That seems an excellent idea - I have been struggling with a Zn complex in a ineffectual way and something like that would help, Eleanor
On Tue, 8 Sep 2020 at 10:40, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > Hi Elanor, > > The distances are in the dictionaries but the angles involve three > different residues so these cannot be in the current dictionary. We could > add the program that generates these restraints to CCP4 though. > > Cheers, > Robbie > > > -----Original Message----- > > From: Eleanor Dodson <eleanor.dod...@york.ac.uk> > > Sent: Tuesday, September 8, 2020 11:38 > > To: Robbie Joosten <robbie_joos...@hotmail.com>; Garib N Murshudov > > <ga...@mrc-lmb.cam.ac.uk> > > Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls <nicholls@mrc- > > lmb.cam.ac.uk> > > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints > > > > Robbie - could that be added to the distributed dictionaries? Zn binding > is > > common and at low resolution distance restraints are not enough.. > > Eleanor > > > > On Tue, 8 Sep 2020 at 10:33, Robbie Joosten <robbie_joos...@hotmail.com > > <mailto:robbie_joos...@hotmail.com> > wrote: > > > > > > Hi Anna, > > > > Yes you can do this in Refmac by adding external restraints. If you > > have structural Zinc sites (Zn coordinated by 4 histidines or > cysteines) you > > can also use PDB-REDO to generate the restraints automatically. The > > restraints are written to the output so you can continue using them in > > Refmac. > > > > HTH, > > Robbie > > > > > -----Original Message----- > > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK > > <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of anna > > > anna > > > Sent: Tuesday, September 8, 2020 11:28 > > > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > > > Subject: [ccp4bb] metal coordination at low resolution - > restraints > > > > > > Dear all, > > > > > > quickly: is there a way to restrain metal coordination geometry > > (even angles) > > > in refmac? > > > > > > I am refining a low resolution structure (3.3A) with 2 zinc > binding > > sites. > > > I am pretty sure about metal position (strong anomalous signal) > > and what > > > are the residues involved in coordination since I solved the apo- > > structure at > > > good resolution and Zn-binding does not induce huge structural > > variations. > > > However, as you can imagine, electron density is poorly defined > > and Refmac > > > gives a very distorted coordination geometry. > > > I noticed that in phenix it is possible to generate restraints > with > > readyset but > > > I'd like to work with refmac. > > > > > > Many thanks for your suggestions. > > > > > > Cheers, > > > Anna > > > > > > ________________________________ > > > > > > > > > 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 > > <http://www.jiscmail.ac.uk/CCP4BB> , a mailing list hosted by > > www.jiscmail.ac.uk <http://www.jiscmail.ac.uk> , terms & conditions are > > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > ######################################################################## 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/
