Hi James,
No, you can't set transparency based on b-factor.
As for the selections, don't use selection keywords (ss) as names.
Cheers,
Tsjerk
On Apr 12, 2015 3:25 PM, "James Starlight" <jmsstarli...@gmail.com> wrote:
> and also a question-
> how it would be possible to do something with the selection based on
> the b-factors
>
> e.g
>
> PyMOL>select ss, b < -0.2
> Selector: selection "ss" defined with 119 atoms.
>
> than I've tried to make visualization of the residues within the ss
> to display residues names from the label context menu, which resulted
> in the
>
> Selector-Error: Misplaced ).
> Selector-Error: Malformed selection.
> ( ss )<--
> Selector-Error: Misplaced ).
> Selector-Error: Malformed selection.
>
> also I've tried just to copy 'ss' to new object:
>
> ( ( name CA+C1*+C1' and ( byres ( ss )<--
> Selector-Error: Misplaced ).
> Selector-Error: Malformed selection.
> ( ss )<--
>
>
> James
>
> 2015-04-12 15:12 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> > 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
> >>> >>> >>>>
> >>> >>> >>>>
> >>> >>> >>>>
> >>> >>> >>>>
> >>> >>> >>>>
> ------------------------------------------------------------------------------
> >>> >>> >>>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> >>> >>> >>>> Develop your own process in accordance with the BPMN 2
> standard
> >>> >>> >>>> Learn Process modeling best practices with Bonita BPM through
> >>> >>> >>>> live
> >>> >>> >>>> exercises
> >>> >>> >>>>
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> >>> >>> >>>> event?utm_
> >>> >>> >>>>
> >>> >>> >>>>
> >>> >>> >>>>
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> >>> >>> >>>> _______________________________________________
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> >>> >>>
> >>> >>>
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> >>> >>> Develop your own process in accordance with the BPMN 2 standard
> >>> >>> Learn Process modeling best practices with Bonita BPM through live
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> >>> >>> event?utm_
> >>> >>>
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> >>> >>> _______________________________________________
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> >>> >>> Info Page:
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> >>> >>> Archives:
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> >>> >>
> >>> >>
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
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> >>> Develop your own process in accordance with the BPMN 2 standard
> >>> Learn Process modeling best practices with Bonita BPM through live
> >>> exercises
> >>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
> >>> event?utm_
> >>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
> >>> _______________________________________________
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> >>
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
>
>
> ------------------------------------------------------------------------------
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