[Chimera-users] Highlighting the H bonds during simulation

Natesh Singh a1468984 at unet.univie.ac.at
Tue Jun 28 06:36:30 PDT 2016

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,
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 at 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

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