Re: [PyMOL] Cartoon visualization of per-residue txt data

[Tsjerk Wassenaar]

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"  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 :
> > 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 :
> >> 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 :
> >>> > 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 :
> >>> >> 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
> >>> >> 
> >>> >> wrote:
> >>> >>>
> >>> >>> so to be more precise the issue is how to ad

Re: [PyMOL] Cartoon visualization of per-residue txt data

[Thomas Holder]

Hi James,

"ss" is a reserved keyword of the selection language, so you should not use it 
as the name of an object or selection.

Cheers,
  Thomas

On 12 Apr 2015, at 09:24, James Starlight  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

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
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
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
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Cartoon visualization of per-residue txt data

[James Starlight]

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 :
> 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 :
>> 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 
>> 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 :
>>> > 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 :
>>> >> 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
>>> >> 
>>> >> 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
>>

Re: [PyMOL] Cartoon visualization of per-residue txt data

[James Starlight]

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 :
> 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 
> 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 :
>> > 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 :
>> >> 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
>> >> 
>> >> 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 

Re: [PyMOL] Cartoon visualization of per-residue txt data

[James Starlight]

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 :
> 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 :
>> 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 
>> 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
>>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
>>> event?ut

Re: [PyMOL] Cartoon visualization of per-residue txt data

[James Starlight]

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 :
> 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 
> 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
>> 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
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

--
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
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
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Cartoon visualization of per-residue txt data

[Osvaldo Martin]

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 
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
> 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
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
​
--
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
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___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] Cartoon visualization of per-residue txt data

[James Starlight]

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
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
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net