Dear All,
As I am practicing new in the crystallography, I am facing some difficulties in
refining the ligand bound structure. Protein I am working with has SG P212121,
it's a dimer. I fitted the ligand on the density with
COOT-->calculate-->Model/Fit/Refine-->Rotate/Translate Zone. Then I merged both
(protein & ligand) the pdb structure and saved the coordinate as .pdb file. By
taking this pdb when I am running restrained refinement it was showing:
Number of atoms : 2508
Number of residues : 319
Number of chains : 3
I am reading library. Please wait.
mon_lib.cif
WARNING : link:SS is found dist = 2.026 ideal_dist= 2.031
ch:AA res: 15 CYS at:SG .->AA res: 29 CYS at:SG
.
WARNING : link:SS is found dist = 2.069 ideal_dist= 2.031
ch:AA res: 30 CYS at:SG .->AA res: 43 CYS at:SG
.
WARNING : link:SS is found dist = 2.031 ideal_dist= 2.031
ch:AA res: 33 CYS at:SG .->AA res: 52 CYS at:SG
.
.....................................................................................................................................................................................
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-9-
--------------------------------
ATTENTION: atom:CD LYS 75 BB is missing in the structure
ATTENTION: atom:CE LYS 75 BB is missing in the structure
ATTENTION: atom:NZ LYS 75 BB is missing in the structure
..................................................................................................................................................................................................................................
ERROR : atom :C1 LIG 900 CC is absent in the library
ERROR : atom :O1 LIG 900 CC is absent in the library
ERROR : atom :C2 LIG 900 CC is absent in the library
ERROR : atom :C3 LIG 900 CC is absent in the library
In the next cycle I put the .cif (newly generated) as LIB in, and rerun the
job. Again it was showing some error like:
Number of atoms : 2508
Number of residues : 319
Number of chains : 3
I am reading library. Please wait.
mon_lib.cif
WARNING : residue: LIG 900 chain:CC
atom: "C28 " is absent in coord_file
atom: "C26 " is absent in coord_file
atom: "C24 " is absent in coord_file
atom: "C1 " is absent in lib description.
atom: "O1 " is absent in lib description.
atom: "C2 " is absent in lib description.
...................................................................................................................................................................................................................
WARNING : LIG : program can not match library description....
program will create complete description for:LIG
* Plotfile: C:\Ccp4Temp\refmac5_temp1.01004_new_LIG_N1.ps
WARNING : residue: LIG 900 chain:CC - rename
"LIG " --> "LIG_N1 "
WARNING : link:SS is found dist = 2.026 ideal_dist= 2.031
ch:AA res: 15 CYS at:SG .->AA res: 29 CYS at:SG
.
--------------------------------------------------------------------------------------------------------------------------------
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-9-
--------------------------------
ATTENTION: atom:CD LYS 75 BB is missing in the structure
ATTENTION: atom:CE LYS 75 BB is missing in the structure
ATTENTION: atom:NZ LYS 75 BB is missing in the structure
ATTENTION: atom:CD LYS 78 BB is missing in the structure
---------------------------------------------------------------------------------------------------------------------------
Important, Important, Important!!!!!
Your coordinate file has a ligand which has either minimum or no description in
the library
A new ligand description has been added to H:/DATA/TR/020312_C5/TR_8_lib.cif
Picture of the new ligand can be viewed using postscript file. See above
Check description in this file and, if satisfied, use it as the input library
Otherwise either edit bond orders manually or use CCP4i Sketcher to view and
edit the ligand
and create a library entry by running libcheck
It is strongly recommended that dictionary entry should be checked carefully
before using it
If you are happy with the library description then use the keyword (MAKE CHECK
NONE)
I.e. do not check correctness of the coordinates
===> Error: New ligand has been encountered. Stopping now
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Refmac_5.6.0117: New ligand has been encountered. Stopping now
Times: User: 0.0s System: 0.0s Elapsed: 0:23
</pre>
</html>
<!--SUMMARY_END--></FONT></B>
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: refmac5 XYZIN
"H:/DATA/TR/020312_C5/tn_2.1_ref1_molrep1_refmac1-coot-0.pdb" XYZOUT
"H:/DATA/TR/020312_C5/tn_2.1_ref1_molrep1_refmac2.pdb" HKLIN
"H:/DATA/TR/020312_C5/tn020312_c5_refmac2.mtz" HKLOUT
"H:/DATA/TR/020312_C5/tn020312_c5_refmac4.mtz" LIBOUT
"H:/DATA/TR/020312_C5/TR_8_lib.cif"
has failed with error message
Refmac_5.6.0117: New ligand has been encountered. Stopping now
***************************************************************************
#CCP4I TERMINATION STATUS 0 Refmac_5.6.0117: New ligand has been encountered.
Stopping now
#CCP4I TERMINATION TIME 12 Mar 2012 08:30:36
#CCP4I TERMINATION OUTPUT_FILES H:/DATA/TR/020312_C5/TR_8_lib.cif TR
Please give me some suggestuion.
Regards,
Dipankar
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