[buster-discuss] Creating link dictionary for a ligand cross-linking two chains

[Florian Sauer]

Dear Buster users,

I'm refining a 3.5 A structure of a Ubiquitin bound protease. The 
Ubiquitin is covalently bound to the protease active site through a 
Propargylamide (AYE) which replaces Ub Gly76 and connects the Ub 
C-terminus and SG of the active site's Cys.

Following the Buster Wiki tutorial 
(https://www.globalphasing.com/buster/wiki/index.cgi?GradeCovalentTutorial) 
I have created a *.cif file with the grade webserver containing the 
ligand including both covalent bonds Gly->AYE->Cys.

I would now like to create a link dictionary using 
covalent_grade_create_linkdic.pl . How can I specify the two covalent 
bonds (1) Gly C - AYE N  and (2) AYE C2 -> Cys SG separately with this 
script?

Thanks in advance for your answers!

Florian

-- 
Dr. Florian Sauer
Rudolf Virchow Zentrum für Experimentelle Biomedizin
Josef-Schneider-Str. 2, Haus D15
97080 Würzburg

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