Dear Chimera Users,
I am analyzing a MD trajectory in chimera. After selecting H binds when I am playing the trajectory, then it always shows the hydrogen bond. Though some of the bonds are broken during the simulation but it always connect the step 1 h bonds connected.. How can I show the h bonds which breaks during the simulation.
Thank you very much for your help. S
Hi S, The H-bonds do not automatically recalculate. Instead of using findhbond one time before playing the trajectory, it should be used at each step. This can be done with a per-frame script. On the MD Movie player dialog, choose "Per-Frame... Define script" and specify that the script is in "Chimera commands." Then enter whatever commands you want to execute at each step. The MD Movie documentation includes an example with calculating H-bonds: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#pe...
In your case it could be as simple as one "findhbond" command. First, I recommend trying the command in the regular Command Line to figure out which keywords and options you want. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html
If there are protein ribbons shown, another command you might want to include in your per-frame script is "ksdssp" to recalculate secondary structure assignments. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
The Trajectories tutorial, part 1, also includes using a per-frame script to calculate H-bonds: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#pa...
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 Jan 28, 2010, at 10:51 AM, snoze pa wrote:
Dear Chimera Users, I am analyzing a MD trajectory in chimera. After selecting H binds when I am playing the trajectory, then it always shows the hydrogen bond. Though some of the bonds are broken during the simulation but it always connect the step 1 h bonds connected.. How can I show the h bonds which breaks during the simulation. Thank you very much for your help. S
Thanks Elaine for your prompt reply. Do you think if it is good to calculate the hbonds after every 10ps snapshot from hbonds menu. I want to count how many hbond are lost with time. When I am using this trick then I can see no more broken hbonds. Also another question related to Relax constraints, it is 0.4 A; what that mean? is it same as donor acceptor atom distance? thank you. S
On Thu, Jan 28, 2010 at 1:09 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi S, The H-bonds do not automatically recalculate. Instead of using findhbond one time before playing the trajectory, it should be used at each step. This can be done with a per-frame script. On the MD Movie player dialog, choose "Per-Frame... Define script" and specify that the script is in "Chimera commands." Then enter whatever commands you want to execute at each step. The MD Movie documentation includes an example with calculating H-bonds: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame
In your case it could be as simple as one "findhbond" command. First, I recommend trying the command in the regular Command Line to figure out which keywords and options you want. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html
If there are protein ribbons shown, another command you might want to include in your per-frame script is "ksdssp" to recalculate secondary structure assignments. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
The Trajectories tutorial, part 1, also includes using a per-frame script to calculate H-bonds: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1
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 Jan 28, 2010, at 10:51 AM, snoze pa wrote:
Dear Chimera Users, I am analyzing a MD trajectory in chimera. After selecting H binds when I am playing the trajectory, then it always shows the hydrogen bond. Though some of the bonds are broken during the simulation but it always connect the step 1 h bonds connected.. How can I show the h bonds which breaks during the simulation. Thank you very much for your help. S
Hi S, If you are recording a movie file, just do it for every step. The playback will be slower but the resulting movie will not. If you are just doing it for your own viewing, it is up to your own judgement how often it should be done. Most accurate would be every step that is in your trajectory, but that will slow down the playback.
As described in the manual, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond...
findhbond uses several different distance and angle cutoffs depending on the donor and acceptor atom types. Those cutoffs are based on very high-resolution small molecule structures, and we have found that for PDB structures in general (macromolecules and typically not as high resolution) the results are best with some relaxation of the strict values. So for example if the strict cutoff is 1.0 A, with 0.4 tolerance, the resulting cutoff would be 1.4 A. 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 Jan 28, 2010, at 1:06 PM, snoze pa wrote:
Thanks Elaine for your prompt reply. Do you think if it is good to calculate the hbonds after every 10ps snapshot from hbonds menu. I want to count how many hbond are lost with time. When I am using this trick then I can see no more broken hbonds. Also another question related to Relax constraints, it is 0.4 A; what that mean? is it same as donor acceptor atom distance? thank you. S
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
On Thu, Jan 28, 2010 at 3:16 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi S, If you are recording a movie file, just do it for every step. The playback will be slower but the resulting movie will not. If you are just doing it for your own viewing, it is up to your own judgement how often it should be done. Most accurate would be every step that is in your trajectory, but that will slow down the playback.
As described in the manual, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria findhbond uses several different distance and angle cutoffs depending on the donor and acceptor atom types. Those cutoffs are based on very high-resolution small molecule structures, and we have found that for PDB structures in general (macromolecules and typically not as high resolution) the results are best with some relaxation of the strict values. So for example if the strict cutoff is 1.0 A, with 0.4 tolerance, the resulting cutoff would be 1.4 A. 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 Jan 28, 2010, at 1:06 PM, snoze pa wrote:
Thanks Elaine for your prompt reply. Do you think if it is good to calculate the hbonds after every 10ps snapshot from hbonds menu. I want to count how many hbond are lost with time. When I am using this trick then I can see no more broken hbonds. Also another question related to Relax constraints, it is 0.4 A; what that mean? is it same as donor acceptor atom distance? thank you. S
Different programs use different methods and cutoffs. You could try setting the tolerances to 0.0 if you feel the default Chimera method is too permissive, but there is no reason to expect exactly the same number of H-bonds from two different programs. You would need to look at VMD documentation to see how theirs are calculated, and at Chimera's (link already sent in previous message) to know how they are calculated, then decide which one you want.
In Chimera, the angle and distance cutoffs depend on the atom types, and the criteria depend on published data (the small molecule structures). In many other programs, the same cutoffs are used no matter which atom types are involved. I don't know how it is done in VMD, however.
I know of one paper where the authors tried both MolProbity (a fancier method) and Chimera and said they usually gave the identical H-bonds: Differences in the risk of celiac disease associated with HLA-DQ2.5 or HLA-DQ2.2 are related to sustained gluten antigen presentation. Fallang LE, Bergseng E, Hotta K, Berg-Larsen A, Kim CY, Sollid LM. Nat Immunol. 2009 Oct;10(10):1096-101
Elaine
On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
I'd say you'd probably want to dump a list of the H bonds to a file in both programs (easy in Chimera at least) and find the differences and then look at the structure where the differences occur and assess for yourself which program is doing a more accurate assessment of the hydrogen bonding.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jan 28, 2010, at 2:53 PM, Elaine Meng wrote:
Different programs use different methods and cutoffs. You could try setting the tolerances to 0.0 if you feel the default Chimera method is too permissive, but there is no reason to expect exactly the same number of H-bonds from two different programs. You would need to look at VMD documentation to see how theirs are calculated, and at Chimera's (link already sent in previous message) to know how they are calculated, then decide which one you want.
In Chimera, the angle and distance cutoffs depend on the atom types, and the criteria depend on published data (the small molecule structures). In many other programs, the same cutoffs are used no matter which atom types are involved. I don't know how it is done in VMD, however.
I know of one paper where the authors tried both MolProbity (a fancier method) and Chimera and said they usually gave the identical H-bonds: Differences in the risk of celiac disease associated with HLA-DQ2.5 or HLA-DQ2.2 are related to sustained gluten antigen presentation. Fallang LE, Bergseng E, Hotta K, Berg-Larsen A, Kim CY, Sollid LM. Nat Immunol. 2009 Oct;10(10):1096-101
Elaine
On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
I forgot to mention: from looking at the images, I would say the Chimera results are more reasonable, because that's how beta-sheets form, with strand-strand hydrogen bonds. In the VMD view, some strands lack H-bonds to the next strand in the sheet, or only have one.
Of course, these statements are only qualitative, but it was my first impression. Elaine
On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
Thanks a lot Elaine! I highly appreciate your help and time.
On Thu, Jan 28, 2010 at 4:59 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
I forgot to mention: from looking at the images, I would say the Chimera results are more reasonable, because that's how beta-sheets form, with strand-strand hydrogen bonds. In the VMD view, some strands lack H-bonds to the next strand in the sheet, or only have one.
Of course, these statements are only qualitative, but it was my first impression. Elaine
On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
I checked the results with molmol and it seems chimera results are correct. I want to save the number of hbonds in each frame. When I use the command hbond in chimera script movie menu command then it prints correct number of hbonds in every frame. Can you help me how to save the results from each frame(total no of hbonds). thank you S
On Thu, Jan 28, 2010 at 4:59 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
I forgot to mention: from looking at the images, I would say the Chimera results are more reasonable, because that's how beta-sheets form, with strand-strand hydrogen bonds. In the VMD view, some strands lack H-bonds to the next strand in the sheet, or only have one.
Of course, these statements are only qualitative, but it was my first impression. Elaine
On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
Hi S, If you wanted only how many H-bonds there are at each step sent to a file, you can just save the contents of the Reply Log (under Favorites menu). You would define the script in MD Movie, then clear the Reply Log, then run the trajectory through from start to end one time (with Loop turned off). Then click Save on the Reply Log to save its contents to a text file.
If you wanted the detailed results of which atoms are H-bonding and their distances at each step, it can be done with the "saveFile" option of the "findhbond" command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html
The MD Movie per-frame script capability allows inserting the frame number in the filename so you can get a different H-bond results file for each step. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#pe...
For example, the per-frame script could have something like
findhbond saveFile ~/Desktop/hbondinfo-<FRAME>.txt
(plus any other options of that command you might want) which puts all the information from frame 1 into hbondinfo-001.txt, frame 2 hbondinfo-002.txt, ... files on my mac Desktop.
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 Jan 29, 2010, at 10:02 AM, snoze pa wrote:
I checked the results with molmol and it seems chimera results are correct. I want to save the number of hbonds in each frame. When I use the command hbond in chimera script movie menu command then it prints correct number of hbonds in every frame. Can you help me how to save the results from each frame(total no of hbonds). thank you S
On Thu, Jan 28, 2010 at 4:59 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
I forgot to mention: from looking at the images, I would say the Chimera results are more reasonable, because that's how beta-sheets form, with strand-strand hydrogen bonds. In the VMD view, some strands lack H- bonds to the next strand in the sheet, or only have one.
Of course, these statements are only qualitative, but it was my first impression. Elaine
On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you very much Elaine. It is working fine now. I was using wrong command
from chimera import runCommand for HbonDNum in range(1, 1000): runCommand("hbonds saveFile ligand.%03d.hbonds" % HbonDNum)
On Fri, Jan 29, 2010 at 1:08 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi S, If you wanted only how many H-bonds there are at each step sent to a file, you can just save the contents of the Reply Log (under Favorites menu). You would define the script in MD Movie, then clear the Reply Log, then run the trajectory through from start to end one time (with Loop turned off). Then click Save on the Reply Log to save its contents to a text file.
If you wanted the detailed results of which atoms are H-bonding and their distances at each step, it can be done with the "saveFile" option of the "findhbond" command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html
The MD Movie per-frame script capability allows inserting the frame number in the filename so you can get a different H-bond results file for each step. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame
For example, the per-frame script could have something like
findhbond saveFile ~/Desktop/hbondinfo-<FRAME>.txt
(plus any other options of that command you might want) which puts all the information from frame 1 into hbondinfo-001.txt, frame 2 hbondinfo-002.txt, ... files on my mac Desktop.
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 Jan 29, 2010, at 10:02 AM, snoze pa wrote:
I checked the results with molmol and it seems chimera results are correct. I want to save the number of hbonds in each frame. When I use the command hbond in chimera script movie menu command then it prints correct number of hbonds in every frame. Can you help me how to save the results from each frame(total no of hbonds). thank you S
On Thu, Jan 28, 2010 at 4:59 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
I forgot to mention: from looking at the images, I would say the Chimera results are more reasonable, because that's how beta-sheets form, with strand-strand hydrogen bonds. In the VMD view, some strands lack H-bonds to the next strand in the sheet, or only have one.
Of course, these statements are only qualitative, but it was my first impression. Elaine
On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Eric Pettersen -
snoze pa