Hi Robbie and Eleanor There are links for Zn-His and Zn-Cys. They meant to be used automatically, obviously something is not entirely right.
Link names are: ZN-CYS It has a bond between Zn and S as well as an angle: ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000 This also removes H of Cys to make covalent bond between Zn and Cys. Similar links are available for Zn and His ND1 and Zn - HIS NE2 Link names are: ZN-HISND ZN-HISNE Again these links have angles between Zn and atoms of His. Angle centred at Zn is missing. But these distances and angles defined in the link it should work fine. Regards Garib > On 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/
