Hi,
I encountered a similar problem, the way I solved it was to edit either the cif
file or the pdb file to make the signifiers either the XX or the Bb the same.
So that they are consistant over the two files.
For example in the one I used one atom had a # afterwards in the pdb file but a
* in the cif file. So I edited the pdb file to also have a * instead of the #.
Hope that helps
Martin Day
________________________________
From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Vinson LIANG
[lwg_conrad_1...@yahoo.com.cn]
Sent: 13 May 2010 15:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to generate lib file for new ligand?
Dear all,
I have fit my ligand into its density with coot. Then, I add the ligand into
the protein's pdb and try to do refine with refmac5. First, the error comes,
error message
Refmac_5.5.0109: New ligand has been encountered. Stopping now
The next time, I input the .cif file generated by the first run of refmac5 and
rerun the program. And the error comes as,
ERROR : atom :04 5CD 225 XX is absent in the library
ATTENTION: atom:4__0 5CD 225 XX is missing in the structure
ERROR : atom :04 5CD 224 Bb is absent in the library
ATTENTION: atom:4__0 5CD 224 Bb is missing in the structure
Number of chains : 7
Total number of monomers : 750
Number of atoms : 3691
Number of missing atoms : 2
Number of rebuilt atoms : 0
Number of unknown atoms : 2
Number of deleted atoms : 0
Number of bonds restraints : 3452
Number of angles restraints : 4672
Number of torsions restraints : 2372
Number of chiralities : 512
Number of planar groups : 612
IERR = 1
There is error. See above
===> Error: Fatal error. Cannot continue
Refmac_5.5.0109: Fatal error. Cannot continue
Times: User: 13.8s System: 0.1s Elapsed: 0:14
Could anybody please help me to solve this problem?
Thank you all for your attention.
Best wishes,
Vinson Liang
