[Chimera-users] FW: How can I find H-bond between ligand and protein residues within selected angstrom?

Williams, Joanne Joanne.Williams at ucsf.edu
Wed Sep 23 13:36:22 PDT 2015



On 9/19/15 1:29 AM, "高木友理子" <kagaribi-firefly at bs.s.u-tokyo.ac.jp>
wrote:

> Dear Chimera creator,
> 
> I use Chimera to analyse protein-ligand interaction.
> Especially, I would like to find H-bond between these.
> I clicked HBonds and tried to search H-bond within selected distance.
> However,I could not.
> I guess the reason is that I was not able to understand "Relax
> constraints" in H-Bond parameter window.
> I ,of course, checked chimera's help.
> What is relax constraints?
> What does 0.4 angstroms indicate? Is this the Max distance between ligand
> and protein residue?
> I would like to find H-bond between them within selected angstrom.
> What should I do to know that?
> Please teach me how to do.
> Thank you for being patient with my English.
> 
> Best regards,
> 
> Yuriko Takagi
> Tokyo university student





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