[Chimera-users] Query (how to find H-bonds)

Elaine Meng meng at cgl.ucsf.edu
Sun Oct 1 10:27:33 PDT 2017

In the image you sent, it IS already showing the ligand.  It is the smaller helix peptide.  Both the protein and ligand are shown as ribbons, with the dashed line drawn between the protein and the peptide ligand.  The dashed line is connecting the protein and the peptide ligand, because in the PDB file, they are the same chain.

In correct PDB format, they would be in different chains, e.g. chain A for the larger protein and chain B.  Your file format is incorrect because there are two different sets of residues 2-9 in the same chain (the protein starts with 2). 

As a favor, I edited your 3_8_sol_3.ref.pdb file to add chain ID “B" to the ligand residues 1-9 at the end (I didn’t bother adding chain ID “A" to the first part, which would have been more work). The edited file is attached.  However, if you have more files, you will have to edit them yourself!  

You can compare the files before and after editing using your favorite text-editor.  Also, see our description of PDB format:

However, because it is all one file (one model in Chimera), you can’t just use “intermodel” to get only the H-bonds between protein and ligand.  You could calculate all of the H-bonds (intramodel), or to get only the H-bonds between the protein and the peptide ligand, you would have to select one of those (for example, using the edited file, command: select :.B ) and then in the H-bond dialog, turn on the option “Only find H-bonds 'with exactly one end selected',” plus any other options you wanted to use.


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> On Sep 30, 2017, at 7:38 PM, Gurudeeban Selvaraj <gurudeeb99 at qq.com> wrote:
> Dear Dr. Elaine
> Thanks! But I want to see protein and ligand (peptide) structure. I could not see ligand, the display shows only protein structure. 
> The file I enclosed is docked result. Instead of ligand there is a dotted line in between the protein.....I could not see this before.
> The attachment file has (2 to 195 protein) and (1-7 peptide). I can see the individual structure in separate file but I could not see in same pdb file (docked result). 
> The tutorial is not helping to fix the issue
> Please make me clear!
> > On Sep 30, 2017, at 4:57 AM, Gurudeeban Selvaraj <gurudeeb99 at qq.com> wrote:
> > 
> > Dear Dr.Elaine,
> >           Thanks for the information. It is working now but some of them I could not see hydrogen bonds (Intra). Now I could not see the ligand structure of the docked result in Chimera.
> > I have enclosed file and snap shot of my issue. Let me know, what will do?
> > 
> > <3_8_sol_3.ref.pdb><image.jpg>

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