimposed structures? Where do I lokk out for it? I have checked the Reply log window, but it gets displayed only for some, whereas for others it does not. Please help..
Thanks,
-Suda
<Reply_log.txt>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Suda Parimala Ravindran