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,
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
residu
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,
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 i
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 t
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 s
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 T
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
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
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 an
Would you help me to place the following information? Thank you.
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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 Bu
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 givin
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
> Joos
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
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: C
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 o
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