Re: [ccp4bb] Problems with HEC in CCP4

[Eugene Osipov]

I want to summarize my findings about the heme library and finish this
thread:

1)The heme coordinates in HEC.cif contain errors for B ring: it is turned
by 90 degrees relatively to heme plane.

2)HEC in PHENIX is not the same as in CCP4. It does not contain coordinates
for heme and could not be used for molecule generation in COOT. But it
contains correct restrains. Particularly, in PHENIX version of HEC.cif CBB
atom excluded from B-ring planarity group, while in CCP4 CBB belongs to
plan-7 group.

I made HEC.cif for myself from both CCP4 and PHENIX versions of HEC.cif.
Maybe someone will find it useful so I attach modified HEC library to this
mail


2018-05-16 1:19 GMT+03:00 Edward A. Berry :

> This is interesting. If the parameters for heme C reflect the molecule
> before linking
> to cysteines in the protein, and the modifications will be made as
> specified by
> link information in the dictionary, then actually heme C (HEC) should be
> the same
> as HEM (heme b, protoheme). HEC is superfluous, unless its definition could
> include the fact that it must be covalently linked.
>
> Heme C is a regular heme like in myoglobin (heme B, protoheme) that has
> been attached to a protein via two cysteines. Each Cys Sg adds across the
> double bond in a vinyl group, the latter consisting of CA connected to ring
> by single bond, CB connected to CA by double bond. Cys Sg attaches to the
> CA atom, and the double bond becomes single.
> However comparing the .cif library files, the double bond in HEC has moved
> from CA=CB to ringC3=CA:
> (third letter B or C in the atom names indicates which vinyl group it is
> in)
>
> ccp4-7.0/lib/data/monomers/h/HEM.cif:
> HEM  CABC3B   single  1.4740.020
> HEM  CBBCAB   double  1.3300.020
>
> HEM  CACC3C   single  1.4740.020
> HEM  CBCCAC   double  1.3290.020
>
> ccp4-7.0/lib/data/monomers/h/HEC.cif:
> HEC  CABC3B   double  1.4830.020
> HEC  CBBCAB   single  1.5100.020
>
> HEC  CACC3C   double  1.4830.020
> HEC  CBCCAC   single  1.5100.020
>
> And when I look at a protein containing HEC in coot, it displays a double
> bond from ring to CA.
> (By the way in coot "get monomer" HEC comes up with one of the pyrrole
> rings flipped 90* from the porphyrin plane!)
>
> I suggest that either:
>  HEC should be exactly like HEM, and the link definition would include:
> link SG to CA, add H to CB, and change the double bond to single;
>
> Or, HEC should be pre-hydrogenated: vinyl is ethyl, and the link
> definition just involves removing H from CA and making the link SG-CA.
>
> eab
>
>
>
> If the parameters for heme c reflect themolecule before linking
> to cysteines in the protein, and the modifications will be made as
> specified by
> link information in the dictionary, then actually heme C (HEC) should be
> the same
> as heme b (protoheme).
>
>
> On 05/15/2018 04:35 AM, Eugene Osipov wrote:
>
>> 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 
>>
>


-- 
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


HEC_updated.cif
Description: Binary data

Re: [ccp4bb] Problems with HEC in CCP4

[Edward A. Berry]

This is interesting. If the parameters for heme C reflect the molecule before 
linking
to cysteines in the protein, and the modifications will be made as specified by
link information in the dictionary, then actually heme C (HEC) should be the 
same
as HEM (heme b, protoheme). HEC is superfluous, unless its definition could
include the fact that it must be covalently linked.

Heme C is a regular heme like in myoglobin (heme B, protoheme) that has been 
attached to a protein via two cysteines. Each Cys Sg adds across the double 
bond in a vinyl group, the latter consisting of CA connected to ring by single 
bond, CB connected to CA by double bond. Cys Sg attaches to the CA atom, and 
the double bond becomes single.
However comparing the .cif library files, the double bond in HEC has moved from 
CA=CB to ringC3=CA:
(third letter B or C in the atom names indicates which vinyl group it is in)

ccp4-7.0/lib/data/monomers/h/HEM.cif:
HEM  CABC3B   single  1.4740.020
HEM  CBBCAB   double  1.3300.020

HEM  CACC3C   single  1.4740.020
HEM  CBCCAC   double  1.3290.020

ccp4-7.0/lib/data/monomers/h/HEC.cif:
HEC  CABC3B   double  1.4830.020
HEC  CBBCAB   single  1.5100.020

HEC  CACC3C   double  1.4830.020
HEC  CBCCAC   single  1.5100.020

And when I look at a protein containing HEC in coot, it displays a double bond 
from ring to CA.
(By the way in coot "get monomer" HEC comes up with one of the pyrrole rings 
flipped 90* from the porphyrin plane!)

I suggest that either:
 HEC should be exactly like HEM, and the link definition would include: link SG 
to CA, add H to CB, and change the double bond to single;

Or, HEC should be pre-hydrogenated: vinyl is ethyl, and the link definition 
just involves removing H from CA and making the link SG-CA.

eab



If the parameters for heme c reflect themolecule before linking
to cysteines in the protein, and the modifications will be made as specified by
link information in the dictionary, then actually heme C (HEC) should be the 
same
as heme b (protoheme).

On 05/15/2018 04:35 AM, Eugene Osipov wrote:

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 

Re: [ccp4bb] Problems with HEC in CCP4

[Christian Roth]

As far as my understanding goes, LINK records will not be replaced by LINKR
records by default. If the Link is in the monomer library one has to delete
th right atoms and the atoms to be linked have to be within a reasonable
distance. Than refmac will automatically recognize that for the two
residues and when the exact atoms are missing than a standard link can be
applied and will be put in and a LINKR record will appear automatically in
the pdb. No LINK statement is necessary and even counterproductive. LINKR
records in Refmac will point to a rich dictionary with not only a simple
length restraint (for LINK record, which is derived from the actual
distance in the pdb! This could be very wrong.) but has also angle
restraints (dihedrals) etc.
If the link is not in the monomer library I personally would always
recommend to create a link dictionary with jligand, which will also create
such an information rich dictionary.
Similar things are possible in other packages as well. Of course that is
only for pdb's, how that works with mmcif and the pdb, no idea at all.

Cheers

Christian


On Tue, May 15, 2018 at 7:11 PM, Robbie Joosten 
wrote:

> Afaik Refmac will apply the right restraints, iff there is only one type
> of LINK between those atoms. Particularly with carbohydrates, it's better
> to be explicit.
>
>
>
> Cheers,
>
> Robbie
>
>
>
> Sent from my Windows 10 phone
>
>
> --
> *From:* Edward A. Berry 
> *Sent:* Tuesday, May 15, 2018 8:07:38 PM
> *To:* Robbie Joosten; CCP4BB@JISCMAIL.AC.UK
>
> *Subject:* Re: [ccp4bb] Problems with HEC in CCP4
>
> Does this mean- if the pdb file has standard PDB link records involving
> HEC, like
> LINK SG  CYS A  32 CAB HEM A  93 1555   1555
> 1.82
> LINK SG  CYS A  35 CAC HEM A  93 1555   1555
> 1.81
> then refmac will look up the necessary modifications in the ccp4
> dictionary?
> Or do we need to tell refmac to apply those mods?
> eab
>
> On 05/15/2018 05:00 AM, Robbie Joosten wrote:
> > 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  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  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
> >
>

Re: [ccp4bb] Problems with HEC in CCP4

[Robbie Joosten]

Afaik Refmac will apply the right restraints, iff there is only one type of 
LINK between those atoms. Particularly with carbohydrates, it's better to be 
explicit.



Cheers,

Robbie



Sent from my Windows 10 phone




From: Edward A. Berry 
Sent: Tuesday, May 15, 2018 8:07:38 PM
To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problems with HEC in CCP4

Does this mean- if the pdb file has standard PDB link records involving HEC, 
like
LINK SG  CYS A  32 CAB HEM A  93 1555   1555  1.82
LINK SG  CYS A  35 CAC HEM A  93 1555   1555  1.81
then refmac will look up the necessary modifications in the ccp4 dictionary?
Or do we need to tell refmac to apply those mods?
eab

On 05/15/2018 05:00 AM, Robbie Joosten wrote:
> 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  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  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>

Re: [ccp4bb] Problems with HEC in CCP4

[Robbie Joosten]

Indeed LINKR replaces the length of the LINK (superfluous) with the identifier 
of the LINK type (useful info). Unfortunately, it is non-standard. mmCIF allows 
a better description of the type of LINK type, but as it has a fixed vocabulary 
it does not allow actual identifiers that would connect it to a restraint 
dictionary.

The auto addition of LINKs at the PDB seems better than before. At least now 
there are no LINKs between mutually exclusive alternate conformations of 
ligands ;)



Cheers,

Robbie



Sent from my Windows 10 phone




From: Clemens Vonrhein 
Sent: Tuesday, May 15, 2018 6:21:35 PM
To: Robbie Joosten
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problems with HEC in CCP4

Hi,

On Tue, May 15, 2018 at 02:21:59PM +, Robbie Joosten wrote:
> 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).

I guess that is not strictly true for the official PDB format
description e.g. at

  
http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#LINK

where we have

  The LINK records specify connectivity between residues that is not
  implied by the primary structure. Connectivity is expressed in terms
  of the atom names. They also include the distance associated with
  the each linkage following the symmetry operations at the end of
  each record.

"Connectivity" doesn't explicitly mean a "chemical bond", although
further down we have

  The atoms involved in bonds between HET groups or between a HET
  group and standard residue are listed.

and other points talk about "linkages" and "bonding". So maybe not
completely clear what is meant here - but let's assume that some kind
of chemical relation is intended (bond, coordination, salt bridge).

However, PDB entries themselves contain a vast amount of LINK records
that are clearly auto-generated by some software step after
deposition: this step seems to use a simple 3.5A cut-off criteria to
list all atoms in close contact. That's why there are all those LINK
records involving HOH waters - and we clearly don't want to introduce
a bond restraint to those waters.

Anyway, apart from the potential issues with LINK records in deposited
PDB entries, those records in PDB files under active refinement don't
really hold a description about the linkage type - only if a program
is either writing content beyond the default length of 78 characters
or by writing non-standard LINK records, i.e. missing the SymOP items
and putting something else there. This can make those LINK records
quite problematic when moving between different programs - the
non-standard LINKR record used by REFMAC (?) seems a cleaner way to
me, being obviously non-standard.

Cheers

Clemens


> 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  on behalf of Eugene Osipov 
> 
> 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 
> 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 
> > 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 an

Re: [ccp4bb] Problems with HEC in CCP4

[Edward A. Berry]

Does this mean- if the pdb file has standard PDB link records involving HEC, 
like
LINK SG  CYS A  32 CAB HEM A  93 1555   1555  1.82
LINK SG  CYS A  35 CAC HEM A  93 1555   1555  1.81
then refmac will look up the necessary modifications in the ccp4 dictionary?
Or do we need to tell refmac to apply those mods?
eab

On 05/15/2018 05:00 AM, Robbie Joosten wrote:

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  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  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>

Re: [ccp4bb] Problems with HEC in CCP4

[Clemens Vonrhein]

Hi,

On Tue, May 15, 2018 at 02:21:59PM +, Robbie Joosten wrote:
> 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).

I guess that is not strictly true for the official PDB format
description e.g. at

  
http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#LINK

where we have

  The LINK records specify connectivity between residues that is not
  implied by the primary structure. Connectivity is expressed in terms
  of the atom names. They also include the distance associated with
  the each linkage following the symmetry operations at the end of
  each record.

"Connectivity" doesn't explicitly mean a "chemical bond", although
further down we have

  The atoms involved in bonds between HET groups or between a HET
  group and standard residue are listed.

and other points talk about "linkages" and "bonding". So maybe not
completely clear what is meant here - but let's assume that some kind
of chemical relation is intended (bond, coordination, salt bridge).

However, PDB entries themselves contain a vast amount of LINK records
that are clearly auto-generated by some software step after
deposition: this step seems to use a simple 3.5A cut-off criteria to
list all atoms in close contact. That's why there are all those LINK
records involving HOH waters - and we clearly don't want to introduce
a bond restraint to those waters.

Anyway, apart from the potential issues with LINK records in deposited
PDB entries, those records in PDB files under active refinement don't
really hold a description about the linkage type - only if a program
is either writing content beyond the default length of 78 characters
or by writing non-standard LINK records, i.e. missing the SymOP items
and putting something else there. This can make those LINK records
quite problematic when moving between different programs - the
non-standard LINKR record used by REFMAC (?) seems a cleaner way to
me, being obviously non-standard.

Cheers

Clemens


> 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  on behalf of Eugene Osipov 
> 
> 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 
> 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 
> > 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 
> > > 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 

Re: [ccp4bb] Problems with HEC in CCP4

[Christian Roth]

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 
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  on behalf of Eugene
> Osipov 
> *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 :
>
>> 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  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  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
>

Re: [ccp4bb] Problems with HEC in CCP4

[Robbie Joosten]

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  on behalf of Eugene Osipov 

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 
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 
> 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 
> > 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>

Re: [ccp4bb] Problems with HEC in CCP4

[Paul Emsley]

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 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 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 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
<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>

Re: [ccp4bb] Problems with HEC in CCP4

[Eugene Osipov]

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 :

> 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  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  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

Re: [ccp4bb] Problems with HEC in CCP4

[Robbie Joosten]

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  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  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>

Re: [ccp4bb] Problems with HEC in CCP4

[Robbie Joosten]

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  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>

[ccp4bb] Problems with HEC in CCP4

[Eugene Osipov]

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