Yes, I know that. My problem is I not only want to know the RMSD, but also see the aligned structures, so that I can compare difference in ligand structure and protein residues around it.
On Fri, Jul 29, 2016 at 11:49 AM, Bermejo, Guillermo (NIH/CIT) [E] < [email protected]> wrote: > Hi Qinhong, > > In terms of structure superposition and RMSD scoring within Xplor-NIH, > ligands are not treated any different than any other molecules (e.g, > protein). Am I missing something from your question? > > Best, > > Guillermo > > > ________________________________________ > From: Val Yu [[email protected]] > Sent: Friday, July 29, 2016 2:34 PM > To: xplor-nih > Subject: [Xplor-nih] Align small molecule in protein > > Hi, > > I know Xplor-NIH can fit my model set based on any selections. But > sometimes I want to compare my ligand structure with ones in other crystal > structures. Is there any software or server which can do this job > conveniently? Thanks. > > -- > Qinhong Yu > Ames' Lab > Department of Chemistry > UC Davis > -- Qinhong Yu Ames' Lab Department of Chemistry UC Davis
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