-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Dipankar,
according to the log-file, the restraints-file was not read in the second time you ran refmac5. It should otherwise be listet in the section underneath "Information from CCP4Interface script" where it is mentioned as "LIBOUT" instead of "LIBIN". Can you confirm the you added the cif-file as "LIB in" in the ccp4i GUI and not "Output lib"? Regards, Tim On 03/12/2012 06:21 AM, Dipankar Manna wrote: > 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 > > ________________________________ > > This e-mail and any files transmitted with it are for the sole use of the > intended recipient(s) and may contain confidential and privileged > information.If you are not the intended recipient, please contact the sender > by reply e-mail and destroy all copies of the original message.Any > unauthorized review, use, disclosure, dissemination, forwarding,printing or > copying of this email or any action taken in reliance on this e-mail is > strictly prohibited and may be unlawful. > > Visit us at http://www.aurigene.com > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPXcvIUxlJ7aRr7hoRAl9eAKDDd6KL/2wQv6FjM+K2xa9fCAIFmQCeNHIk eQmRYwAhquwmrIN9+TBF/iI= =+vHN -----END PGP SIGNATURE-----
