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
