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[ccp4bb] Refmac library trouble -
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: doctoral or post-doctoral position x-ray crystallography of ion channels
From: Chris Ulens chris {- dot -} ulens {- at -} MED {- dot -} KULEUVEN {- dot -} BE
Date: 2009-01-13		Next message:
Subject: Re: Refmac library trouble -
From: junfeng liu jliu {- at -} NIMR {- dot -} MRC {- dot -} AC {- dot -} UK
Date: 2009-01-13


Subject: Refmac library trouble -
From: Jonathan Marvin Caruthers Jonathan {- dot -} Caruthers {- at -} COLORADO {- dot -} EDU
Date: 2009-01-13

All:



I'm trying to run Refmac with a heme not present in the default libraries. Unfortunately, I can't get the library sketcher to create a library description file and get the following error message:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
MON : HEO
-------------
Output file :/home/caruthej/bo3/ccp4/bo3A_19
Input user lib:/home/caruthej/bo3/ccp4/HEO_bondlist.cif
-------------
Keywords:
HFLAG : Y
COOR : N
LCOOR : Y
SRCH : N
REF : Y
NODIST: N
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.11
_lib_update 15/04/05
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2433
with complete description : 449
NUMBER OF MODIFICATIONS : 46
NUMBER OF LINKS : 64
I am reading libraries. Please wait.
- energy parameters
- monomer"s description (links & mod )
I am reading library. Please wait.
- monomer"s description
WARNING : monomer:HEO - has the minimal description.
WARNING: there is not metal chirality for:FE
WARNING : /subroutine CALC_VOBSN/
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: libcheck
has failed with error message
CCP4: Fatal error, see above.
***************************************************************************


#CCP4I TERMINATION STATUS 0 " CCP4: Fatal error, see above."
#CCP4I TERMINATION TIME 12 Jan 2009 17:18:58
#CCP4I MESSAGE Task failed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>


(I didn't know an Fe ion HAS a chirality, but leave that aside for the moment)

Exasperated, I went and downloaded a library file for heme o from the ligand expo at the PDB (ligand depo) along with a clean PDB the accompanied the .cif file. When I ran Refmac with this library file, I got the following error:

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

ch:KK res: 64 CYS at:O .->ch:KK res: 68 MET at:SD .
--------------------------------
--- title of input coord file ---

PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-XX
--------------------------------
WARNING : atom :FE HEO GG1002 is absent in the library
WARNING : atom :CHA HEO GG1002 is absent in the library
WARNING : atom :CHB HEO GG1002 is absent in the library
WARNING : atom :CHC HEO GG1002 is absent in the library
WARNING : atom :CHD HEO GG1002 is absent in the library
WARNING : atom :NA HEO GG1002 is absent in the library
WARNING : atom :C1A HEO GG1002 is absent in the library
WARNING : atom :C2A HEO GG1002 is absent in the library
WARNING : atom :C3A HEO GG1002 is absent in the library
WARNING : atom :C4A HEO GG1002 is absent in the library
WARNING : atom :CMA HEO GG1002 is absent in the library
WARNING : atom :CAA HEO GG1002 is absent in the library
WARNING : atom :CBA HEO GG1002 is absent in the library
WARNING : atom :CGA HEO GG1002 is absent in the library
WARNING : atom :O1A HEO GG1002 is absent in the library
WARNING : atom :O2A HEO GG1002 is absent in the library
WARNING : atom :NB HEO GG1002 is absent in the library
WARNING : atom :C1B HEO GG1002 is absent in the library
WARNING : atom :C2B HEO GG1002 is absent in the library
WARNING : atom :C3B HEO GG1002 is absent in the library
... and more ...
WARNING : HEO GG1002 : first atom of the tree is absent
WARNING : HEO GG1002 : last atom of the tree is absent
Number of chains : 12
Total number of monomers : 2507
Number of atoms : 19782
Number of missing atoms : 0
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0

Number of bonds restraints : 20412
Number of angles restraints : 27840
Number of torsions restraints : 14230
Number of chiralities : 3106
Number of planar groups : 3402
IERR = 1

There is error. See above
===> Error: Fatal error. Cannot continue
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: refmac5 XYZIN "/home/caruthej/bo3/ccp4/test5.pdb" XYZOUT "/home/caruthej/bo3/ccp4/bo3A_26_2_pdb_1.tmp" HKLIN "/home/caruthej/bo3/ccp4/merged_freer.mtz" HKLOUT "/home/caruthej/bo3/ccp4/bo3A_26_4_mtz_1.tmp" LIBIN "/home/caruthej/bo3/ccp4/heo1.cif" TLSIN "/home/caruthej/bo3/ccp4/opt.tls" LIBOUT "/home/caruthej/bo3/ccp4/bo3A_26_lib.cif"
has failed with error message
Refmac_5.2.0019: Fatal error. Cannot continue
***************************************************************************


#CCP4I TERMINATION STATUS 0 Refmac_5.2.0019: Fatal error. Cannot continue
#CCP4I TERMINATION TIME 13 Jan 2009 12:57:36
#CCP4I MESSAGE Task failed

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Needless to say, chain G is the heme, the residue number is 1002, and the coordinates ARE present in the input file. I can only surmise that this has something to do with the library file and that the files present at ligand depo that I downloaded are not the problem and that something I'm not doing correctly is. Anybody have any ideas? This has really been driving me nuts.



thanks,


Jon Caruthers
Stowell Lab
University of Colorado

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: doctoral or post-doctoral position x-ray crystallography of ion channels
From: Chris Ulens chris {- dot -} ulens {- at -} MED {- dot -} KULEUVEN {- dot -} BE
Date: 2009-01-13		Next message:
Subject: Re: Refmac library trouble -
From: junfeng liu jliu {- at -} NIMR {- dot -} MRC {- dot -} AC {- dot -} UK
Date: 2009-01-13
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