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
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?
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) ?
James
2014-09-22 10:21 GMT+02:00 James Starlight <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>:
>
> 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>
>> 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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