[sharp-discuss] problems with 3.0.15
Clemens Vonrhein
vonrhein@globalphasing.com
Tue, 4 Feb 2003 07:57:22 +0000
--BHMq0+oGliEfCAkH
Content-Type: multipart/mixed; boundary="S6vg04ofUPzW4qJg"
Content-Disposition: inline
--S6vg04ofUPzW4qJg
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable
Dear all,
yes - I'm aware of that bug (which appears when more than one
molecule/asu is assumed). I had planned an update release of Sushi
3.0.16 for a couple of weeks now (but got distracted by various other
things). Anyway, in the meantime you can apply the attached patch as
follows:
% cd $BDG_home/bin/sharp/autoSHARP
% cp -p getinfo.sh getinfo.sh.saved
% patch getinfo.sh < getinfo.sh.diff
This should cure that problem. Sorry about the inconvenience.
Cheers
Clemens
On Mon, Feb 03, 2003 at 03:54:16PM -0500, Doug Bailey wrote:
> Hello Everyone,
>=20
> I recently upgraded to SHARP 2.01 / Sushi 3.0.15 and now things seemed to=
=20
> have stop working.
>=20
> I had a user submit a known working job just to test things out. In the=
=20
> logfile, Step 1.1 Initial Check seems to complete but then things hang in=
=20
> what looks like Step 1.2 Extracting Additional Info. After this there is =
no=20
> additional info placed in the logfile. It looks like the process,=20
> getinfo.sh is hung. We let things run for over an hour.
>=20
> Any help would be greatly appreciated.
>=20
> Thanks,
> Doug
>=20
>=20
>=20
>=20
>=20
> Douglas Bailey E-mail: baileyd@ncifcrf.gov
> NCI-FCRDC Ph: 301-846-5328
> 7th Street, Ft. Detrick Cell: 301-748-2170
> Frederick, Maryland 21702 Fax: 301-846-6128
>=20
>=20
>=20
> _______________________________________________
> 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 Tel: +44-(0)1223-353033
* Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************
--S6vg04ofUPzW4qJg
Content-Type: text/plain; charset=us-ascii
Content-Disposition: attachment; filename="getinfo.sh.diff"
Index: getinfo.sh
===================================================================
RCS file: /home/somasys/Repository/Sushi/bin/sharp/autoSHARP/getinfo.sh,v
retrieving revision 1.15.4.3.2.3
retrieving revision 1.15.4.3.2.4
diff -r1.15.4.3.2.3 -r1.15.4.3.2.4
67,72c67,70
< if [ `grep -c "getinfo.sh" .autoSHARP` -eq 0 ]; then
< echo "# ----------------------------------------" >> .autoSHARP
< echo "# Automatic generated values" >> .autoSHARP
< echo "# (by script getinfo.sh)" >> .autoSHARP
< echo "# ----------------------------------------" >> .autoSHARP
< fi
---
> echo "# ----------------------------------------" >> .autoSHARP
> echo "# Automatic generated values" >> .autoSHARP
> echo "# (by script getinfo.sh)" >> .autoSHARP
> echo "# ----------------------------------------" >> .autoSHARP
74c72
< HtmlSection "Each dataset"
---
> HtmlSection "Getting additional information from each dataset"
219a218,219
> autoSHARP_nmol=1
> echo " autoSHARP_nmol=\"1\"" >> .autoSHARP
221a222
> autoSHARP_NresAsu=`echo $autoSHARP_nres $autoSHARP_nmol | awk '{if(NF==2){print $1*$2}else{print $1}}'`
228c229,230
< wilkb=`wilsonmtz $BDG_datafiles/$data $fmid $smid $autoSHARP_nres ${autoSHARP_SubDir}/wilson_${iden}.${autoSHARP_logext} $reso`
---
> wilkb=`wilsonmtz $BDG_datafiles/$data $fmid $smid $autoSHARP_NresAsu \
> ${autoSHARP_SubDir}/wilson_${iden}.${autoSHARP_logext} $reso`
237c239,241
< HtmlNote -e "/manual/autoSHARP3.html#getinfoWilson" "Wilson scale factor K and temperature factor B = $wilkb (based on $autoSHARP_nmol molecule`autoSHARP_plural $autoSHARP_nmol`)"
---
> HtmlNote -e "/manual/autoSHARP3.html#getinfoWilson" \
> "Wilson scale factor K and temperature factor B = $wilkb (based " \
> "on $autoSHARP_nmol molecule`autoSHARP_plural $autoSHARP_nmol`)"
239c243,245
< solc=`awk '/fraction of unit cell occupied by atoms/{printf("%5.1f",100*(1.0-$(NF-1)))}' ${autoSHARP_SubDir}/wilson_${iden}.${autoSHARP_logext}`
---
> solc=`awk '/fraction of unit cell occupied by atoms/{
> printf("%5.1f",100*(1.0-$(NF-1)))}' \
> ${autoSHARP_SubDir}/wilson_${iden}.${autoSHARP_logext}`
246,247c252,255
< mean_fs2_resh=`awk '/ TOTALS /{x=t}{if (NF>1){t=$NF}}END{print x}' ${autoSHARP_SubDir}/wilson_${iden}.${autoSHARP_logext}`
< HtmlNote -e "/manual/autoSHARP3.html#getinfoFstat" "<F> =$mean_f; <sd> =$mean_s; <F>/<sd>=$mean_fs1; <F/sd>=$mean_fs2"
---
> mean_fs2_resh=`awk '/ TOTALS /{x=t}{if (NF>1){t=$NF}}END{print x}' \
> ${autoSHARP_SubDir}/wilson_${iden}.${autoSHARP_logext}`
> HtmlNote -e "/manual/autoSHARP3.html#getinfoFstat" \
> "<F> =$mean_f; <sd> =$mean_s; <F>/<sd>=$mean_fs1; <F/sd>=$mean_fs2"
271c279
< solc=`solventmtz $BDG_datafiles/$data $fmid $smid $autoSHARP_nres`
---
> solc=`solventmtz $BDG_datafiles/$data $fmid $smid $autoSHARP_NresAsu`
314c322,323
< wave_step=`echo $wave_max $wave_min | awk '{printf("%f",($1-$2)/1000)}'`
---
> # allow a small factor around the min/max wavelengths given
> wave_step=`echo $wave_max $wave_min | awk '{printf("%f",((1.1*$1)-(0.91*$2))/1000)}'`
595a605,606
> autoSHARP_nmol=1
> echo " autoSHARP_nmol=\"$autoSHARP_nmol\"" >> .autoSHARP
600c611
< HtmlSection -e "/manual/autoSHARP3.html#getinfoMatthews" "Matthews Coefficient"
---
> HtmlSection -e "/manual/autoSHARP3.html#getinfoMatthews" "Matthews Coefficient, solvent content"
660c671
< echo "<tr><td> </td><td align=center><b>$nmol</b></td><td align=center>$vm</td><td align=center>$solc</td></tr>"
---
> echo "<tr><td> </td><td align=center><b><font size=+2>$nmol</font></b></td><td align=center>$vm</td><td align=center>$solc</td></tr>"
679c690,693
< HtmlNote "updating number of residues ($autoSHARP_nres) and molecular weight ($autoSHARP_molw Da)"
---
> autoSHARP_NresAsu=`echo $autoSHARP_nres $autoSHARP_nmol | awk '{if(NF==2){print $1*$2}else{print $1}}'`
> autoSHARP_MolwAsu=`echo $autoSHARP_molw $autoSHARP_nmol | awk '{if(NF==2){print $1*$2}else{print $1}}'`
> HtmlNote "updating number of residues ($autoSHARP_NresAsu) and molecular " \
> "weight ($autoSHARP_MolwAsu Da) in asymmetric unit"
690c704,705
< wilkb=`wilsonmtz $BDG_datafiles/$data $fmid $smid $autoSHARP_nres ${autoSHARP_SubDir}/wilson_${iden}.${autoSHARP_logext} $reso`
---
> wilkb=`wilsonmtz $BDG_datafiles/$data $fmid $smid $autoSHARP_NresAsu \
> ${autoSHARP_SubDir}/wilson_${iden}.${autoSHARP_logext} $reso`
695a711
> iset=`expr $iset + 1`
700c716
< [ "$autoSHARP_pirf" != "None" ]; then
---
> [ "X$autoSHARP_pirf" != "XNone" ]; then
720a737
> echo " # molecular weight of monomer" >> .autoSHARP
721a739
> echo " # number of residues in monomer" >> .autoSHARP
722a741
> echo " # number of monomers in asu" >> .autoSHARP
--S6vg04ofUPzW4qJg--
--BHMq0+oGliEfCAkH
Content-Type: application/pgp-signature
Content-Disposition: inline
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.2.1 (GNU/Linux)
iD8DBQE+P3Jh4f+nTPEF25QRAigZAJ9GlcN8DyOwE9VmlSCjqpy9QUrb3gCeMalm
v0bKDJrtAKotzIiNqyKP/6c=
=Xj7r
-----END PGP SIGNATURE-----
--BHMq0+oGliEfCAkH--