If you have a smiles string or some representation of your ligand ACEDRG will make sensible restraints. Ekeanor
On Fri, 1 May 2020 at 10:50, Barone, Matthias <bar...@fmp-berlin.de> wrote: > do you mean earlier whne coot was connected to phenix during the > refinement? If you load the pdb and the mtz directly into coot, you have to > load the cif file beofre starting the real space refinement in coot. > > > Dr. Matthias Barone > > AG Kuehne, Rational Drug Design > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Muhammad > Bashir Khan <m...@ualberta.ca> > *Sent:* Friday, May 1, 2020 2:25:56 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Ligand Refinement in coot > > ReadySet > > On Thu, Apr 30, 2020 at 6:23 PM Sharan Karade <sharankar...@gmail.com> > wrote: > >> Hi, >> I think, you can generate new restrain file for your ligand and load >> before you do refine in COOT for next time. I have query that, how did you >> generate restrain file for ligand (elbow or readyset in phenix)?. >> >> >> >> >> On Thu, Apr 30, 2020 at 5:06 PM Muhammad Bashir Khan <m...@ualberta.ca> >> wrote: >> >>> Hi Folks; >>> >>> I want to ask about the ligand refinement in coot. Earlier I was able to >>> refine the ligand in the coot using real space refine zone but now by some >>> reason when I want to refine the ligand in coot it asks me >>> "Refinement setup failure failed to find restrained for XYZ". Do not know >>> what happen to the restrained file >>> >>> All your suggestion will be highly appreciated >>> >>> Bashir >>> >>> -- >>> ------------------------------------------------------ >>> Muhammad Bashir Khan, Ph.D. >>> Research Associate >>> Department of Biochemistry >>> Medical Science Bldg. >>> Lab 3-27 >>> University of Alberta >>> Edmonton AB, T6G 2H7 >>> >>> Phone: 780-492-4577- >>> e-mail: m...@ualberta.ca <cbroo...@ualberta.ca> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> >> >> >> -- >> Sharan Karade >> Postdoc-fellow >> IBBR-UMD, 9600 Gudelsky Dr, >> Rockville >> Maryland 20850 >> >> >> > > -- > ------------------------------------------------------ > Muhammad Bashir Khan, Ph.D. > Research Associate > Department of Biochemistry > Medical Science Bldg. > Lab 3-27 > University of Alberta > Edmonton AB, T6G 2H7 > > Phone: 780-492-4577- > e-mail: m...@ualberta.ca <cbroo...@ualberta.ca> > > ------------------------------ > > 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
