[ccp4bb] How to generate cif file?

2014-09-26 Thread Gaelle PESCE 

Dear all,

In my protein structure I found a modified Tyrosine that is covalently 
bound to a nucleotide by a phosphodiester bound.


I am having problem to generate the library description for such a 
modification. Would someone have any ideas on how to generate such a cif 
file?


Thanks in advance.

Regards,

Gaelle

Re: [ccp4bb] How to generate cif file?

2014-09-26 Thread Robbie Joosten 
HI Gaelle,

If both the nucleotide already exists in the PDB (you can check on
LigandExpo), you can just create a LINK description with Jligand in CCP4.
See this tutorial:
http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html
If you have the cif file with the LINK description, you can just load it in
Refmac. You also need to add a LINK record to you PDB file. Jligand will
give you an example record.

HTH,
Robbie

 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Gaelle PESCE
 Sent: Friday, September 26, 2014 12:52
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] How to generate cif file?
 
 Dear all,
 
 
 
 In my protein structure I found a modified Tyrosine that is covalently
bound
 to a nucleotide by a phosphodiester bound.
 
 I am having problem to generate the library description for such a
 modification. Would someone have any ideas on how to generate such a cif
 file?
 
 
 
 Thanks in advance.
 
 
 
 Regards,
 
 Gaelle