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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 | ||
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PRINT_CORRELATIONS=FALSE ! this is not yet in the official BUILT=20171111 | 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 | |||