Highlighting the H bonds during simulation
Dear Sir, How could I highlight the formation and breakdown of Hbonds with the ligand to that of residues during the md simulation. I tried using the script (per-frame commands) chain @ca ~disp solvent hb line 2 color yellow reveal true Using this command, highlights all Hbonds in the system during the simulation, but I would like to see only Hbond interactions with ligand to that of nearby residues. How could I do this? what would be the appropriate per-frame script? Looking forward for the guidance. Best regards, Natesh Uni.Wien
Hi Natesh, The exact commands would depend on your system (how to specify the ligand), but I can at least give you an example. If “select ligand” selects only your ligand, it could be something like chain @ca ~disp solvent select ligand; hb selRestrict cross line 2 color yellow reveal true; ~select If “select ligand” doesn’t select only your ligand of interest, you would need to instead use its residue number(s) or names to select it. Basically this uses the “selRestrict” option of “hbonds” to limit the detection to just H-bonds with one end in the selected ligand. I put the select and unselect commands in the same line (separated with semicolons) so that the green selection outline will not show up. Putting the commands in the same line separated by semicolons hides the intermediate states. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/usageconventions.html> 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 May 31, 2016, at 2:21 AM, Natesh Singh <a1468984@unet.univie.ac.at> wrote:
Dear Sir,
How could I highlight the formation and breakdown of Hbonds with the ligand to that of residues during the md simulation. I tried using the script (per-frame commands)
chain @ca ~disp solvent hb line 2 color yellow reveal true
Using this command, highlights all Hbonds in the system during the simulation, but I would like to see only Hbond interactions with ligand to that of nearby residues. How could I do this? what would be the appropriate per-frame script?
Looking forward for the guidance.
Best regards, Natesh Uni.Wien
Dear Elaine, Thanks for help. The script worked out fine. I have another two queries: A. When I run the per frame script and record the movie, then I could not see the original h-bond width in the movie which I had changed from pseudobondgroup panel (line width: 5.0 from 1.0), though line style from bold to dashed could be seen in the movie. The new width is properly displayed in the chimera window but not reflecting in the movie. B. I would like to know how chimera is clustering the trajectory.., on what basis the number of clusters are obtained and what cut off is used during the process. I think based on pairwise rmsd matrix it's doing the clustering and cut off is used to identify the unique clusters. I could not find the same in the documentation so it would be nice if could shade some light on this. I was thinking if chimera could also give cluster map of the trajectory, where we could see different clusters and distances between them. Best regards, Natesh Uni. Wien Am 01.06.2016 00:51, schrieb Elaine Meng:
Hi Natesh, The exact commands would depend on your system (how to specify the ligand), but I can at least give you an example. If “select ligand” selects only your ligand, it could be something like
chain @ca ~disp solvent select ligand; hb selRestrict cross line 2 color yellow reveal true; ~select
If “select ligand” doesn’t select only your ligand of interest, you would need to instead use its residue number(s) or names to select it.
Basically this uses the “selRestrict” option of “hbonds” to limit the detection to just H-bonds with one end in the selected ligand. I put the select and unselect commands in the same line (separated with semicolons) so that the green selection outline will not show up. Putting the commands in the same line separated by semicolons hides the intermediate states. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/usageconventions.html>
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 May 31, 2016, at 2:21 AM, Natesh Singh <a1468984@unet.univie.ac.at> wrote:
Dear Sir,
How could I highlight the formation and breakdown of Hbonds with the ligand to that of residues during the md simulation. I tried using the script (per-frame commands)
chain @ca ~disp solvent hb line 2 color yellow reveal true
Using this command, highlights all Hbonds in the system during the simulation, but I would like to see only Hbond interactions with ligand to that of nearby residues. How could I do this? what would be the appropriate per-frame script?
Looking forward for the guidance.
Best regards, Natesh Uni.Wien
Hi Natesh, (A) This is a common issue discussed in previous posts, for example <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-October/008025.html> ...and in the “Tips for Saving Images" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#sstip> Basically, your system can only draw a line up to a certain pixel width. When you save a high-res image (more pixels than shown in the Chimera window), especially with supersampling (which makes the initial image NxN times larger than the final image), what you get in the final image may be proportionally thinner than in the Chimera window. You can see what final width is possible by choosing menu: File… Save Image. The resulting dialog will report (near the bottom) the maximum attainable linewidth in the final image given the requested image dimensions and the supersampling level. Decreasing the supersampling level and/or image dimensions will increase the linewidth in the final saved result. Generally supersampling is nice because it smooths edges (pixel stairsteps less visible), so I would first see if 2x2 supersampling solves the problem before turning it off (setting it to 1x1). The movie-saving dialog from MD Movie also has this supersampling option, but it does not report what the final linewidth will be… that’s why I suggest looking at the main save-image dialog to decide what level to use, even though you won’t be using that dialog directly. (B) the clustering methodology is described in the paper cited in the Ensemble Cluster manpage: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/en...> An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Kelley LA, Gardner SP, Sutcliffe MJ. Protein Eng. 1996 Nov;9(11):1063-5. <http://peds.oxfordjournals.org/content/9/11/1063.long> (free full text) I agree it could be useful if the clusters and the inter-cluster distances could be written out to the Log or a text file, or even exported to Cytoscape for network visualization, but we have not implemented any of those, sorry. 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 Jun 28, 2016, at 6:36 AM, Natesh Singh <a1468984@unet.univie.ac.at> wrote:
Dear Elaine, Thanks for help. The script worked out fine.
I have another two queries: A. When I run the per frame script and record the movie, then I could not see the original h-bond width in the movie which I had changed from pseudobondgroup panel (line width: 5.0 from 1.0), though line style from bold to dashed could be seen in the movie. The new width is properly displayed in the chimera window but not reflecting in the movie.
B. I would like to know how chimera is clustering the trajectory.., on what basis the number of clusters are obtained and what cut off is used during the process. I think based on pairwise rmsd matrix it's doing the clustering and cut off is used to identify the unique clusters. I could not find the same in the documentation so it would be nice if could shade some light on this. I was thinking if chimera could also give cluster map of the trajectory, where we could see different clusters and distances between them.
Best regards, Natesh Uni. Wien
participants (2)
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Elaine Meng -
Natesh Singh