Technically, if I recall that correct from my memory, if the link is in the monomer library and the correct atoms are deleted, Refmac will use the link from the library and create a LINKR record. I am not sure right now if they are handled properly in the deposition process.
Cheers Christian On Tue, May 15, 2018 at 4:21 PM, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > Hi Eugene, > > > > A link describes a chemical bond between two residues. With each LINK > modifications of the residues are described (e.g. leaving atoms and, in > this case, changes of local chemistry such as bond orders). > > Each LINK type has a unique identifier that points to the descriptions in > the CCP4 dictionary. Did you add those names (HEC-something, I don’t know > them by hart)? And is your CCP4 up to date? > > > > Cheers, > > Robbie > > > > Sent from my Windows 10 phone > > > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eugene > Osipov <e.m.osi...@gmail.com> > *Sent:* Tuesday, May 15, 2018 2:53:49 PM > > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Problems with HEC in CCP4 > > Hi Robbie, > I thought LINK just adds another bond restrain to the refinement procedure > and does not affect already existing restrains in library cif file. Am I > wrong? > Also, what do you mean by "modify the chemistry"? > Just to test your suggestion, I have added LINKs for heme c vynil groups > in 4qo5 and ran refinement in refmac 5.8. I took F(+) from deposited cif > file as F and SigF(+) as SIGF. After refinement HEC601 and HEC604 have > incorrect position of CBC atom. > Note: I took 4qo5 just as example of cytochrome c to show issues with HEC > and do not intend to insult authors of original paper. > > 2018-05-15 12:00 GMT+03:00 Robbie Joosten <robbie_joos...@hotmail.com>: > >> 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> >> > > > > -- > 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 >
