As far as my understanding goes, LINK records will not be replaced by LINKR records by default. If the Link is in the monomer library one has to delete th right atoms and the atoms to be linked have to be within a reasonable distance. Than refmac will automatically recognize that for the two residues and when the exact atoms are missing than a standard link can be applied and will be put in and a LINKR record will appear automatically in the pdb. No LINK statement is necessary and even counterproductive. LINKR records in Refmac will point to a rich dictionary with not only a simple length restraint (for LINK record, which is derived from the actual distance in the pdb! This could be very wrong.) but has also angle restraints (dihedrals....) etc. If the link is not in the monomer library I personally would always recommend to create a link dictionary with jligand, which will also create such an information rich dictionary. Similar things are possible in other packages as well. Of course that is only for pdb's, how that works with mmcif and the pdb, no idea at all.
Cheers Christian On Tue, May 15, 2018 at 7:11 PM, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > Afaik Refmac will apply the right restraints, iff there is only one type > of LINK between those atoms. Particularly with carbohydrates, it's better > to be explicit. > > > > Cheers, > > Robbie > > > > Sent from my Windows 10 phone > > > ------------------------------ > *From:* Edward A. Berry <ber...@upstate.edu> > *Sent:* Tuesday, May 15, 2018 8:07:38 PM > *To:* Robbie Joosten; CCP4BB@JISCMAIL.AC.UK > > *Subject:* Re: [ccp4bb] Problems with HEC in CCP4 > > Does this mean- if the pdb file has standard PDB link records involving > HEC, like > LINK SG CYS A 32 CAB HEM A 93 1555 1555 > 1.82 > LINK SG CYS A 35 CAC HEM A 93 1555 1555 > 1.81 > then refmac will look up the necessary modifications in the ccp4 > dictionary? > Or do we need to tell refmac to apply those mods? > eab > > On 05/15/2018 05:00 AM, Robbie Joosten wrote: > > Addendum: > > > > 4qo5 actually lacks the right LINK records altogether. It will only work > if you add these by hand. Perhaps you should ask the depositors or the PDB > to add the appropriate LINK records. > > > > Cheers, > > Robbie > > > >> -----Original Message----- > >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Robbie > >> Joosten > >> Sent: Tuesday, May 15, 2018 10:51 > >> To: CCP4BB@JISCMAIL.AC.UK > >> Subject: Re: [ccp4bb] Problems with HEC in CCP4 > >> > >> Hi Eugene, > >> > >> The problem is not in the HEC.cif file but with the LINKs which modify > the > >> chemistry. These were fixed a while ago and the LINKs were added to the > >> CCP4 dictionary. I thought these were released already. If not, they > will be > >> soon. > >> > >> Cheers, > >> Robbie > >> > >>> -----Original Message----- > >>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of > >> Eugene > >>> Osipov > >>> Sent: Tuesday, May 15, 2018 10:36 > >>> To: CCP4BB@JISCMAIL.AC.UK > >>> Subject: [ccp4bb] Problems with HEC in CCP4 > >>> > >>> Dear CCP4 developers, > >>> please fix errors with heme c dictionary file HEC.cif. > >>> Edward Berry described this problem in detail 4 years ago: > >>> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36393.html > >>> This error already affects deposited entries, e.g.: 4QO5 clearly > >>> contains errors in vynil groups of heme c. > >>> > >>> > >>> -- > >>> > >>> Eugene Osipov > >>> Junior Research Scientist > >>> Laboratory of Enzyme Engineering > >>> A.N. Bach Institute of Biochemistry > >>> Russian Academy of Sciences > >>> Leninsky pr. 33, 119071 Moscow, Russia > >>> e-mail: e.m.osi...@gmail.com <mailto:e.m.osi...@gmail.com > <e.m.osi...@gmail.com>> >
