[sharp-discuss] Sharp Error -log file
Clemens Vonrhein
vonrhein@globalphasing.com
Fri, 6 Feb 2004 13:15:39 +0000
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Hi Sam,
ok: the problem is related to the setting of $CCP4_SCR. This is set to
something like /tmp/$USER by default in the normal CCP4 setup
script. The advantage is, that each user has they're own specific
scratch directory. The disadvantage is, that on most systems these
scratch directories are cleaned up on a regular basis and these
subdirectories are deleted (that's why the normal CCP4 setup script
tries to create $CCP4_SCR if it doesn't exist).
Now I don't like that design (purely personal taste) and I usually
have scratch space set to plain old /tmp - which will always exist and
will always be writable by any user. To keep things tidy, all
SHARP/autoSHARP scripts will create temporary files with unique names
in the various scratch disks.
So you should change the settings for $CCP4_SCR and $BINSORT_SCR in
the various $BDG_home/machines/*/ccp4.setup files to point to an
always existing directory, e.g. /tmp. The error you get (see your log
file) is that
/verytemp/ztmp
doesn't exist. Maybe it is local to a specific machine and you try to
run things on a different machine?=20
Cheers
Clemens
On Wed, Feb 04, 2004 at 06:58:02PM -0000, Arulandu, Arockiasamy wrote:
> Dear Clemens
>=20
> here is the log file with the error message. wish that helps.
>=20
> sam
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> >>>>>>>>>
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> [sam@xtallo ~]$ cat eden-unique.log
> <B><FONT COLOR=3D"#FF0000"><!--SUMMARY_BEGIN-->
> <pre>
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> 1###############################################################
> ###############################################################
> ###############################################################
> ### CCP4 4.2: MTZDUMP version 4.2 : 06/08/02##
> ###############################################################
> User: Run date: 2/ 4/04 Run time:10:37:29
>=20
>=20
> Please reference: Collaborative Computational Project, Number 4. 1994.
> "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,=
760-763.
>=20
> as well as any specific reference in the program write-up.
>=20
>=20
> <!--SUMMARY_END--></FONT></B>
> List reflection: 0
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> (Q)QOPEN: file opened on unit 1 Status: READONLY
> <B><FONT COLOR=3D"#FF0000"><!--SUMMARY_BEGIN-->
> Logical Name: HKLIN Filename: eden.mtz
> <!--SUMMARY_END--></FONT></B>
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> * Title:
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> .
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> * Number of Columns =3D 25
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> * Number of Reflections =3D 18176
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> * Missing value set to NaN in input mtz file
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> * There is no History information in this MTZ file
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> * Column Labels :
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> H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent
> PHIcent FOMcent Fmap PHImap FHref PHIHref
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> * Column Types :
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> H H H I F P W R R F P F Q A A A A R F P W F P F P
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> * Cell Dimensions :
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> 66.8340 66.8340 166.7070 90.0000 90.0000 120.0000
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> * Resolution Range :
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> 0.00030 0.27699 ( 57.735 - 1.900 A )
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> * There is no sort order recorded in the MTZ header
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> * Space group =3D P6522 (number 179)
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> OVERALL FILE STATISTICS for resolution range 0.000 - 0.277
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
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> Col Sort Min Max Num % Mean Mean Resolution Ty=
pe Column
> num order Missing complete abs. Low High =
label
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> 1 ASC 0 30 0 100.00 14.2 14.2 57.74 1.90 =
H H
> 2 NONE 0 17 0 100.00 5.1 5.1 57.74 1.90 =
H K
> 3 NONE 0 87 0 100.00 33.0 33.0 57.74 1.90 =
H L
> 4 NONE 2.0 24.0 0 100.00 21.65 21.65 57.74 1.90 =
I NUMORB
> 5 NONE 0.0 2402.5 95 99.48 156.20 156.20 32.77 1.90 =
F FB
> 6 NONE -180.0 180.0 95 99.48 5.22 89.77 32.77 1.90 =
P PHIB
> 7 NONE 0.000 1.000 95 99.48 0.639 0.639 32.77 1.90 =
W FOM
> 8 NONE -881.1 782.6 95 99.48 -0.12 47.88 32.77 1.90 =
R HX
> 9 NONE-1040.5 964.7 95 99.48 -0.02 46.00 32.77 1.90 =
R HY
> 10 NONE 0.0 1113.9 95 99.48 74.71 74.71 32.77 1.90 =
F FH
> 11 NONE -180.0 180.0 95 99.48 -5.85 89.80 32.77 1.90 =
P PHIH
> 12 NONE 0.1 2554.9 95 99.48 198.41 198.41 32.77 1.90 =
F FP
> 13 NONE 1.7 38.4 95 99.48 5.53 5.53 32.77 1.90 =
Q SIGFP
> 14 NONE-1615.3 2402.0 95 99.48 -0.36 16.25 32.77 1.90 =
A HLA
> 15 NONE-3096.2 931.6 95 99.48 -0.47 15.59 32.77 1.90 =
A HLB
> 16 NONE -686.8 403.8 95 99.48 -0.37 6.66 32.77 1.90 =
A HLC
> 17 NONE -563.3 1047.4 95 99.48 -0.05 6.34 32.77 1.90 =
A HLD
> 18 NONE 0.7 897.1 95 99.48 21.69 21.69 32.77 1.90 =
R HL0
> 19 NONE 0.0 2811.8 95 99.48 152.20 152.20 32.77 1.90 =
F Fcent
> 20 NONE -179.9 180.0 95 99.48 6.18 90.07 32.77 1.90 =
P=20
> PHIcent
> 21 NONE 0.000 1.000 95 99.48 0.671 0.671 32.77 1.90 =
W=20
> FOMcent
> 22 NONE 0.0 2405.6 95 99.48 156.55 156.55 32.77 1.90 =
F Fmap
> 23 NONE -180.0 180.0 95 99.48 5.17 89.81 32.77 1.90 =
P PHImap
> 24 NONE 0.0 1122.5 95 99.48 75.90 75.90 32.77 1.90 =
F FHref
> 25 NONE -180.0 180.0 95 99.48 -6.05 90.53 32.77 1.90 =
P=20
> PHIHref
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> No. of reflections used in FILE STATISTICS 18176
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> <B><FONT COLOR=3D"#FF0000"><!--SUMMARY_BEGIN-->
> MTZDUMP: NO REFLECTIONS LISTED
> Times: User: 0.3s System: 0.0s Elapsed: 0:00
> </pre>
> <!--SUMMARY_END--></FONT></B>
> <B><FONT COLOR=3D"#FF0000"><!--SUMMARY_BEGIN-->
> </html>
> <!--SUMMARY_END--></FONT></B>
> <B><FONT COLOR=3D"#FF0000"><!--SUMMARY_BEGIN-->
> <pre>
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> 1###############################################################
> ###############################################################
> ###############################################################
> ### CCP4 4.2: UNIQUE version 4.2 : 09/08/02##
> ###############################################################
> User: Run date: 2/ 4/04 Run time:10:37:29
>=20
>=20
> Please reference: Collaborative Computational Project, Number 4. 1994.
> "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,=
760-763.
>=20
> as well as any specific reference in the program write-up.
>=20
>=20
> <!--SUMMARY_END--></FONT></B>
> Data line--- CELL 66.8340 66.8340 166.7070 90.0000 90.0000 1=
20.0000
> Data line--- SYMM 179
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> FORMATTED OLD file opened on unit 24
> <B><FONT COLOR=3D"#FF0000"><!--SUMMARY_BEGIN-->
> Logical name: SYMOP, Filename: /yusr/pomp/sharp3/database/symop
> <!--SUMMARY_END--></FONT></B>
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> Data line--- RESO 1.900
> Data line--- LABO F=3DFUNI SIGF=3DSIGFUNI
> Data line--- END
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> Reciprocal space symmetry
> Space group: P6522 (179) Point group: 622 Laue group: 6/mmm
> Asymmetric unit: [6/mmm] hkl:h>=3D0, k>=3D0, l>=3D0 with h>=3Dk
>=20
> Original indices for reflection hkl with symmetry number ISYM
>=20
> Bijvoet positive
> ISYM ISYM ISYM ISYM
> ISYM 1 +h,+k,+l 7 -h,-k,+l 13 +k,+h,-l 19 -k,-h,-l
> ISYM 3 -h-k,+h,+l 9 +h+k,-h,+l 15 +h,-h-k,-l 21 -h,+h+k=
,-l
> ISYM 5 +k,-h-k,+l 11 -k,+h+k,+l 17 -h-k,+k,-l 23 +h+k,-k=
,-l
>=20
> Bijvoet negative
> ISYM ISYM ISYM ISYM
> ISYM 2 -h,-k,-l 8 +h,+k,-l 14 -k,-h,+l 20 +k,+h,+l
> ISYM 4 +h+k,-h,-l 10 -h-k,+h,-l 16 -h,+h+k,+l 22 +h,-h-k=
,+l
> ISYM 6 -k,+h+k,-l 12 +k,-h-k,-l 18 +h+k,-k,+l 24 -h-k,+k=
,+l
>=20
> <B><FONT COLOR=3D"#FF0000"><!--SUMMARY_BEGIN-->
> Last system error message:
> No such file or directory
> UNIQUE: CCP4_QOPEN: can't open /verytemp/ztmp/42317149.mtz
> Times: User: 0.1s System: 0.0s Elapsed: 0:01
> </pre>
> <!--SUMMARY_END--></FONT></B>
> <B><FONT COLOR=3D"#FF0000"><!--SUMMARY_BEGIN-->
> </html>
> <!--SUMMARY_END--></FONT></B>
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> "Arulandu, Arockiasamy" <sam001@neo.tamu.edu> said:
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> >=20
> > Dear Clemens,
> >=20
> > Your earlier suggestion helped me pass the CAD error and now i am stuck=
in the
> > further step, running Autosharp. Runs o.k up to Density Mopdification a=
nd
> > stops at DM step with the error message " unable to uniqueify file eden=
.mtz!".
> >=20
> > I very much appreciate if you have any inputs.
> >=20
> > thank you
> > sam
> >=20
> >=20
>=20
>=20
>=20
> --=20
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> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
--=20
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park=20
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************
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