[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

sfcheck



***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Hello:

I couldn't get the SFCHECK to run ( CCP4 3.4).  Can anybody help?
Apparently there is problem either with the PDB file or the sym lib
file. (What is symlib.blc anyway?)

Thank you very much.

/Yafeng Xue



The model (PDB) file (the first lines) used:
########################################################
CRYST1   75.580   75.580   32.710  90.00  90.00 120.00 P3121         6
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.013231  0.007639  0.000000        0.00000
SCALE2      0.000000  0.015278  0.000000        0.00000
SCALE3      0.000000  0.000000  0.030572        0.00000
ATOM      1  CB  VAL A   1      16.037  45.286  -6.874  1.00 22.76
C
ATOM      2  CG1 VAL A   1      15.338  46.197  -5.871  1.00 25.19
C
ATOM      3  CG2 VAL A   1      17.285  44.685  -6.236  1.00 26.03
C
ATOM      4  C   VAL A   1      14.494  43.335  -6.319  1.00 19.98
C
ATOM      5  O   VAL A   1      13.376  43.618  -5.840  1.00 20.27
O
ATOM      6  N   VAL A   1      13.975  44.825  -8.191  1.00 22.18
N

########################################################

The log file (from the interactive section) is given below:

########################################################
ascl5 48% sfcheck

  --- SFCHECK --- /Vers 5.3; 09.04.1998/

  Do you want to have FILE-DOCUMENT /sfcheck.log/ ? /<N>/Y/:


 Input file with model (format PDB or CIF or BLANC)
        Type file name with extention or just CR /it means without this
file/
        Extention "crd" means BLANC file, "cif" - CIFile
 FILE_C:test.pdb

 Input file with Fobs (format  ASCII (CIF or PDB) or BLANC or MTZ)
        Type file name with extention or just CR /it means without this
file/
        Extention "dat" means BLANC file, extention "mtz" means MTZ file
 FILE_SF:/usr/people/yafeng/u11/pcn/ccp4/g8d2/g8d2_freeR.mtz
  INPUT FILE :/usr/people/yafeng/u11/pcn/ccp4/g8d2/g8d2_freeR.mtz;
  (Q)QOPEN allocated #  1
 User:   yafeng               Logical Name:
/usr/people/yafeng/u11/pcn/ccp4/g8d2/g8d2_freeR.mtz
 Status: READONLY   Filename:
/usr/people/yafeng/u11/pcn/ccp4/g8d2/g8d2_freeR.mtz
  -----------------------------------
 --- MTZ file : /usr/people/yafeng/u11/pcn/ccp4/g8d2/g8d2_freeR.mtz

   No  Label                       type

     1  H                               H
     2  K                               H
     3  L                               H
     4  F                               F
     5  SIGF                            Q
     6  FreeRflag                       R
  -----------------------------------
 #
 #     Keywords:
 #
 #NOMIT:   <0>        - number of cycles of omit procedure, 2 is a good
 #                      choice. Note: omit procedure takes time!
 #MAP:    <N>/Y       - Y - extract density map will be created
 #OUT:   <N>/Y/A      - Y - create new Fobs CIFile
 #                      A - with anisothermal correction
 #
 #     Next keywords are necessary if there is only Fobs file and
 #     this file has not information about space group and cell
parameters
 #     In this case you must define cell parameters and space group name
 #     or space group number and setting
 #
 #GROUP:   < >        - space group name, use capital letter
 #CELL: <0,0,0,0,0,0> - cell parameters: a,b,c,alpha,beta,gamma
 #NSG:     <1>        - space group number /from <1> to 230 /
 #SETT:    <2>        - setting /1 or 2,for monoclinic and trigonal
groups only/
 #
 #     Next keywords are necessary only for MTZ file
 #
 #F:        < >       - label of F or F(+)
 #SIGF:     < >       - label of sigma F or sigma F(+)
 #F-:       < >       - label of F(+)
 #SIGF-:    < >       - label of sigma F(-)
 #FREE:     < >       - label of Free_flag
 #I:        < >       - label of I or I(+)
 #SIGI:     < >       - label of sigma I or  sigma I(+)
 #I-:       < >       - label of I(-)
 #SIGI-:    < >       - label of sigma I(-)
 #
 #             Program creates:
 #                  new CIFile of Fobs:     sfcheck.hkl
 #                  file with extract
 #                  density around model:   sfcheck_ext.dat
 #                  /CCP4 format/
 #

 #---  type "key_word   parameters" and/or ---
 #---  type "CR" for to run program        ---
 -->F F  
 -->SIGF SIGF
 -->FREE FreeRflag
 -->
  (Q)QOPEN allocated #  1
 User:   yafeng               Logical Name:
/usr/people/yafeng/u11/pcn/ccp4/g8d2/g8d2_freeR.mtz
 Status: READONLY   Filename:
/usr/people/yafeng/u11/pcn/ccp4/g8d2/g8d2_freeR.mtz
  OUTPUT FILE :sfcheck_mtz.cif;

 FORMATTED      UNKNOWN file opened on unit  22
 Logical name: sfcheck_mtz.cif, Full name: sfcheck_mtz.cif

  (Q)QOPEN allocated #  1
 User:   yafeng               Logical Name:
/usr/people/yafeng/u11/pcn/ccp4/g8d2/g8d2_freeR.mtz
 Status: READONLY   Filename:
/usr/people/yafeng/u11/pcn/ccp4/g8d2/g8d2_freeR.mtz
 * Input Program Labels :
 
 H K L F SIGF F(-) SIGF(-) FC PHIC W FPART PHIPART PHIB FOM FREE DP
SIGDP ISYM
 DUM1 DUM2 DUM3 DUM4 DUM5 DUM6 DUM7 DUM8 DUM9 DUM10 IDUM1 IDUM2 IDUM3
IDUM4 IDUM5
 IDUM6 IDUM7 IDUM8 IDUM9 IDUM10 I(+) SIGI(+) I(-) SIGI(-)
 
 * Input File Labels :
 
 H K L F SIGF FreeRflag
 
 * Lookup Table : the number indicates the input column no.
 * Array element n corresponds to the nth program label
 
     1    2    3    4    5    0    0    0    0    0    0    0    0    0
6
     0    0    0    0    0    0    0    0    0    0    0    0    0    0
0
     0    0    0    0    0    0    0    0    0    0    0    0
 
N,hkl,F,sig,stat :    5000    16   12   12         29.82           6.380
o
N,hkl,F,sig,stat :   10000    25    9   -5         41.73           8.112
o
  -----------------------------
Number of reflections output :    13027

 --- read file of coordinates       ---
  ERR: OPEN FILE /FOR READ/
         PATH :`
                        &p&p
         NAME :symlib;
    EXTENTION :blc;
  ERROR:  can't  open  symlib.blc
  ERR: can't find space group name in symlib.blc
             -->P 1<--
       default space group is P1
  ERROR: in CHECK_CRD