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Subject:

Re: Problems with HEC in CCP4

From:

Paul Emsley <[log in to unmask]>

Reply-To:

Paul Emsley <[log in to unmask]>

Date:

Tue, 15 May 2018 14:05:24 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (91 lines)

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 <[log in to unmask] <mailto:[log in to unmask]>>:
> 
>     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 <[log in to unmask] <mailto:[log in to unmask]>> On Behalf Of Robbie
>      > Joosten
>      > Sent: Tuesday, May 15, 2018 10:51
>      > To: [log in to unmask] <mailto:[log in to unmask]>
>      > 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 <[log in to unmask] <mailto:[log in to unmask]>> On Behalf Of
>      > Eugene
>      > > Osipov
>      > > Sent: Tuesday, May 15, 2018 10:36
>      > > To: [log in to unmask] <mailto:[log in to unmask]>
>      > > 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:
>      > > [log in to unmask]" target="_blank">https:[log in to unmask]
>     <[log in to unmask]" target="_blank">https:[log in to unmask]>
>      > > 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: [log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask]
>     <mailto:[log in to unmask]>>
> 
> 
> 
> 
> -- 
> 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: [log in to unmask] <mailto:[log in to unmask]>

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