Hi James -
On Sep 22, 2014, at 4:30 AM, James Starlight
<jmsstarli...@gmail.com<mailto:jmsstarli...@gmail.com>> wrote:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
# dock each model to the ligand
for pdb in $receptors/*.pdb; do
filename=$(basename "$pdb")
M=${filename/.pdb/}
echo "Processing of ${M} is initiated..."
#remove water and ions; change EMD to TER
grep -v "ATOM.*\(WAT\|NA+\|Cl-\)" $pdb | sed -e 's/^END/TER/g' >
${dirr}/temp/${M}_clean.pdb
#superimsoposition using pymol against reference
pymol $ref ${dirr}/temp/${M}_clean.pdb -c -q -d "super $M, $R and resi 2-280;
save ./superimposed/${M}_aligned.pdb, $M" > ./superimposed/pymol_${M}.log
cp $ref ./superimposed
done
Glad it worked for you.
two additional questions:
1) will it possible to use more flexibility in case of the selection of region
for alignment in reference structure?
super $M, $R and resi 2-280
For instance I'd like to select all residues which are part of the alpha
helixes of the reference. how it should be done?
Try `$R and resi 2-280 and ss h`. See
http://www.pymolwiki.org/index.php/Property_Selectors for more info. (That
page comes up as the very first result for me on Google with “pymol select
secondary structure” as the search term.)
2) what advantages could give me tmalign method for the superimposition in
comparison to super and ce programs? does the coordinates of the reference will
not changed after alignment of each mobile on it (like fitting in case of
super) ?
>From the description here (http://www.pymolwiki.org/index.php/TMalign) that
>TMalign, like CEalign, can be useful for structures in the “twilight zone,”
>where sequence alignment by `align` or structural alignment by `super` may not
>provide a good fit. For any of the programs, though, only the mobile
>structures should move; the target/reference coordinates should always remain
>unchanged.
Cheers,
Jared
James
2014-09-22 10:21 GMT+02:00 James Starlight
<jmsstarli...@gmail.com<mailto:jmsstarli...@gmail.com>>:
Hi Jared,
many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)
2014-09-19 20:19 GMT+02:00 Sampson, Jared
<jared.samp...@nyumc.org<mailto:jared.samp...@nyumc.org>>:
Hi James -
I don’t have any experience with Profit. However, instead of using "something
like” PyMOL’s `super` command as you asked, you could actually use `super` in
your shell session by launching PyMOL in command line
mode<http://www.pymolwiki.org/index.php/Command_Line_Options>. Of course, you
would need to modify it according to your file naming scheme, but here’s a
working example.
###
#!/bin/bash
REF=reference.pdb
# grab some related pdb files to use and make one of them the reference
# (obviously you won’t have to do this)
i=0
for pdb in 1bbd 7fab 1dba 1plg 1nl0; do
pymol -c -d "fetch ${pdb}, mobile${i}, async=0; save mobile${i}.pdb"
i=$((i+1))
done
mv mobile0.pdb $REF
# align all the mobile files to a selection in the reference file
i=1
for MOB in mobile*.pdb; do
# strip the extensions
R=$(echo $REF | sed 's/\.pdb$//')
M=$(echo $MOB | sed 's/\.pdb$//')
# superimpose and save aligned mobile coordinates
pymol $REF $MOB -c -q -d "super $M, $R and resi 1-110; save
${M}_aligned.pdb"
done
pymol mobile*_aligned.pdb
###
You could also use CEalign if you need something citable, just switch the order
of the arguments to it: `cealign $R and resi 1-110, $M`.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Sep 19, 2014, at 6:03 AM, James Starlight
<jmsstarli...@gmail.com<mailto:jmsstarli...@gmail.com>> wrote:
Dear all,
I still need some help regarding some algorithm for structural superimposition
of my mobile structures regarding one specified reference using some fitting
method (to avoid changing in the position of the reference.pdb which is very
important for me!)=>something like super command in pymol. Using ProFit I have
faced with some errors during superimposition regarding the chosing reference
(in case where there were some differences in the positions of ref and mob
structures its alignment was not perfect (the mob had not been fully aligned on
the ref) obtaining very big RMSD (20 A!) as the result although its actual
value should be in range of 2-5 A. I'll be thankful for possible sollutions of
this problem using Profit is there are users experienced with this software (mb
it should to define fitting zones or atom subsets more accurately but I have no
ideas here ) or any other alternatives which could be used as parts of the
shell script.
James
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