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sfcheck
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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 :Ç`Ý
òì&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