Thank you very much!
Kind regards,
James
2014-09-22 18:50 GMT+02:00 Sampson, Jared <jared.samp...@nyumc.org>:
> Hi James -
>
> On Sep 22, 2014, at 4:30 AM, James Starlight <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>:
>
>> 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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