Content:

Introduction

Since accurate data processing (after a good experiment) is often crucial to the success of experimental phasing, we will show some examples starting right from the raw diffraction images here. They can be used to see how to run autoPROC and feed the resulting scaled and merged data into autoSHARP for structure solution and initial model building.

Usually, you would run autoSHARP with all defaults - but if this is a tutorial with some time limits, you could also try adding e.g. the -fast flag to your command line. And to run really fast, we can also switch off the ARP/wARP automatic building by setting

export i_can_run_arpwarp=0    # bash
   - or -
setenv i_can_run_arpwarp 0    # tcsh/csh

(to only use Buccaneer at the model building stage).

Examples

4PXY

dataset size = 1.5G
see also: https://www.rcsb.org/structure/4PXY
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=4pxy

# getting raw diffraction data:
[ ! -d 4PXY ] && mkdir 4PXY && ( cd 4PXY && wget https://data.proteindiffraction.org/jcsg/deposited/psi_biology/2014/SP17051A_4pxy.tz ; tar -xvf SP17051A_4pxy.tz && rm SP17051A_4pxy.tz && ln -s . Images )

cd 4PXY

# getting sequence (of monomer)
wget -O 4PXY/4PXY.seq "http://www.rcsb.org/fasta/entry/4PXY"

# running autoPROC (data processing)
process -I Images  -d autoPROC > autoPROC.lis &
firefox autoPROC/summary.html &

# running autoSHARP (experimental phasing, density modification and initial model building))
run_autoSHARP.sh -seq 4PXY.seq -ha Se -wvl  peak -sca autoPROC/aimless.sca -id autoSHARP.01 > autoSHARP.01.lis &
firefox autoSHARP.01/LISTautoSHARP.html &

5C66

dataset size = 2.1G
see also: https://www.rcsb.org/structure/5C66
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=5c66

 # getting raw diffraction data:
 [ ! -d 5C66 ] && mkdir 5C66 && ( cd 5C66 && rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/456 . && ln -s 456 Images )

 cd 5C66

 # getting sequence (of monomer)
 wget -O 5C66/5C66.seq "http://www.rcsb.org/fasta/entry/5C66"

 # running autoPROC (data processing)
 process -I Images  -d autoPROC > autoPROC.lis &
 firefox autoPROC/summary.html &

 # running autoSHARP (experimental phasing, density modification and initial model building))
 run_autoSHARP.sh -seq 5C66.seq -ha Zn -nsit 3 -wvl  peak -sca autoPROC/aimless.sca -id autoSHARP.01 > autoSHARP.01.lis &
 firefox autoSHARP.01/LISTautoSHARP.html &

6NJK

dataset size = 4.2G
see also: https://www.rcsb.org/structure/6NJK
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=6njk

 # getting raw diffraction data:
 [ ! -d 6NJK ] && mkdir 6NJK && ( cd 6NJK && wget https://data.proteindiffraction.org/csgid/IDP97254_6njk.tar.bz2 ; tar -xvf IDP97254_6njk.tar.bz2 && rm IDP97254_6njk.tar.bz2 && ln -s IDP97254_6njk/data Images )

 cd 6NJK

 # getting sequence (of monomer)
 wget -O 6NJK/6NJK.seq "http://www.rcsb.org/fasta/entry/6NJK"

 # running autoPROC (data processing)
 process -I Images ReverseRotationAxis=yes -d autoPROC > autoPROC.lis &
 firefox autoPROC/summary.html &

 # running autoSHARP (experimental phasing, density modification and initial model building))
 run_autoSHARP.sh -seq 6NJK.seq -ha Se -wvl  peak -sca autoPROC/aimless.sca -id autoSHARP.01 > autoSHARP.01.lis &
 firefox autoSHARP.01/LISTautoSHARP.html &

6NJ1

dataset size = 4.3G
see also: https://www.rcsb.org/structure/6NJ1
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=6nj1

 # getting raw diffraction data:
 [ ! -d 6NJ1 ] && mkdir 6NJ1 && ( cd 6NJ1 && wget https://data.proteindiffraction.org/csgid/IDP97248_6nj1.tar.bz2 ; tar -xvf IDP97248_6nj1.tar.bz2 && rm IDP97248_6nj1.tar.bz2 && ln -s IDP97248_6nj1/data Images )

 cd 6NJ1

 # getting sequence (of monomer)
 wget -O 6NJ1/6NJ1.seq "http://www.rcsb.org/fasta/entry/6NJ1"

 # running autoPROC (data processing)
 process -I Images ReverseRotationAxis=yes -d autoPROC > autoPROC.lis &
 firefox autoPROC/summary.html &

 # running autoSHARP (experimental phasing, density modification and initial model building))
 run_autoSHARP.sh -seq 6NJ1.seq -ha Se -wvl  peak -sca autoPROC/aimless.sca -id autoSHARP.01 > autoSHARP.01.lis &
 firefox autoSHARP.01/LISTautoSHARP.html &

5SZC

dataset size = 5.3G
see also: https://www.rcsb.org/structure/5SZC
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=5szc

 # getting raw diffraction data:
 [ ! -d 5SZC ] && mkdir 5SZC && ( cd 5SZC && rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/359 . && ln -s 359 Images )

 cd 5SZC

 # getting sequence (of monomer)
 wget -O 5SZC/5SZC.seq "http://www.rcsb.org/fasta/entry/5SZC"

 # running autoPROC (data processing)
 process -I Images  -d autoPROC > autoPROC.lis &
 firefox autoPROC/summary.html &

 # running autoSHARP (experimental phasing, density modification and initial model building))
 run_autoSHARP.sh -seq 5SZC.seq -ha Se -wvl  peak -sca autoPROC/aimless.sca -id autoSHARP.01 > autoSHARP.01.lis &
 firefox autoSHARP.01/LISTautoSHARP.html &

6NFD

dataset size = 5.9G
see also: https://www.rcsb.org/structure/6NFD
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=6nfd

 # getting raw diffraction data:
 [ ! -d 6NFD ] && mkdir 6NFD && ( cd 6NFD && wget https://data.proteindiffraction.org/csgid/IDP97199_6nfd.tar.bz2 ; tar -xvf IDP97199_6nfd.tar.bz2 && rm IDP97199_6nfd.tar.bz2 && ln -s IDP97199_6nfd/data Images )

 cd 6NFD

 # getting sequence (of monomer)
 wget -O 6NFD/6NFD.seq "http://www.rcsb.org/fasta/entry/6NFD"

 # running autoPROC (data processing)
 process -I Images ReverseRotationAxis=yes -d autoPROC > autoPROC.lis &
 firefox autoPROC/summary.html &

 # running autoSHARP (experimental phasing, density modification and initial model building))
 run_autoSHARP.sh -seq 6NFD.seq -ha Se -wvl  peak -sca autoPROC/aimless.sca -id autoSHARP.01 > autoSHARP.01.lis &
 firefox autoSHARP.01/LISTautoSHARP.html &

4LER

dataset size = 7.9G
see also: https://www.rcsb.org/structure/4LER
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=4ler

 # getting raw diffraction data:
 [ ! -d 4LER ] && mkdir 4LER && ( cd 4LER && wget https://data.proteindiffraction.org/jcsg/deposited/psi_biology/2013/GS7807N_4ler.tz ; tar -xvf GS7807N_4ler.tz && rm GS7807N_4ler.tz && ln -s . Images )

 cd 4LER

 # getting sequence (of monomer)
 wget -O 4LER/4LER.seq "http://www.rcsb.org/fasta/entry/4LER"

 # running autoPROC (data processing)
 process -I Images  -d autoPROC > autoPROC.lis &
 firefox autoPROC/summary.html &

 # running autoSHARP (experimental phasing, density modification and initial model building))
 run_autoSHARP.sh -seq 4LER.seq -ha Se -wvl  peak -sca autoPROC/aimless_0.97852.sca -id autoSHARP.01 > autoSHARP.01.lis &
 firefox autoSHARP.01/LISTautoSHARP.html &

5OD9

dataset size = 8.5G
see also: https://www.rcsb.org/structure/5OD9
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=5od9

# getting raw diffraction data:
[ ! -d 5OD9 ] && mkdir 5OD9 && ( cd 5OD9 && wget https://data.proteindiffraction.org/other/Mid1sc9_5od9.tar.bz2 ; tar -xvf Mid1sc9_5od9.tar.bz2 && rm Mid1sc9_5od9.tar.bz2 && ln -s Mid1sc9_5od9/data Images )

cd 5OD9

# getting sequence (of monomer)
wget -O 5OD9/5OD9.seq "http://www.rcsb.org/fasta/entry/5OD9"

# running autoPROC (data processing)
process -I Images  -d autoPROC > autoPROC.lis &
firefox autoPROC/summary.html &

# running autoSHARP (experimental phasing, density modification and initial model building))
run_autoSHARP.sh -seq 5OD9.seq -ha Zn -nsit 4 -wvl  peak -sca autoPROC/aimless.sca -id autoSHARP.01 > autoSHARP.01.lis &
firefox autoSHARP.01/LISTautoSHARP.html &

5B8D

dataset size = 8.9G
see also: https://www.rcsb.org/structure/5B8D
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=5b8d

 # getting raw diffraction data:
 [ ! -d 5B8D ] && mkdir 5B8D && ( cd 5B8D && wget https://data.proteindiffraction.org/sgc/HDAC6-x304_5b8d.tar.bz2 ; tar -xvf HDAC6-x304_5b8d.tar.bz2 && rm HDAC6-x304_5b8d.tar.bz2 && ln -s HDAC6-x304_5b8d/data Images )

 cd 5B8D

 # getting sequence (of monomer)
 wget -O 5B8D/5B8D.seq "http://www.rcsb.org/fasta/entry/5B8D"

 # running autoPROC (data processing)
 process -I Images  -d autoPROC > autoPROC.lis &
 firefox autoPROC/summary.html &

 # running autoSHARP (experimental phasing, density modification and initial model building))
 run_autoSHARP.sh -seq 5B8D.seq -ha Zn -nsit 3 -wvl  peak -sca autoPROC/aimless.sca -id autoSHARP.01 > autoSHARP.01.lis &
 firefox autoSHARP.01/LISTautoSHARP.html &

5KH9

dataset size = 8.9G
see also: https://www.rcsb.org/structure/5KH9
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=5kh9

# getting raw diffraction data:
[ ! -d 5KH9 ] && mkdir 5KH9 && ( cd 5KH9 && wget https://data.proteindiffraction.org/sgc/HDAC6-x469_5kh9.tar.bz2 ; tar -xvf HDAC6-x469_5kh9.tar.bz2 && rm HDAC6-x469_5kh9.tar.bz2 && ln -s HDAC6-x469_5kh9/data Images )

cd 5KH9

# getting sequence (of monomer)
wget -O 5KH9/5KH9.seq "http://www.rcsb.org/fasta/entry/5KH9"

# running autoPROC (data processing)
process -I Images  -d autoPROC > autoPROC.lis &
firefox autoPROC/summary.html &

# running autoSHARP (experimental phasing, density modification and initial model building))
run_autoSHARP.sh -seq 5KH9.seq -ha Zn -nsit 3 -wvl  peak -sca autoPROC/aimless.sca -id autoSHARP.01 > autoSHARP.01.lis &
firefox autoSHARP.01/LISTautoSHARP.html &

ExamplesAutoProcAutoSharp