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  >
>

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 

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 
> >:
> 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 

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 

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 
> >:
> 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 

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 
>>
>
>
>
> --
> 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 
>:
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 
> > >



--
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

[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 >:

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  
>




--
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

[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 
>



-- 
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] CCP4BB Digest - 13 May 2018 to 14 May 2018 (#2018-119)

[Yaoqi Zhou]

Would you help me to place the following information? Thank you.

Dear CCP4ers,
Looking for collaborators to annotate articles relevant to your research

If you have published any article indexed by PUBMED, we invite you to join the 
RELISH (relevant literature search) consortium, whereby annotating the degree 
of relevance for 60 recommended articles to your paper you will be eligible to 
become one of the co-authors on a high-impact, open-database paper.

Each participant’s task will be as follows. Visit 
https://pubmed.ict.griffith.edu.au/register/, input a recent article indexed by 
PubMed (preferably one which you have authored), and annotate all 60 
recommended articles for their relevance regarding the input article.

For more details, please visit 
http://sparks-lab.org/Call-for-participation3.html

Thank you for your interest.

Yaoqi Zhou

Professor & Research Leader

Institute for Glycomics

Griffith University, Gold Coast Campus

Re: [ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

[Kay Diederichs]

Hi Wim,

I would use pdbset and the I213 symops to generate 23 copies of the ASU 
contents, and append them to the existing I213 PDB file. The resulting P1 PDB 
file has the same cell constants as the I213 one.

But that's probably not what you want?

Kay

On Tue, 15 May 2018 10:51:15 +0200, Wim Burmeister  
wrote:

>
>  
>  http-equiv="Content-Type">
>  
>  
>Hello,
>does anybody have a script which transforms the pdb file of a
>structure in I-centred I213 into a pdb file based on the
>corresponding primitive P1 unit cell ? A rotation matrix would also
>do� which uses the matrix of the transformation from one coordinate
>system to the other combined with the orthogonalisation convention
>for the P1 cell.
>Best
>Wim
>-- 
>Wim Burmeister
>  Professeur
>  size="1">Institut de Biologie Structurale (IBS) CIBB
>  size="1">71 avenue des Martyrs
>CS 
> 20192  face="Helvetica, Arial, sans-serif">
>38044 Grenoble Cedex 9, FRANCE  face="Helvetica, Arial, sans-serif">
>E-mail: size="1"> href="mailto:wim.burmeis...@ibs.fr;>wim.burmeis...@ibs.fr  face="Helvetica, Arial, sans-serif">  lang="fr-FR">
>  Tel:��� +33 (0) 457 42 87 41�� Fax: +33 (0) 476 20 94 
> 00
>href="http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/;>face="Helvetica, Arial, sans-serif">lang="fr-FR">website
>href="https://www.openstreetmap.org/?mlat=45.20762mlon=5.69255#map=17/45.20762/5.69255;>size="1">face="Helvetica, Arial, 
> sans-serif">map
>
>  
>  
>

Re: [ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

[Eleanor Dodson]

Well - if you use reindex to change the reflections from I213 to P1 the log
file gives the rotation matrix need to convert I213 coordinates using the
same convention.
There are various clever inputs to reindex which allow you to do this

Then you can use

pdbset   xyzin I213.pdb xyzout P1.pdb giving that matrix.
>From the doc..

ROTATE [INVERT] [MATRIX|EULER|POLAR] values

Define rotational transformation, either as MATRIX (this keyword may be
omitted) followed by 9 numbers (r11 r12 r13 r21 r22 r23 r31 r32 r33), by
keyword EULER followed by Eulerian angles alpha, beta, gamma (as in ALMN
), or by keyword POLAR followed by
polar angles omega, phi, kappa (as in POLARRFN
). This transformation will be
applied to all atoms. The SHIFT
 command may be used to
define a translation in addition. The transformation defined by ROTATE &
SHIFT, or by TRANSFORM ,
is applied after any SYMGEN 
operation. Multiple definitions of ROTATE or TRANSFORM, or of SHIFT will
NOT be concatenated: only the last will be effective.


Eleanor



On 15 May 2018 at 09:51, Wim Burmeister  wrote:

> Hello,
> does anybody have a script which transforms the pdb file of a structure in
> I-centred I213 into a pdb file based on the corresponding primitive P1 unit
> cell ? A rotation matrix would also do  which uses the matrix of the
> transformation from one coordinate system to the other combined with the
> orthogonalisation convention for the P1 cell.
> Best
> Wim
> --
>
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs
> 
> CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website
> 
> map
> 
>
>
>

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 

[ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

[Wim Burmeister]

  
  
Hello,
does anybody have a script which transforms the pdb file of a
structure in I-centred I213 into a pdb file based on the
corresponding primitive P1 unit cell ? A rotation matrix would also
do  which uses the matrix of the transformation from one coordinate
system to the other combined with the orthogonalisation convention
for the P1 cell.
Best
Wim
-- 
Wim Burmeister
  Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs
CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
  Tel:    +33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website
map

  
  

[ccp4bb] Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK

[David Barford]

Dear colleagues,

Please see below an advert for the position of Protein Crystallography Facility 
Manager at the MRC Laboratory of Molecular Biology.


Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, 
Cambridge, UK

The MRC Laboratory of Molecular Biology (LMB) seeks to appoint a Protein 
Crystallography Facility Manager. The LMB is one of the birthplaces of 
structural biology and remains at the forefront of methods development as 
protein crystallography is a critical technique for understanding the 
mechanisms of macromolecular complexes, one of the major goals of the LMB. The 
post-holder will provide support to researchers from all Divisions of the LMB 
in the collection of X-ray diffraction data using both synchrotrons and 
in-house X-ray facilities, will maintain and develop the in-house facilities, 
will provide expert advice and support during subsequent structure 
determinations, and will act as the coordinator for LMB's synchrotron access. 
It is expected that there will be the opportunity for collaboration on 
structural projects with research groups at the LMB.


The successful applicant will have several years of post-doctoral experience in 
the field of protein crystallography including data collection at synchrotrons 
and all aspects of structure determination. Excellent communication and 
inter-personal skills are required because the post will involve interacting 
with a diverse range of scientists with different levels of expertise.

Closing date for applications: 11th June 2018

For further details and information on how to apply please visit:

https://mrc.tal.net/vx/appcentre-ext/candidate/post/1707/en-GB 

Informal enquires should be addressed to

Dr. David Barford. E.mail: dbarf...@mrc-lmb.cam.ac.uk 

Dr. Jan Löwe. E.mail: j...@mrc-lmb.cam.ac.uk 


___

Dr. David Barford

Structural Studies Division
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge CB2 0QH, UK.

e.mail: dbarf...@mrc-lmb.cam.ac.uk

Tel. +44 (0)1223 267075