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<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Robbie > Joosten > Sent: Tuesday, May 15, 2018 10:51 > To: CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of > Eugene > > Osipov > > Sent: Tuesday, May 15, 2018 10:36 > > To: CCP4BB@JISCMAIL.AC.UK<mailto: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> > > <mailto: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<mailto:e.m.osi...@gmail.com>
