Lei, The DeGrado lab developed a tool that would do just what you seek to do and could function as a PyMOL plugin. I played with it a few years ago after I found an interesting cation-pi sandwhich in my structure. I e-mailed then with the author, hoping to link the tool to the entire current PDB inventory, but then had to move on to another project, so am not certain how updated it is now. Have a look at the tool and documentation here: http://degradolab.org/suns/ It is reported in 2014 by Gonzalez et al, here: https://www.ncbi.nlm.nih.gov/pubmed/25079944
Regards, Emily. On Wed, Jan 8, 2020 at 7:57 AM Zheng, Lei <lei.zh...@uth.tmc.edu> wrote: > Dear CCP4ers, > > > > We identify a potential ion binding site formed by four residues in a > structure. I want to search if any other structures have a similar local > residual geometry. Is there any programs to perform such a searching? For > example, to search in Protein Data Bank using coordinates of the binding > site residues? I appreciate your suggestions. > > > > Happy New Year! > > Lei > > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
