Hello Eugene,
Andrey Lebedev has written a nice tutorial using JLigand for ligands:
ftp://ftp.ccp4.ac.uk/JLigand/index.html
You want, in particular, the "A new link..." section. You should work your way through it - you will find it
enlightening.
Regards,
Paul.
On 15/05/2018 13:53, Eugene Osipov wrote:
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 <[email protected]
<mailto:[email protected]>>:
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 <[email protected]
<mailto:[email protected]>> On Behalf Of Robbie
> Joosten
> Sent: Tuesday, May 15, 2018 10:51
> To: [email protected] <mailto:[email protected]>
> 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 <[email protected]
<mailto:[email protected]>> On Behalf Of
> Eugene
> > Osipov
> > Sent: Tuesday, May 15, 2018 10:36
> > To: [email protected] <mailto:[email protected]>
> > 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/[email protected]/msg36393.html
<https://www.mail-archive.com/[email protected]/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: [email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
--
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: [email protected] <mailto:[email protected]>
