Hi I thank everybody for their nice suggestions. I am happy that my doubts are clear now.
Kahkashan On Wed, Aug 22, 2018 at 5:51 AM, Ian Tickle <ianj...@gmail.com> wrote: > > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
