I can't phosphorylate a residue
It looks as if it's trying to create a file in $CLIBD (ccp4/lib/data)
which doesn't belong to me (as is usual I would have thought)
It shouldn't put it there, should it?
Phil
(monomer-molecule-from-3-let-code "SEP" "")
/public/xtal/ccp4-6.1/ccp4-6.0.99c/bin/libcheck
:
: --- LIBCHECK --- /Vers 4.2.3 ; 28.07.2006/
:
:
: Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /<N>/Y/A :
: N - means without DOC-file
: Y - with new contents
: A - means to keep old contents and add new information
: with DOC-file program creates batch file: libcheck.bat
: _DOC:
:
: #
: # Keywords:
: #
: #FILE_L: < > - additional library, " " means without this file
: #MON: < > - give info about this monomer
: # if = * , give list all monomers in the library
: #FILE_PDB: < > - input PDB_file ," " means without this file
: #FILE_SMILE: < > - input SMILE_file ," " means without this fil e
: #FILE_SDF: < > - input SDF file, " " means without this file
: #FILE_MOL: < > - input MOL file, " " means without this file
: # use keyword MON as compound_id
: #FILE_CIF: < > - input CIFile ," " means without this file
: #FILE_CSD: < > - input CSD CIFile," " means without this file
: #HFLAG: <Y>/A/N - Y - hydrogen atoms where they are
: # A - with all hydrogen atoms
: # N - without hydrogen atoms
: #IND: <N>/Y - Y - create index of mon_lib.cif
: # output file: "new_mon_lib_ind.cif"
: #FILE_O: <libcheck > - output files /library,coords,ps/, name without
: # extention
: #FILE_L2: < > - additional library (FILE_L) will be added to this
library
: # in this case program performs only adding
: #ANGLE: <0.0> - rotation angle for picture ( around X )
: #LIST: <M>/S/L - S short output, L - long, M - medium
: #REF: <Y>/S,N,0 - 0 no refinement of new monomer
: # N only crd->ang and ang->crd
: # S plus torsion ref, Y plus restr.ref
: #
: #TEST: <0> - for program testing only
: #COOR: <N>/Y - use Vobs from coords instead Videal
: #LCOOR: <Y>/N - Y use coords from lib description
: #NODIST: <N>/Y - Y not read the distributed library
: # (only with FILE_L)
: #SRCH: <N>/Y/0 - Y - global search, 0 - for MON from PDB_file
: # (only with NODIST = N)
:
: #--- type "keyword parameters" and/or ---
: #--- press key "CR" to run program ---
: --> --> MON : SEP
: -------------
: -------------
: Keywords:
: HFLAG : Y
: COOR : N
: LCOOR : Y
: SRCH : N
: REF : Y
: NODIST: N
: ------------------------------
: --- LIBRARY OF MONOMERS ---
: _lib_name mon_lib
: _lib_version 4.13
: _lib_update 18/01/08
: ------------------------------
: NUMBER OF MONOMERS IN THE LIBRARY : 2436
: with complete description : 455
: NUMBER OF MODIFICATIONS : 47
: 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
: * CIFile : libcheck_SEP.cif
: * PDBfile : libcheck_SEP.pdb
: * Plotfile: libcheck_SEP.ps
: I am writing new description to
: file: libcheck.lib
exit status: 0
INFO:: libcheck status: 0
/public/xtal/ccp4-6.1/ccp4-6.0.99c/bin/refmac5
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
:<html> <!-- CCP4 HTML LOGFILE -->
:<hr>
:<!--SUMMARY_END--></FONT></B>
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
:<pre>
:
: ###############################################################
: ###############################################################
: ###############################################################
: ### CCP4 6.0.99c: Refmac_5.4.0067 version 5.4.0067 : 17/01/08##
: ###############################################################
: User: pre Run date: 3/ 6/2008 Run time: 17:17:04
:
:
: Please reference: Collaborative Computational Project, Number 4. 1994.
: "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst.
D50, 760-763.
: as well as any specific reference in the program write-up.
:
:<!--SUMMARY_END--></FONT></B>
: $TEXT:Reference1: $$ comment $$
: "Refinement of Macromolecular Structures by the Maximum-Likelihood
Method:"
: G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
: Acta Crystallogr. D53, 240-255
: EU Validation contract: BIO2CT-92-0524
:
: $$
: $SUMMARY :Reference1: $$ Refmac: $$
: :TEXT:Reference1: $$
:
: Data line ---> MODE NEWENTRY
: Data line ---> END
:===> Warning: Reflections file has not been defined
:===> Warning: Switching to the idealisation mode
:
: **** Input and Default parameters# ****
:
:
:Input coordinate file. Logical name - XYZIN actual file name -
libcheck_SEP.pdb
:Output coordinate file. Logical name - XYZOUT actual file name -
monomer-SEP.pdb
:
: Refinement type : Idealisation
:
:
: **** Makecif parameters ****
:
:Dictionary files for
restraints : /public/xtal/ccp4-6.1/ccp4-6.0.99c/lib/data/monomers/mon*cif
:Parameters for new entry and
VDW: /public/xtal/ccp4-6.1/ccp4-6.0.99c/lib/data/monomers/ener_lib.cif
:===> Warning: LIBIN has been defined but it is not a file
: Apart from amino acids and DNA/RNA all monomers will be checked to
see if atom names and connectivity is correct
: Hydrogens will be restored in their riding positions
: hydrogens will be written to the output file
: Links between monomers will be checked. Only those links present in
the coordinate file will be used
: Standard sugar links will be analysed and used
: For new ligands "ideal restraint" values will be taken from the
energetic libary ener_lib.cif
: Symmetry related links will be analysed and used
: Cis peptides will be found and used automatically
:
:
:
:
:Monitoring style is "MEDIUM". Complete information will be printed out
in the
:first and last cycle. In all other cycles minimum information will be
printed out
:Sigma cutoffs for printing out outliers
:If deviation of restraint parameter > alpha*sigma then information will
be printed out
:Distance outliers 10.000
:Angle outliers 10.000
:Torsion outliers 10.000
:Chiral volume outliers 10.000
:Plane outliers 10.000
:Non-bonding outliers 10.000
:---------------------------------------------------------------
:
: Input file :libcheck_SEP.pdb
: ------------------------------
: --- LIBRARY OF MONOMERS ---
: _lib_name mon_lib
: _lib_version 4.13
: _lib_update 18/01/08
: ------------------------------
Last system error message: Permission denied
Refmac_5.4.0067: Open failed:
File: /public/xtal/ccp4-6.1/ccp4-6.0.99c/lib/data/libcheck_SEP.cif
: Open failed: Unit: 7,
File: /public/xtal/ccp4-6.1/ccp4-6.0.99c/lib/data/libcheck_SEP.cif
(logical: /public/xtal/ccp4-6.1/ccp4-6.0.99c/lib/data/libcheck_SEP.cif)
:<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
: Refmac_5.4.0067: Open failed:
File: /public/xtal/ccp4-6.1/ccp4-6.0.99c/lib/data/libcheck_SEP.cif
:Times: User: 1.0s System: 0.0s Elapsed: 0:01
:</pre>
:</html>
:<!--SUMMARY_END--></FONT></B>
exit status: 1
DEBUG:: libcheck-minimal? returns #f
(get-monomer "SEP")
