[sharp-discuss] need help using autosharp
Clemens Vonrhein
vonrhein@globalphasing.com
Tue, 18 Mar 2003 18:10:19 +0000
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Hi,
there is a small bug in 3.0.15 when you have more than 1 molecule/asu
(and the sequence file doesn't reflect that).
If you are running Sushi 3.0.15 please apply the attached patch:
% cd $BDG_home/bin/sharp/autoSHARP
% patch getinfo.sh < getinfo.sh.diff
I _hope_ that cures it ...
Clemens
On Tue, Mar 18, 2003 at 05:48:05PM +0000, madhavan br wrote:
>=20
> Hi all,
>=20
> My autoSHARP for heavy atom refining seems to stop after
> calculating Matthew's coeffecient without giving any error message. I
> checked my mtz file and it looks ok. Can somebody help me resolving
> this problem. In my STDERR logfile there's a mention of BDG trace BPT
> error. I've no idea what this means.
>=20
> Thanks,
>=20
> Maddy
> _________________________________________________________________
>=20
> Call US for just Rs. 5. [1]Get a phone card
> _______________________________________________ sharp-discuss mailing
> list sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
>=20
> References
>=20
> 1. http://g.msn.com/8HMUENIN/2746
--=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)
***************************************************************
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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
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