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SSX-PepT Se: Difference between revisions
→generating XSCALE.INP for scaling
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mkdir <attendee_name>_SSX (e.g. Greta_SSX) | mkdir <attendee_name>_SSX (e.g. Greta_SSX) | ||
cd <attendee_name>_SSX | cd <attendee_name>_SSX | ||
find ../tutorial_data/PepT_SE_145/ -name xtal* > | find ../tutorial_data/PepT_SE_145/ -name xtal* > XSCALE.INP | ||
sed -i s/^/INPUT_FILE=/ | sed -i s/^/INPUT_FILE=/ XSCALE.INP | ||
paste this into the header: | paste this into the header: | ||
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== scale everything together == | == scale everything together == | ||
rm xscale.inp | rm xscale.inp | ||
xscale_par | xscale_par | ||
-->have a look at XSCALE.LP | -->have a look at XSCALE.LP | ||
== run xscale_isocluster == | == run xscale_isocluster == | ||
xscale_isocluster -dim 3 all_145.hkl | xscale_isocluster -dim 3 -i all_145.hkl | tee XSCALE_ISOCLUSTER.LP | ||
--> check output | --> check output on screen (which is saved on XSCALE_ISOCLUSTER.LP). The program says that we obtain 4 clusters. Check with coot: | ||
coot iso.pdb | |||
coot iso.pdb | |||
We don't really see the clusters as separate when looking at iso.pdb in coot. So let us just take the 4 clusters that xscale_isocluster detects as an opportunity to use groups of data sets for further work, without implying any deeper meaning of the clusters. | |||
== look at the 4 clusters == | == look at the 4 clusters == | ||
load iso.1.pdb into coot. Also load iso.2.pdb , iso.3.pdb, iso.4.pdb and use the Display Manager for switching the clusters on/off | |||
load | |||
== decide which clusters one would take for structure solution == | == decide which clusters one would take for structure solution == | ||
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cp XSCALE.LP XSCALE_old.LP | cp XSCALE.LP XSCALE_old.LP | ||
awk '{ one = $1 ; getline ; print one " " $7 " " $8;getline}' XSCALE.1.INP |grep 'INPUT_FILE' >temp | awk '/INPUT_FILE/{ one = $1 ; getline ; print one " " $7 " " $8;getline}' XSCALE.1.INP |grep 'INPUT_FILE' >temp | ||
awk '{ one = $1 ; getline ; print one " " $7 " " $8;getline}' XSCALE.4.INP |grep 'INPUT_FILE'>>temp | awk '/INPUT_FILE/{ one = $1 ; getline ; print one " " $7 " " $8;getline}' XSCALE.4.INP |grep 'INPUT_FILE'>>temp | ||
sort -nr -k2 temp >temp1 | sort -nr -k2 temp >temp1 | ||
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OUTPUT_FILE=1+4.hkl | OUTPUT_FILE=1+4.hkl | ||
SAVE_CORRECTION_IMAGES=FALSE | SAVE_CORRECTION_IMAGES=FALSE | ||
PRINT_CORRELATIONS=FALSE | PRINT_CORRELATIONS=FALSE ! this is not yet in the official BUILT=20171111 | ||
WFAC1=1 | WFAC1=1 | ||
Alternatively, solve the structure with only cluster 1 ! | |||
== solve structure with [[ccp4com:SHELX C/D/E|SHELX C/D/E]] == | == solve structure with [[ccp4com:SHELX C/D/E|SHELX C/D/E]] == | ||
(use [[ccp4com:hkl2map|hkl2map]])! | (use [[ccp4com:hkl2map|hkl2map]])! There are 458 residues, out of which 18 are SeMet, in PepT. | ||
== Notes == | |||
other option: run xscale_isocluster with the option -clu 1 and sort by strength, take the upper ones and solve the structure. | other option: run xscale_isocluster with the option -clu 1 and sort by strength, take the upper ones and solve the structure. | ||
Or | |||
run xscale_isocluster with the option -clu 1 and sort by strength*cos(angle), take the upper ones and solve the structure. | |||
That would be | |||
awk '/INPUT_FILE/{ one = $1 ; getline ; print one " " $7*cos($8*3.14159/180) " " $8;getline}' XSCALE.1.INP |grep INPUT_FILE >temp | |||
awk '/INPUT_FILE/{ one = $1 ; getline ; print one " " $7*cos($8*3.14159/180) " " $8;getline}' XSCALE.4.INP |grep INPUT_FILE >>temp | |||
sort -nr -k2 temp >temp1 | |||