We focus mainly on non-H clashes. Careful inspection of H-clashes can sometimes lead to an improvement of the structure (better conformer). Very often we find the listed H-clashes "unavoidable", i.e. under the given data and converged refinement we cannot do anything anyway. So a very serious H-clash is checked, otherwise mostly not.
Jan Dohnalek On Fri, Aug 17, 2018 at 6:27 PM Firdous Tarique <kahkashantari...@gmail.com> wrote: > Hello everyone. > > I have a basic question. When a validation report of a coordinate is > generated we often come across a term known as "Too-Close Contacts". > First of all can somebody please explain me what is the shortest > interatomic distance between the two atoms which is permissible ? > Next, in this list there are Non-H and H columns list, their Interatomic > distance and Clash overlap. I could see two types of clashes in my > validation report. One in which interatomic distance between the two atom > (one is always a modeled H) ranges from 1.7-2.4A, and clash overlap from > 04-1.0. The other in which the interatomic distance between two atom is > greater than 2.2A and the clash overlap is between 0.4-0.6 (always between > two non H-atoms). > > So my question is that out of so many clashes shown in the list which are > one which actually need to be fixed and can't be ignored specially because > one of my ligand is an amino acid which is showing lots of these H clashes > (interatomic distance less than 1.5A). > > Regards > > Kahkashan > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
