Re: [ccp4bb] RMSD between structures of homologous proteins

2014-08-13 Thread Prof. K. Sekar
Sreetama, See the following URL whether it is useful to solve your issue http://cluster.physics.iisc.ernet.in/3dss/ best, Sekar Dear all,    When calculating the RMSD between structures of homologous proteins, where there are large changes in the loop region(s), which RMSD should

Re: [ccp4bb] Comparison of Water Positions across PDBs

2013-11-06 Thread Prof. K. Sekar
Dear all, there is a tool to identify invariant water molecules in homologous protein structures and the tool can be accessed via http://cluster.physics.iisc.ernet.in/3dss/ best, Sekar Thanks Bernhard    you have helpfully distinguished between the two processes - there is certainly a

Re: [ccp4bb] Data mining interactions in the PDB

2013-10-28 Thread Prof. K. Sekar
How about this server http://iris.physics.iisc.ernet.in/psap/ On 10/29/2013 03:23 AM, Katherine Sippel wrote: Hi all, I was wondering if anyone knew of a software or server to mine the PDB for a specific class of interactions? I've tried PDBeMotif without much luck and I thought I'd

Re: [ccp4bb] Rfree flag

2013-02-27 Thread Prof. K. Sekar
Dear Kavya, It is not so. It is not mandatory. best, Sekar Dear users, Is it mandatory to use the same reflections for Rfree calculations of a ligand bound data as that of its native? Thank you With Regards Kavya -- This message has been scanned for viruses and dangerous