Hi, also, it helps to keep in mind that some clashes may actually be valid interactions that are labeled as 'clashes' by validation software that is simply not sophisticated enough to distinguish between bad steric clashes and chemically/physically favorable valid interactions. For an example, please refer to results we show in our full quantum refinement of a small structure done as part of quantum refinement project (www.qrefine.com):
http://scripts.iucr.org/cgi-bin/paper?S2059798317016746 All the best, Pavel 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
