One way of approaching such modelling uncertainties is to build explicitly a number of likely models, refine them and examine the difference maps carefully to see whether you can convince yourself that one model is clearly better than the others. At least then you will know whether the alternatives are distinguishable Phil
Sent from my iPad > On 23 Jul 2020, at 18:12, Reza Khayat <rkha...@ccny.cuny.edu> wrote: > > > Tried the homologues thing. There are homologues and I've done the fitting, > but this is what I consider to be subjective. I'm certain the referee will > ask: Given the quality of density for the nucleotide, how certain are the > authors that a different fit is not possible? Have other fit poses been > considered? > > > > Reza > > > > Reza Khayat, PhD > Assistant Professor > City College of New York > Department of Chemistry and Biochemistry > New York, NY 10031 > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jon Cooper > <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> > Sent: Thursday, July 23, 2020 1:07 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP > > Hello, do you have any homologues in the PDB with ATP, etc, bound as a guide? > Coot is pretty good at fitting known ligands, and unknown ones, too! > > > -------- Original Message -------- > On 23 Jul 2020, 17:53, Reza Khayat < rkha...@ccny.cuny.edu> wrote: > > Hi, > > > > Can folks suggest programs for objectively docking ATP/ADP molecules into > density? Our density is not so good, probably because of occupancy, and we'd > like a less subjecting approach for modeling. Thanks. > > > > Best wishes, > Reza > > > > Reza Khayat, PhD > Assistant Professor > City College of New York > Department of Chemistry and Biochemistry > New York, NY 10031 > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
