Dear David and Rob,
thanks a lot for your help and your suggestions.
Following your suggestions I found in Coot the very neat solution "Make
link (click 2 atoms ...): Much better than my previous dinosaur approach.
Thanks again and all the best,
Gerlind
On 03/06/2021 20:17, David Briggs wrote:
Hi Gerlind,
Rob Nicholls gave a talk on how to deal with covalent linkages using
AceDrg at CCP4 study weekend in 2020.
https://youtu.be/p4oTJ0bjD3M <https://youtu.be/p4oTJ0bjD3M>
And Paul Emsley has written up a guide about it...
https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html
Hopefully these will be useful for you.
Good luck,
Dave
--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs
------------------------------------------------------------------------
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
Gerlind Sulzenbacher <gerlind.sulzenbac...@univ-amu.fr>
*Sent:* Thursday, June 3, 2021 7:10:12 PM
*To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
*Subject:* [ccp4bb] help needed with link description
External Sender: Use caution.
Dear all,
I am going litteraly mad (or just old).
I would like to make a covalent link between a carbohydrate moiety and
and ASP of my well-cheered protein.
The identifier for the carbohydrate moiety is MAD, chain C, res number 1.
The link is established between C5 of MAD and OD2 of ASP 518, chain A.
In the mad_monlib.cif I added the following:
data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
ASP-MAD ASP . . MAD . .
bond_ASP-OD2_=_MAD-C5
#
data_link_ASP-MAD
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
ASP-MAD 1 OD2 2 C5 . 1.370 0.040
In the entry PDB file I added the line:
LINK OD2 ASP A 518 C5 MAD C 1
The log file of REFMAC tells me
INFO: link is found (not be used) dist= 1.370 ideal_dist= 1.370
ch:AAA res: 518 ASP at:OD2 .->ch:CCC res:
1 MAD at:C5 .
And the expression "not be used" is certainly the case, as the distance
of the covalent bond changes from 1.37 to 1.6 Å.
The data resolution is 1.8 Å.
If somebody could please point out what I am doing wrong, I'd be very
grateful.
With best wishes,
Gerlind
--
Gerlind Sulzenbacher
Architecture et Fonction des Macromolécules Biologiques
UMR7257 CNRS, Aix-Marseille Université
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel +33 491 82 55 66
Fax +33 491 26 67 20
E-mail: gerlind.sulzenbac...@univ-amu.fr
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--
Gerlind Sulzenbacher
Architecture et Fonction des Macromolécules Biologiques
UMR7257 CNRS, Aix-Marseille Université
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel +33 491 82 55 66
Fax +33 491 26 67 20
E-mail: gerlind.sulzenbac...@univ-amu.fr
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