Hi I agree with Pavel. Last time I checked the validation didn't take account of Calpha - H ... O or N hydrogen bonds (also involving other polarised C atoms), even though these are well-documented.
Cheers -- Ian On Wed, 22 Aug 2018 at 10:42, Pavel Afonine <pafon...@gmail.com> wrote: > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
