Hi Tsjerk,
the interesting option for coloring which I found to set sensitivity
of the visualization in my case:
spectrum b, red_orange_white, minimum=-1, maximum=0.1
are there any same commands to set transparency level according to the
B-factor value? Here the issue is with the proper selection
E.g
PyMOL>select not-relevent, b > 0
results only in small atoms selected
and
PyMOL>select ss, b = 0
Selector-Error: Invalid selection.
b<--
Regards,
James
2015-04-10 21:12 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
> Hi James,
>
> The selection keyword 'b' exists for just that purpose: to make selections
> based on the b-factor value.
>
> color red, b > 0
>
> Cheers,
>
> Tsjerk
>
> On Fri, Apr 10, 2015 at 5:19 PM, James Starlight <jmsstarli...@gmail.com>
> wrote:
>>
>> some specification regarding B-factors visualization for my task:
>>
>> is it possible within the open pymol session
>>
>> 1) to select only residues with non-zero B-factors as specified
>> selection (here I would like to present it as the stics and display it
>> names as the label)
>>
>> 2) to define residues with zero B-factors as another specified
>> selection (for those one I'd like to apply specified color filter for
>> instance and transparency as for not relevant in my case)
>>
>> Thanks!
>>
>> J
>>
>> 2015-04-10 15:27 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>> > Hi Osvaldo and thank you very much- it works perfect!
>> >
>> > The only question which I have- is it possible to modify existing
>> > color-pattern of the B-factor colouring (from the spectrum
>> > visualization)? for instance I need to colour by white all residues
>> > with 0.0 B-factors and as the rainbow from cold to hot gradient
>> > residues with non-zero B-factors: where residues with most negative
>> > values should correspond to the hot colours, and with positive - to
>> > cold (because here this valus in fact correspond to the binding free
>> > energy so more negative- better contribution to dG).
>> >
>> >
>> > Thanks again,
>> >
>> > James
>> >
>> > 2015-04-10 14:44 GMT+02:00 Osvaldo Martin <aloctavo...@gmail.com>:
>> >> Hi James,
>> >>
>> >> cmd.alter() is not working because you forget the to add the "".
>> >>
>> >> You can use PyMol as a regular Python library, write an script and then
>> >> run
>> >> it, from the command line, as:
>> >>
>> >> python my_script.py
>> >>
>> >> Your script should looks like the following:
>> >>
>> >> import __main__
>> >> __main__.pymol_argv = ['pymol','-qc'] # Pymol: quiet and no GUI
>> >> import pymol
>> >> from pymol import cmd, stored
>> >> pymol.finish_launching()
>> >> import other_useful_library
>> >>
>> >> cmd.load("OR5P3_androstenone.pdb")
>> >>
>> >> # open the file of new values (just 1 column of numbers, one for each
>> >> alpha carbon)
>> >> inFile = open("OR5P3_androstenone.dat", 'r')
>> >>
>> >> # create the global, stored array
>> >> newB = []
>> >>
>> >> # read the new B factors from file
>> >> for line in inFile.readlines(): newB.append( float(line) )
>> >>
>> >> # close the input file
>> >> inFile.close()
>> >>
>> >> # clear out the old B Factors
>> >> cmd.alter("OR5P3_androstenone", "b=0.0")
>> >>
>> >> # update the B Factors with new properties
>> >> cmd.alter("OR5P3_androstenone and n. CA", "b=newB.pop(0)")
>> >>
>> >> # color the protein based on the new B Factors of the alpha carbons
>> >> cmd.spectrum("b", "OR5P3_androstenone and n. CA")
>> >>
>> >> # save new pdb
>> >> cmd.save("OR5P3_androstenone_newBFactors.pdb", "OR5P3_androstenone")
>> >>
>> >> Cheers,
>> >> Osvaldo.
>> >>
>> >>
>> >> On Fri, Apr 10, 2015 at 9:03 AM, James Starlight
>> >> <jmsstarli...@gmail.com>
>> >> wrote:
>> >>>
>> >>> so to be more precise the issue is how to adapt the following script
>> >>> (which used python interpetator directly from pymol to change
>> >>> B-factors within loaded pdb) to use it as the external script loaded
>> >>> from command line e.g pymol -r script.py
>> >>>
>> >>> # here the code what should I to adapt:
>> >>>
>> >>> cmd.load("OR5P3_androstenone.pdb")
>> >>>
>> >>> # open the file of new values (just 1 column of numbers, one for each
>> >>> alpha carbon)
>> >>> inFile = open("OR5P3_androstenone.dat", 'r')
>> >>>
>> >>> # create the global, stored array
>> >>> newB = []
>> >>>
>> >>> # read the new B factors from file
>> >>> for line in inFile.readlines(): newB.append( float(line) )
>> >>>
>> >>> # close the input file
>> >>> inFile.close()
>> >>>
>> >>> # clear out the old B Factors
>> >>> cmd.alter(OR5P3_androstenone, b=0.0)
>> >>>
>> >>> # update the B Factors with new properties
>> >>> cmd.alter(OR5P3_androstenone and n. CA, b=newB.pop(0))
>> >>>
>> >>> # color the protein based on the new B Factors of the alpha carbons
>> >>> cmd.spectrum("b", "OR5P3_androstenone and n. CA")
>> >>>
>> >>> # save new pdb
>> >>> cmd.save("OR5P3_androstenone_newBFactors.pdb", "OR5P3_androstenone")
>> >>>
>> >>>
>> >>>
>> >>> # so as you can see here I tried to move some pynol command like alter
>> >>> to the cmd.alter with its options but the script didn't worked.
>> >>>
>> >>> J.
>> >>>
>> >>> 2015-04-09 16:52 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>> >>> > also to specify:
>> >>> >
>> >>> > I've already done this for one pdb and one dat file using just
>> >>> > sequence command from the pymol with loaded protA.pdb
>> >>> >
>> >>> > inFile = open("./test.dat", 'r')
>> >>> >
>> >>> > # create the global, stored array
>> >>> > stored.newB = []
>> >>> >
>> >>> > # read the new B factors from file
>> >>> > for line in inFile.readlines(): stored.newB.append( float(line) )
>> >>> >
>> >>> > # close the input file
>> >>> > inFile.close()
>> >>> >
>> >>> > # clear out the old B Factors
>> >>> > alter protA, b=0.0
>> >>> >
>> >>> > # update the B Factors with new properties
>> >>> > alter protA and n. CA, b=stored.newB.pop(0)
>> >>> >
>> >>> > # color the protein based on the new B Factors of the alpha carbons
>> >>> > cmd.spectrum("b", "protA and n. CA")
>> >>> >
>> >>> >
>> >>> > now the idea using below bash script which superimpose each pdb with
>> >>> > each log to call pymol from the terminal each time for each pdb and
>> >>> > load to it corresponded dat file producing as the result new pdb
>> >>> > with
>> >>> > new B-factors (taken from the dat log)
>> >>> >
>> >>> >
>> >>> > #!/bin/bash
>> >>> >
>> >>> > workdir=/data2/Gleb/script/Simulations/activation/5p3_decomposition_visu
>> >>> > pdb_all=${workdir}/complexes
>> >>> > logs_all=${workdir}/logs
>> >>> >
>> >>> > # where final pdb will be saved
>> >>> > output=${workdir}/outputs
>> >>> >
>> >>> >
>> >>> > #looping of pdbs
>> >>> > for pdb in ${pdb_all}/*.pdb; do # ????
>> >>> > pdb_n_full=$(basename "${pdb}")
>> >>> > pdb_n="${pdb_n_full%.*}"
>> >>> > Complexes=("${Complexes[@]}" "${pdb_n}");
>> >>> > echo ${pdb_n} "has been added to the list!"
>> >>> > done
>> >>> > #sort elements within ${Complexes[@]} lists!!
>> >>> > #echo "The pdb list consist of:" ${Complexes[@]}
>> >>> > #echo "Total number of pdbs:" ${#Complexes[@]}
>> >>> >
>> >>> > #looping of tops
>> >>> > for log in ${logs_all}/*.dat; do # ????
>> >>> > log_n_full=$(basename "${log}")
>> >>> > log_n="${log_n_full%.*}"
>> >>> > Logs=("${Logs[@]}" "${log_n}");
>> >>> > echo ${log_n} "has been added to the list!"
>> >>> > done
>> >>> > #sort elements within ${Logs[@] lists!!
>> >>> > #echo "The DAT list consist of:" ${Logs[@]}
>> >>> > #echo "Total number of logs:" ${#Logs[@]}
>> >>> >
>> >>> >
>> >>> > # So I need only to define how I will use pymol with each pair of
>> >>> > log
>> >>> > and pdb
>> >>> > #proceed each pdb in pymol using elements from both lists
>> >>> > for i in $(seq 1 ${#Logs[@]}); do
>> >>> > # print what pdb and what DAT will be used within this loop
>> >>> > echo ${Logs[i]}
>> >>> > echo ${Complexes[i]}
>> >>> > # here run pymol using i pdb with corresponded i dat !!
>> >>> > #done
>> >>> >
>> >>> >
>> >>> > I will be thankful for any ideas in the last part of that script!
>> >>> >
>> >>> >
>> >>> > James
>> >>> >
>> >>> > 2015-04-09 16:15 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>> >>> >> thanks for the information! Here I ask to provide me with some more
>> >>> >> help because I'm not a big expert in the python .
>> >>> >>
>> >>> >> For instance I have 2 folders- one with 10 pdb's corresponded to
>> >>> >> the
>> >>> >> 10 complexes of one receptor (289 residues) docked with 10
>> >>> >> different
>> >>> >> ligands; the second one is the 10 the_same_name.dat files
>> >>> >> corresponded
>> >>> >> to the 10 logs having 1 column with the values per each residue
>> >>> >> (totally 289 values) of the receptor. I need to associate each pdb
>> >>> >> with each dat to exchange existing B-factors within each pdb onto
>> >>> >> the
>> >>> >> values taken from the corresponded.dat files and associate it's
>> >>> >> directly to the C-alpha atoms of each complex for instance. Will it
>> >>> >> be
>> >>> >> better to rewrite here the script from the PyMol Wiki or to use
>> >>> >> data2bfactor.py (here as I found I need to modify my dat logs
>> >>> >> including to them number of receptor residues and chainID).
>> >>> >>
>> >>> >> James
>> >>> >>
>> >>> >> 2015-04-08 19:00 GMT+02:00 Osvaldo Martin <aloctavo...@gmail.com>:
>> >>> >>> Hi James,
>> >>> >>>
>> >>> >>> I think what you want to do is to load your data to the b-factor
>> >>> >>> column of
>> >>> >>> the pdb file and then ask PyMol to color the protein according to
>> >>> >>> the
>> >>> >>> b-factor values. Try with this example from the PyMol wiki and let
>> >>> >>> us
>> >>> >>> know
>> >>> >>> if you find some trouble.
>> >>> >>>
>> >>> >>> Regards,
>> >>> >>> Osvaldo.
>> >>> >>>
>> >>> >>> On Wed, Apr 8, 2015 at 1:47 PM, James Starlight
>> >>> >>> <jmsstarli...@gmail.com>
>> >>> >>> wrote:
>> >>> >>>>
>> >>> >>>> Dear Pymol users!
>> >>> >>>>
>> >>> >>>> For better visualization of the MMGBSA outputs from MD performed
>> >>> >>>> for
>> >>> >>>> 10
>> >>> >>>> ligands
>> >>> >>>> agains 1 receptor-target I wonder to map per-residue
>> >>> >>>> decomposition
>> >>> >>>> data from each of the systems onto the receptor's 3D structure.
>> >>> >>>> Eventually I'd like to produce 10 cartoon diagrams which would
>> >>> >>>> differs
>> >>> >>>> in the coloring according to the difference in the contribution
>> >>> >>>> of
>> >>> >>>> residues from the receptor's cavity to binding for different
>> >>> >>>> ligands.
>> >>> >>>> I will be very thankful if someone provide me with ideas of how
>> >>> >>>> such
>> >>> >>>> visualization could be done using receptors structure,
>> >>> >>>> decomposition
>> >>> >>>> logs as the inputs and/or pymol. Here some general idea whig
>> >>> >>>> came in
>> >>> >>>> mind- import column from the mmgbsa.log directly (with number of
>> >>> >>>> rows= number of receptors residues) to the receptor.pdb B-factors
>> >>> >>>> column (for instance making meaningful value for C-alpha atom and
>> >>> >>>> 0
>> >>> >>>> for the rest). Will be very thankful for some examples of how it
>> >>> >>>> could
>> >>> >>>> be achieved e.g using combination of awk_sed if more trivial way
>> >>> >>>> is
>> >>> >>>> not exist.
>> >>> >>>>
>> >>> >>>>
>> >>> >>>> Thanks for help!!
>> >>> >>>>
>> >>> >>>> James
>> >>> >>>>
>> >>> >>>>
>> >>> >>>>
>> >>> >>>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
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