Re: [ccp4bb] Conserved water

2017-06-07 Thread Andres Libreros
Thanks everyone for the tips. Actually, I need this information to improve my analysis on drug/protein interaction. Best regards:) Gerardo A. Libreros Universidade de São Paulo Laboratório de Biologia Estrutural Aplicada Sent from my iPhone > On 7 Jun 2017, at 18:34, Jared Sampson

Re: [ccp4bb] Conserved water

2017-06-07 Thread Edward A. Berry
Easiest way is to line up molecule pairs or chain pairs in COOT and see if there are equivalent waters. If the number of waters is too large to inspect manually, save the superposed structures to disk, grep out the waters from each into a separate files, and use a program like

Re: [ccp4bb] Conserved water

2017-06-07 Thread benjamin bax
How about WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design? Ben On 7 Jun 2017, at 07:59, Eleanor Dodson wrote: Many years ago I wrote code to label waters with a code related to the residue/atom they were

Re: [ccp4bb] Conserved water

2017-06-07 Thread Eleanor Dodson
Many years ago I wrote code to label waters with a code related to the residue/atom they were Hbonded to , so then you could check whether all OH TYR 227 in each chain had an associated water.. But it used non-standard water naming .. Easiest way is to line up molecule pairs or chain pairs in

[ccp4bb] Conserved water

2017-06-06 Thread gerardo andres
Hi everyone, does anyone know any strategy or program (besides pywater) to identify conserved waters in a protein? Thanks,  Gerardo

[ccp4bb] Conserved water positions in low resolution refinement?

2013-11-02 Thread Guenter Fritz
Dear all, and especially all of you involved in the development of refinement programs, in low resolution refinement we always include structural information we actually do not see in the electron density (side chains, riding hydrogens) since we know that these atoms are there. But what about

Re: [ccp4bb] RE : [ccp4bb] Conserved water positions in low resolution refinement?

2013-11-02 Thread Guenter Fritz
board [CCP4BB@JISCMAIL.AC.UK] de la part de Guenter Fritz [guenter.fr...@uni-konstanz.de] Date d'envoi : samedi 2 novembre 2013 16:04 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Conserved water positions in low resolution refinement? Dear all, and especially all of you involved in the development