[PyMOL] View of the ligand binding site
Dear Pymol users I am looking for a possibility to automatize orientation of the camera on the ligand binding cavity working with different protein-ligand complexes. Is it possible to calculate centroid of the ligand and then orient the view of it ? Many thanks in advance Cheers, Enrico ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] setting specific state in no-gui mode
Dear Pymol Users!
I am using pymol in batch mode to select specific state from the
multi-state object and then save screen-shoot and the pse session for
it.
cmd.set('state','5','my_object*')
cmd.png('image.png',dpi=50,ray=1)
cmd.save('session.pse')
The problem is that in the pse session I may see only the selected
state. I've tried to change the states using arrows in the GUI but it
always frozen to the state selected before saving the pse session. Is
it possible via some command to reset to the default (1) state before
saving the pymol session ?
Cheers,
Enrico
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[PyMOL] handling of multiple files in batch mode
Dear Pymol Users!
My Pymol batch script loads all pdb filles from the output directory
split states and saves the pse session
pymol "${output}"/*.pdb -c -d "
from pymol import cmd
#cmd.load('${output}/*.pdb')
cmd.set('grid_mode','1')
cmd.orient()
cmd.bg_color('white')
cmd.show('sticks', 'not polymer')
cmd.show('spheres', 'not polymer')
cmd.set('stick_radius', '0.12', 'not polymer')
cmd.set('sphere_scale', '0.20', 'not polymer')
cmd.save('${output_pse}/${project}.pse')
"
1) As you may see I load the filles using bash syntax as *.pdb. Is it
possible to do it directly in the pymol script e.g. using glob ? Could
you please show me the example of such syntax?
e.g. I''e already tried #cmd.load('${output}/*.pdb')
but it did not recognize the pattern.
2) is it possible to print the name of each separate pdb in the
splitted grid display?
Many thanks in advance!
Cheers
Enrico
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[PyMOL] hydrogen-bonds detected in the protein-ligand complexes
Dear Pymol users!
Another question related to the analysis of the multi-model pdb
obtained from protein-ligand docking calculations.
I am using pymol to visualise protein-ligand interactions between each
pose predicted by docking and protein in my script:
preset.ligand_cartoon('my_pdb*',_self=cmd)
then I may use the following command to switch to the state in
multi_model pdb, which could be important:
cmd.set('state','5','my_pdb*')
Is it possible to print the number of the state which has
1) the maximal number of the hydrogen bonds?
2) has a particular hydrogen bond of my interest?
Cheers,
Enrico
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Re: [PyMOL] Analysis of docking results in multi-model format
just as an update of my first topic. Is there any possibility to associate any plugin or external tool (rdkit) to calculate pharmacophore model for each docking pose loaded in multi-model format (i) as well as for the ligand in X-ray structure (ii) and then compare i with ii in order to find instantly the docking pose which is more similar to X-ray structure according to some part of the pharmacophore shared between the both molecules ? чт, 24 мар. 2022 г. в 14:11, Enrico Martinez : > > Dear Pymol Users! > I am dealing with the analysis of the results of protein-ligand > docking poses representing the multi-model pdb. I need to find a > possibility (e.g. via some script that could be executed in the pymol) > to compare each docking pose with the X-ray structure (loaded as the > separate model in pymol) in order to find automatically the model (= > docking solution) which may fit better to it (e.g. via estimating RMSD > of some part of the ligand in each docking solution compared to the > X-ray structure). > > Assuming that the both pdbs ((docking poses, and X-ray structure)) > have been superimposed (based on the protein atoms) how could I > automatically switch to the model (in the ensemble) with the identical > position of the ligand as in the X-ray structure? I would be grateful > for any suggestions > With kind regards, > Enrico ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Analysis of docking results in multi-model format
Hello Joel, Actually I am using VINA that indeed provides us with these RMSD values. However the goal is to compare the docking poses with the X-ray structure containing another (but very similar in terms of the functional groups) ligand. I've already tried some pymol built-in commands like pair_fit but I could not adapt it to the multi-model pdb in order to select "on-the-fly" the pose which has better similarity to the pose observed in the X-ray structure. Cheers, Enrico пт, 25 мар. 2022 г. в 01:28, Joel Tyndall : > > Hi Enrico, > > Which docking protocol are you using as this may already have RMSD to a > reference ligand and presentation of best poses (based on scoring) > > Joel > > -Original Message- > From: Enrico Martinez > Sent: Friday, 25 March 2022 2:11 AM > To: pymol-users > Subject: [PyMOL] Analysis of docking results in multi-model format > > Dear Pymol Users! > I am dealing with the analysis of the results of protein-ligand docking poses > representing the multi-model pdb. I need to find a possibility (e.g. via > some script that could be executed in the pymol) to compare each docking pose > with the X-ray structure (loaded as the separate model in pymol) in order to > find automatically the model (= docking solution) which may fit better to it > (e.g. via estimating RMSD of some part of the ligand in each docking solution > compared to the X-ray structure). > > Assuming that the both pdbs ((docking poses, and X-ray structure)) have been > superimposed (based on the protein atoms) how could I automatically switch to > the model (in the ensemble) with the identical position of the ligand as in > the X-ray structure? I would be grateful for any suggestions With kind > regards, Enrico > > > ___ > PyMOL-users mailing list > Archives: > https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.netdata=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7C5801f6d4300c4429df4008da0d996aa8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637837249971556989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=%2FH4rWyrcccM8UDMCjpXhzfhvbWIRK7iVxT3WTHhd11Q%3Dreserved=0 > Unsubscribe: > https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribedata=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7C5801f6d4300c4429df4008da0d996aa8%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637837249971556989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=W1bYxrtg1zExUmoFtA3srAUsOc8PAODG2QimqwEY%2FQw%3Dreserved=0 ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Analysis of docking results in multi-model format
Dear Pymol Users! I am dealing with the analysis of the results of protein-ligand docking poses representing the multi-model pdb. I need to find a possibility (e.g. via some script that could be executed in the pymol) to compare each docking pose with the X-ray structure (loaded as the separate model in pymol) in order to find automatically the model (= docking solution) which may fit better to it (e.g. via estimating RMSD of some part of the ligand in each docking solution compared to the X-ray structure). Assuming that the both pdbs ((docking poses, and X-ray structure)) have been superimposed (based on the protein atoms) how could I automatically switch to the model (in the ensemble) with the identical position of the ligand as in the X-ray structure? I would be grateful for any suggestions With kind regards, Enrico ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] fixing atom order in multi-model pdb
Dear Pymol Users!
I am dealing with the multi-model pdb containing the docking poses
that were merged with the protein atoms. Initially the part containing
the ligand poses also included some flexible side-chains of the
receptor (obtained from VINA) that were subsequently merged ( in each
model) with the static part of the protein using some script.
The complex may be correctly visualised in pymol, however (due to the
reorganizations of the atoms in the protein part) there are some
problems in the visualisations of the interatomic interactions between
the static part of the protein and the ligands.
May we use some pymol in no-gui mode to "fix" the atomic order problem
in the loaded pdb (in each models!) and then save it as a new pdb?
Here is the model of the workflow:
pymol -c -d "
from pymol import cmddb')
cmd.load('complex.pdb')
# execute some command to fix atom order in the multi-model pdb
cmd.save('complex_fixed_pdb.pdb')
"
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[PyMOL] saving info regarding protein-ligand interactions in the log
Dear Pymol users! I am using a multi-model pdb containing the 80 predicted docking solutions as well as the receptor (the both presented in each frame). I need to calculate all hydrogen bonds (and possible other interactions) observed in each frame (=docking solution)? I've already used pymol for the visualizations of the interactions, and find it very useful for the visual inspection. May I use some pymol script in order that I could save the information regarding the observed interactions in the log file? Many thanks in advance Cheers, Enrico ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] intermezzo plugin for analysis of protein-ligand interactions
I have tried to do it in the same way and saw the same errors. I may think that it does not work with the latest pymol.. May someone suggest to me some other plugin which could be useful to describe protein-ligand contacts (electrostatic, vdW etc )? Many thanks !! Enrico пт, 18 февр. 2022 г. в 13:49, Saurabh Gayali : > > I was able to install it by downloading the zip file for the web version link > and installing inside pymol for the local file. > > > However, it shows an error for initialization: > > When using Fetch URl mode, it shows charmap error. > > > > Saurabh Gayali / Post Doctoral Fellow > saurabh.gay...@gmail.com / +91 8800412916 > > > Noida, UP, India > > > > Sender notified by > Mailtrack 18/02/22, 06:19:03 pm > > On Thu, Feb 17, 2022 at 4:16 PM Enrico Martinez > wrote: >> >> Dear Pymol Users! >> I am looking for some pymol plugin for the detailed analysis of >> protein-ligand interactions. I have already seen: >> http://mordred.bioc.cam.ac.uk/intermezzo/ >> but I could not understand how I could install it ( I am using pymol >> 2.4 pro installed on my MACBOOK and it seems to me that the package >> had been developed for the previous release). >> >> On the site I found: >> >> "Additionally, it will soon also be possible to install the plugin >> using the "Install from PyMOLWiki" and "Install from Repository" >> sections." >> >> but eventually I could not find it in pymolWIKI. >> >> May you suggest some other solutions which would work with my pymol version ? >> >> Many thanks in advance >> Enrico >> >> >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] intermezzo plugin for analysis of protein-ligand interactions
Dear Pymol Users! I am looking for some pymol plugin for the detailed analysis of protein-ligand interactions. I have already seen: http://mordred.bioc.cam.ac.uk/intermezzo/ but I could not understand how I could install it ( I am using pymol 2.4 pro installed on my MACBOOK and it seems to me that the package had been developed for the previous release). On the site I found: "Additionally, it will soon also be possible to install the plugin using the "Install from PyMOLWiki" and "Install from Repository" sections." but eventually I could not find it in pymolWIKI. May you suggest some other solutions which would work with my pymol version ? Many thanks in advance Enrico ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] visualisations of the hydrogen bonds using preset.ligand_cartoon
Dear Pymol Users!
I wonder to ask regarding the algorithm implemented in pymol for the
calculation of the hydrogen bonds between ligand and protein using
preset.ligand_cartoon demonstrating the interactions?
I've just compared predicted hydrogen bonds for the same complex that
I could observe with Chim*ra and found that there were differences:
pymol tends to predict more hydrogen bonds considering additional
interactions located on the longer distances. Are there some built-in
commands in pymol that would allow me to modulate geometrical criteria
(cut-offs?) for the hydrogen bonds search assuming that I am operating
with multi-model pdb (results of docking) using command:
preset.ligand_cartoon('my_pdb*',_self=cmd)
Many thanks in advance
Cheers
Enrico
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Re: [PyMOL] distance-based selection of the side-chains
You are right, thank you!
Cheers,
Enrico
чт, 27 янв. 2022 г. в 13:32, Ali Saad Kusay :
>
> Hi Enrico,
>
> I think it's because you are selecting side chains, glycine has no sidechain
> and alanine has single carbon atom side chain so this representation won't
> work for it. You would need to remove the sidechains from the selection to
> make it apply to the backbone atoms, i.e. cmd.select('rep lines and poly)
>
> Cheers,
>
> Ali
>
> On 27/1/22, 11:22 pm, "Enrico Martinez" wrote:
>
> additional question in the same field:
> as I've mentioned before, before applying distance-based filtering, I
> would like to change the representation of the lines to ball-and-stick
> for the residues involved in the interactions:
> cmd.select('rep lines and sidechain')
> cmd.show_as('sticks', 'sele')
> cmd.set('stick_radius', '0.10')
> cmd.set('stick_ball', 'on')
> cmd.set('stick_ball_ratio', '2.2')
>
> I've just noticed that some residues remain their "line"
> representation, notably for hydrophobic (Gly, Ala) residues. How could
> it be fixed ?
>
> чт, 27 янв. 2022 г. в 12:38, Enrico Martinez :
> >
> > Thank you very much, Ali!!
> > Cheers,
> > Enrico
> >
> > чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay
> :
> > >
> > > Hi Enrico,
> > >
> > > You need to use the byres or br. Selection
> (https://protect-au.mimecast.com/s/4MzUCROND2uvY6pqpi9A9Zw?domain=pymolwiki.org)
> > >
> > > I.e:
> > > cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
> > >
> > > Also, consider hiding all protein residues and showing only the ones
> near the protein, i.e.:
> > > cmd.show('sticks','br. poly within 4 of resn XXX')
> > > ^ Where 4 is the distance and XXX should be substituted with the
> residue name of the ligand
> > >
> > > Cheers,
> > >
> > > Ali
> > >
> > > On 27/1/22, 10:12 pm, "Enrico Martinez"
> wrote:
> > >
> > > Dear Pymol Users!
> > > I am working on the visualization of the protein-ligand contacts
> > > identified using
> > > preset.ligand_cartoon('pdb',_self=cmd)
> > > Since the command also displays some residues, which are not
> involved
> > > in the interactions (with the radicals located too far away) with
> the
> > > ligand, I need to filter the displayed side-chains focusing only
> on
> > > the important interactions. I am using a distance-based criterion
> for
> > > the selection of the residues which I am going to hide.
> > >
> > > this is what I've already tried:
> > >
> > > # display visible side chains as the sticks
> > > cmd.select('rep lines and visible and sidechain')
> > > cmd.show('sticks', 'sele')
> > > # select all visible sticks of the sidechains far away from the
> ligand
> > > cmd.select('sidechain & (rep sticks & visible beyond 4 of not
> polymer)')
> > > cmd.hide('everything', 'sele')
> > >
> > > the problem is that the "select" command with such syntax, always
> > > selects the ATOMS, but not the whole side-chains. Is it possible
> to
> > > hide the whole side-chain using such syntax as well as it's
> displayed
> > > label?
> > > Many thanks in advance!
> > > Enrico
> > >
> > >
> > > ___
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> https://protect-au.mimecast.com/s/_G8ICVARKgCxBJEoESz5b82?domain=mail-archive.com
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> > >
> > >
>
>
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Re: [PyMOL] distance-based selection of the side-chains
additional question in the same field:
as I've mentioned before, before applying distance-based filtering, I
would like to change the representation of the lines to ball-and-stick
for the residues involved in the interactions:
cmd.select('rep lines and sidechain')
cmd.show_as('sticks', 'sele')
cmd.set('stick_radius', '0.10')
cmd.set('stick_ball', 'on')
cmd.set('stick_ball_ratio', '2.2')
I've just noticed that some residues remain their "line"
representation, notably for hydrophobic (Gly, Ala) residues. How could
it be fixed ?
чт, 27 янв. 2022 г. в 12:38, Enrico Martinez :
>
> Thank you very much, Ali!!
> Cheers,
> Enrico
>
> чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay :
> >
> > Hi Enrico,
> >
> > You need to use the byres or br. Selection
> > (https://pymolwiki.org/index.php/Selection_Algebra)
> >
> > I.e:
> > cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
> >
> > Also, consider hiding all protein residues and showing only the ones near
> > the protein, i.e.:
> > cmd.show('sticks','br. poly within 4 of resn XXX')
> > ^ Where 4 is the distance and XXX should be substituted with the residue
> > name of the ligand
> >
> > Cheers,
> >
> > Ali
> >
> > On 27/1/22, 10:12 pm, "Enrico Martinez" wrote:
> >
> > Dear Pymol Users!
> > I am working on the visualization of the protein-ligand contacts
> > identified using
> > preset.ligand_cartoon('pdb',_self=cmd)
> > Since the command also displays some residues, which are not involved
> > in the interactions (with the radicals located too far away) with the
> > ligand, I need to filter the displayed side-chains focusing only on
> > the important interactions. I am using a distance-based criterion for
> > the selection of the residues which I am going to hide.
> >
> > this is what I've already tried:
> >
> > # display visible side chains as the sticks
> > cmd.select('rep lines and visible and sidechain')
> > cmd.show('sticks', 'sele')
> > # select all visible sticks of the sidechains far away from the ligand
> > cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
> > cmd.hide('everything', 'sele')
> >
> > the problem is that the "select" command with such syntax, always
> > selects the ATOMS, but not the whole side-chains. Is it possible to
> > hide the whole side-chain using such syntax as well as it's displayed
> > label?
> > Many thanks in advance!
> > Enrico
> >
> >
> > ___
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> > Archives:
> > https://protect-au.mimecast.com/s/utRJClx1Nji2GrWxqIGRZsc?domain=mail-archive.com
> > Unsubscribe:
> > https://protect-au.mimecast.com/s/XwNECmO5glujXxVzLuOSHPJ?domain=sourceforge.net
> >
> >
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Re: [PyMOL] distance-based selection of the side-chains
Thank you very much, Ali!!
Cheers,
Enrico
чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay :
>
> Hi Enrico,
>
> You need to use the byres or br. Selection
> (https://pymolwiki.org/index.php/Selection_Algebra)
>
> I.e:
> cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
>
> Also, consider hiding all protein residues and showing only the ones near the
> protein, i.e.:
> cmd.show('sticks','br. poly within 4 of resn XXX')
> ^ Where 4 is the distance and XXX should be substituted with the residue name
> of the ligand
>
> Cheers,
>
> Ali
>
> On 27/1/22, 10:12 pm, "Enrico Martinez" wrote:
>
> Dear Pymol Users!
> I am working on the visualization of the protein-ligand contacts
> identified using
> preset.ligand_cartoon('pdb',_self=cmd)
> Since the command also displays some residues, which are not involved
> in the interactions (with the radicals located too far away) with the
> ligand, I need to filter the displayed side-chains focusing only on
> the important interactions. I am using a distance-based criterion for
> the selection of the residues which I am going to hide.
>
> this is what I've already tried:
>
> # display visible side chains as the sticks
> cmd.select('rep lines and visible and sidechain')
> cmd.show('sticks', 'sele')
> # select all visible sticks of the sidechains far away from the ligand
> cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
> cmd.hide('everything', 'sele')
>
> the problem is that the "select" command with such syntax, always
> selects the ATOMS, but not the whole side-chains. Is it possible to
> hide the whole side-chain using such syntax as well as it's displayed
> label?
> Many thanks in advance!
> Enrico
>
>
> ___
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>
>
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[PyMOL] distance-based selection of the side-chains
Dear Pymol Users!
I am working on the visualization of the protein-ligand contacts
identified using
preset.ligand_cartoon('pdb',_self=cmd)
Since the command also displays some residues, which are not involved
in the interactions (with the radicals located too far away) with the
ligand, I need to filter the displayed side-chains focusing only on
the important interactions. I am using a distance-based criterion for
the selection of the residues which I am going to hide.
this is what I've already tried:
# display visible side chains as the sticks
cmd.select('rep lines and visible and sidechain')
cmd.show('sticks', 'sele')
# select all visible sticks of the sidechains far away from the ligand
cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
cmd.hide('everything', 'sele')
the problem is that the "select" command with such syntax, always
selects the ATOMS, but not the whole side-chains. Is it possible to
hide the whole side-chain using such syntax as well as it's displayed
label?
Many thanks in advance!
Enrico
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Re: [PyMOL] problem with ray of PNG using pymol in non-gui mode
yep, it is not possible actually to switch off the Ray using no-gui mode in
pymol ( i've just read another topic on this case). BTW I found that the
problem of the disappearing of carton is mor related to the transparency,
since it had already been set for the surface as well. In the case when I
set it both for cartoon and surface, the cartoon diagram is lost :-)
here is my script:
cmd.set('transparency_mode','1')
cmd.set('transparency', '0.7', '${output}* and polymer')
cmd.set('cartoon_transparency', '0.3', '${output}* and polymer')
пт, 21 янв. 2022 г. в 05:40, Saurabh Gayali :
> Have you tried setting ray_trace_mode?
> Info here: https://pymolwiki.org/index.php/Ray
>
> --
>
> *Saurabh Gayali* / Post Doctoral Fellow
> saurabh.gay...@gmail.com / +91 8800412916
>
> *CSIR-IGIB*
> <http://example.com/>New Delhi, India
>
>
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> 21/01/22,
> 10:10:28 am
>
> On Thu, Jan 20, 2022 at 11:02 PM Enrico Martinez
> wrote:
>
>> Dear Pymol Users!
>> I've faced the problem of saving a PNG image without ray using the png
>> command in non-gui mode. First if I do it in pymol gui
>> #cmd.png('test.png',width=800,height=800,ray=0)
>> .. it produces fine image (without ray)
>>
>> However if I execute the same command inside of my bash sript:
>>
>> $pymol -c -d "
>> from pymol import cmd
>> from pymol import preset
>> cmd.load('my_pdb.pdb')
>> cmd.show('surface', 'my_pdb and polymer')
>> cmd.set('surface_color', 'default', 'my_pdb and polymer')
>> cmd.set('transparency', '0.8', 'my_pdb and polymer')
>> cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
>>
>> cmd.png('${vizu}/${output}_${lig_name}_interact_rep${i}.png',width=${image},height=${image},ray=0)
>> "
>>
>> Eventually It produces the correct pymol session but on the PNG image
>> I do not see any cartoon representation (only transparent surface) of
>> my protein. I did some tests and found that using non-gui mode (like
>> in the script shown above) pymol always sets the ray flag to ray=1
>> even if it is disabled in my script. Is there any way to disable ray
>> (ray=0) in my script besides setting it in the cmd.png?
>> Many thanks in advance!
>> Enrico
>>
>>
>> ___
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[PyMOL] problem with ray of PNG using pymol in non-gui mode
Dear Pymol Users!
I've faced the problem of saving a PNG image without ray using the png
command in non-gui mode. First if I do it in pymol gui
#cmd.png('test.png',width=800,height=800,ray=0)
.. it produces fine image (without ray)
However if I execute the same command inside of my bash sript:
$pymol -c -d "
from pymol import cmd
from pymol import preset
cmd.load('my_pdb.pdb')
cmd.show('surface', 'my_pdb and polymer')
cmd.set('surface_color', 'default', 'my_pdb and polymer')
cmd.set('transparency', '0.8', 'my_pdb and polymer')
cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
cmd.png('${vizu}/${output}_${lig_name}_interact_rep${i}.png',width=${image},height=${image},ray=0)
"
Eventually It produces the correct pymol session but on the PNG image
I do not see any cartoon representation (only transparent surface) of
my protein. I did some tests and found that using non-gui mode (like
in the script shown above) pymol always sets the ray flag to ray=1
even if it is disabled in my script. Is there any way to disable ray
(ray=0) in my script besides setting it in the cmd.png?
Many thanks in advance!
Enrico
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[PyMOL] ball-and-stick representatation of the ligand and non-polar contacts
I am using the combination of two presets to visualise protein-ligand
interactions:
1) to visualise protein-ligand contacts
preset.ligand_cartoon('${output}*',_self=cmd)
2) and then to change the representation of the ligand:
preset.ball_and_stick(selection='my_system and not polymer', mode=1)
Unfortunately after the execution of the second command I do not see
anymore dashed yellow lines for non-polar contacts between protein and
ligand
Is there any quick command, which may return it for a multi-model file
and better to change the color of the dotted line from yellow
(default) to another color (blue)?
Thank you in advance!
Enrico
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[PyMOL] How may I color surface using spectral palette ?
Dear All,
I am working on the visualization of the transparent surface in my
model. For the moment I found only one possibility for non-monotone
coloring palette of the surface, using
cmd.set('surface_color', 'default')
How may I color the surface using some spectrum (e.g. from orange to
yellow) or alternatively according to the electrostatic properties of
the amino-acids?
Thank you in advance
Enrico
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[PyMOL] conversion of the small molecules from sdf to mol2
Dear Pymol users, dear Friends!
I have a question regarding file conversion of the small organic
molecules, which is not directly related to pymol but I believe that I
may use it for the solution.
I am dealing with the conversion of SDF file (2d formulas) to mol2
format (3d coordinates)
Usually I use it in one line command with babel
obabel --gen3d -isdf ligands.sdf -omol2 > ligands.mol2
It creates a multi-model mol2 file, that I may open in pymol and split
the molecules manually using split_states command:
pymol ligands.mol2
cmd.split_states('ligands', 'prefix=conf')
This creates several separate objects conf0001, conf0002 etc that I
may save as the individual mol2.
Alternatively I may obtain individual mol2 filles for each model of the SDF:
obabel ./ligands.sdf -O ./babel/conf.mol2 --gen3d -m
which creates separate files conf1.mol2 , conf2.mol2 .. confN.mol2
that I may load in pymol in one command from terminal
pymol ./babel/conf*.mol2
The problem that the name of the initial model stored in the initial sdf, as:
name_of_the_ligand
always lost during conversion from sdf to mol2 (regardless of the way
of the conversion). So the mol2 files always lack their initials
defined from sdf :-)
Could you suggest some trick to associate the name of the model (From
initial sdf) to the corresponding object loaded in pymol or
alternatively keep them during the conversion?
Many thanks in advance!
Enrico
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Re: [PyMOL] Set label for visible amino acids
Dear Vijay,
thank you very much, it works very good. Magic! :-)
Cheers,
Enrico
ср, 12 янв. 2022 г. в 13:53, Dr. Vijay Masand :
>
> Dear Enrico
> Use the following command:
> label n. CA & all within 5 of organic, "%s%s" % (resn,resi)
> The above command will label all CA atoms within 5 angstrom from Organic
> molecule with residue number and name.
> I have collected a good number of commands for showing ligand-protein
> complexes.
>
> With Warm Regards
> Dr. Vijay H. Masand
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/
>
>
>
> On Wed, Jan 12, 2022 at 5:55 PM Enrico Martinez
> wrote:
>>
>> exactly we may do it in the context meny for the particular selection
>> (we do not need to select a particular residues, so ..)
>> but may we create the same label using label command as well ??
>> cmd.label('sele', 'resn')
>> I think something should be used instead of 'resn'. there is also
>> option 'resi' which shows only the number of the amino acid. So I need
>> to combine "resn" and "resi"
>> :-)
>>
>> вт, 11 янв. 2022 г. в 21:27, Oganesyan, Vaheh
>> :
>> >
>> > For label like ‘R87’ I manually do “label /s309/B/H/ARG`87/CA, ‘R87’”
>> >
>> >
>> >
>> > Vaheh
>> >
>> >
>> >
>> > From: Enrico Martinez
>> > Sent: Tuesday, January 11, 2022 12:34 PM
>> > To: pymol-users
>> > Subject: [PyMOL] Set label for visible amino acids
>> >
>> >
>> >
>> > Dear Pymol users!
>> > Here is the chain of the pymol commands that I am using to label the
>> > visible amino-acids shown as lines in the current pymol session.
>> > cmd.select('name CA and rep lines')
>> > cmd.label('sele', 'resn')
>> > cmd.set('label_font_id', '14')
>> > cmd.set('label_color', 'indigo')
>> > cmd.set('label_position', '3,0,0')
>> > It produces nice labeling according to the amino acid name (example
>> > Tyr). How it would be possible to indicate additionally the number of
>> > the amino acid like Tyr-119 or simply using one letter code + the
>> > number?
>> > Many thanks in advance
>> > Enrico
>> >
>> >
>> > ___
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>> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> > Unsubscribe:
>> > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>> ___
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Re: [PyMOL] Set label for visible amino acids
exactly we may do it in the context meny for the particular selection
(we do not need to select a particular residues, so ..)
but may we create the same label using label command as well ??
cmd.label('sele', 'resn')
I think something should be used instead of 'resn'. there is also
option 'resi' which shows only the number of the amino acid. So I need
to combine "resn" and "resi"
:-)
вт, 11 янв. 2022 г. в 21:27, Oganesyan, Vaheh :
>
> For label like ‘R87’ I manually do “label /s309/B/H/ARG`87/CA, ‘R87’”
>
>
>
> Vaheh
>
>
>
> From: Enrico Martinez
> Sent: Tuesday, January 11, 2022 12:34 PM
> To: pymol-users
> Subject: [PyMOL] Set label for visible amino acids
>
>
>
> Dear Pymol users!
> Here is the chain of the pymol commands that I am using to label the
> visible amino-acids shown as lines in the current pymol session.
> cmd.select('name CA and rep lines')
> cmd.label('sele', 'resn')
> cmd.set('label_font_id', '14')
> cmd.set('label_color', 'indigo')
> cmd.set('label_position', '3,0,0')
> It produces nice labeling according to the amino acid name (example
> Tyr). How it would be possible to indicate additionally the number of
> the amino acid like Tyr-119 or simply using one letter code + the
> number?
> Many thanks in advance
> Enrico
>
>
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Re: [PyMOL] Visualisation of protein-ligand interactions using cmd
I've just found the list of the presets:
https://pymolwiki.org/index.php/Preset
so a new question is still about preset.ligand_cartoon.
It works well, but shows me too much information. Is it possible to
limit the set of the identified residues e.g. to indicating only the
residues involved in the hydrogen bonds/ salt bridges?
Thank you in advance!
Enrico
вт, 11 янв. 2022 г. в 18:10, Enrico Martinez :
>
> Thank you very much Jared!
> Could you tell me if you have some cool present for the surface
> representations ?
>
> For example I am using the following script to visualize the surface
> of the protein around the ligand binding site:
> cmd.show('surface', 'polymer within 15 of complex* and not polymer')
> cmd.set('surface_color','marine','polymer')
> cmd.set('transparency', '0.4')
> cmd.hide('cartoon', 'all')
> cmd.png('image.png',width=${image},height=${image},dpi=50,ray=1)
>
> It produces a good looking image but the surface looks monotone. How
> could I improve its representation using some preset??
> Cheers,
> Enrico
>
> вт, 11 янв. 2022 г. в 15:58, Jared Sampson :
> >
> > Hi Enrico -
> >
> > If you want to reproduce GUI actions programmatically, you can see what
> > happens under the hood for most things by opening a log file:
> >
> > log_open log.pml
> >
> > then perform the desired action and the Python API version of the
> > corresponding command will be written to the log file. For example, for
> > the ligand sites > cartoon action menu item, this would be:
> >
> > preset.ligand_cartoon("myobject",_self=cmd)
> >
> > If you want to use this in a script I think you'll also have to do:
> >
> > from pymol import preset
> >
> > Hope that helps.
> >
> > Cheers,
> > Jared
> >
> >
> > On Tue, Jan 11, 2022 at 5:21 AM Enrico Martinez
> > wrote:
> >>
> >> Dear Pymol Users!
> >> Is it possible to visualize protein-ligand interactions (which
> >> normally is achieved in GUI via a - > present -> ligand sites
> >> using some combination of the pymol commands, which could be scripted
> >> using cmd. syntax ?
> >> I've found this explanation
> >> https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts
> >> but did not understand quite well how it works.
> >> I would be grateful for the example of the commands which show the
> >> polar contacts (I am mostly interested in hydrogen bonds) in my pymol
> >> session without calling each time the GUI menu.
> >> Many thanks in advance!
> >> Enrico
> >>
> >>
> >> ___
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[PyMOL] Set label for visible amino acids
Dear Pymol users!
Here is the chain of the pymol commands that I am using to label the
visible amino-acids shown as lines in the current pymol session.
cmd.select('name CA and rep lines')
cmd.label('sele', 'resn')
cmd.set('label_font_id', '14')
cmd.set('label_color', 'indigo')
cmd.set('label_position', '3,0,0')
It produces nice labeling according to the amino acid name (example
Tyr). How it would be possible to indicate additionally the number of
the amino acid like Tyr-119 or simply using one letter code + the
number?
Many thanks in advance
Enrico
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Re: [PyMOL] Visualisation of protein-ligand interactions using cmd
Thank you very much Jared!
Could you tell me if you have some cool present for the surface
representations ?
For example I am using the following script to visualize the surface
of the protein around the ligand binding site:
cmd.show('surface', 'polymer within 15 of complex* and not polymer')
cmd.set('surface_color','marine','polymer')
cmd.set('transparency', '0.4')
cmd.hide('cartoon', 'all')
cmd.png('image.png',width=${image},height=${image},dpi=50,ray=1)
It produces a good looking image but the surface looks monotone. How
could I improve its representation using some preset??
Cheers,
Enrico
вт, 11 янв. 2022 г. в 15:58, Jared Sampson :
>
> Hi Enrico -
>
> If you want to reproduce GUI actions programmatically, you can see what
> happens under the hood for most things by opening a log file:
>
> log_open log.pml
>
> then perform the desired action and the Python API version of the
> corresponding command will be written to the log file. For example, for the
> ligand sites > cartoon action menu item, this would be:
>
> preset.ligand_cartoon("myobject",_self=cmd)
>
> If you want to use this in a script I think you'll also have to do:
>
> from pymol import preset
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Tue, Jan 11, 2022 at 5:21 AM Enrico Martinez
> wrote:
>>
>> Dear Pymol Users!
>> Is it possible to visualize protein-ligand interactions (which
>> normally is achieved in GUI via a - > present -> ligand sites
>> using some combination of the pymol commands, which could be scripted
>> using cmd. syntax ?
>> I've found this explanation
>> https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts
>> but did not understand quite well how it works.
>> I would be grateful for the example of the commands which show the
>> polar contacts (I am mostly interested in hydrogen bonds) in my pymol
>> session without calling each time the GUI menu.
>> Many thanks in advance!
>> Enrico
>>
>>
>> ___
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>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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[PyMOL] Visualisation of protein-ligand interactions using cmd
Dear Pymol Users! Is it possible to visualize protein-ligand interactions (which normally is achieved in GUI via a - > present -> ligand sites using some combination of the pymol commands, which could be scripted using cmd. syntax ? I've found this explanation https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts but did not understand quite well how it works. I would be grateful for the example of the commands which show the polar contacts (I am mostly interested in hydrogen bonds) in my pymol session without calling each time the GUI menu. Many thanks in advance! Enrico ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] visualisation of ligand conformations predicted in Docking
Dear Pymol Users! I am working on the visualization of the ligand binding poses predicted by protein-ligand docking. Having 88 solutions I split these states into different states and then set transparency=0.8 to each of them, in order to visualize them as the "cloud" of the conformational space of the ligand predicted in docking. I also selected the best docking pose (always the first model) and colored it in Red without the transparency. The problem is that, during the visualization, on the png graph, the best docking pose looks to be on the second plane compared to others (transparent) poses. How could I always move this model on the first plane compared to other aligned ligand poses? P.S. I tried to enclose the PNG to my message but it seems that it could not pass the moderator filter .. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] surface representation of the protein-ligand interactions
Right, thank you, Blaine!
It works very well now! Actually there was a problem in the selection
from my part so..
I will play with the surfaces a little bit and then will update this
topic with my questions :-)
Cheers,
Enrico
пн, 10 янв. 2022 г. в 16:25, Mooers, Blaine H.M. (HSC)
:
>
> Hi Enrico,
>
> You do not need the first line of your script.
>
> This one-liner worked for me in the terminal.
>
> pymol -c -d
> "cmd.fetch('3nd3');cmd.show('surface');cmd.set('transparency','0.5');cmd.save('surf.pse');cmd.png('surf.png')"
>
> You might test reversing the order of the cmd.png() and cmd.save() commands.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
>
> From: Ali Saad Kusay via PyMOL-users [pymol-users@lists.sourceforge.net]
> Sent: Monday, January 10, 2022 8:48 AM
> To: Enrico Martinez
> Cc: pymol-users
> Subject: [EXTERNAL] Re: [PyMOL] surface representation of the protein-ligand
> interactions
>
> Hi Enrico,
>
> This is beyond my understanding, try and run this bash script without making
> the surface transparent (to figure out if the issue comes from the
> transparency)
>
> Also try the rebuild command before saving the image:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Rebuild=DwIGaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh=QM8ZtM6vxjrnYB0Cs6BSV-M8WweuPuuTS1xLMGYQdKU=
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
> On 10/1/22, 11:10 pm, "Enrico Martinez" wrote:
>
> Thank you very much,Ali!
> just one question: when I do the surface calculations using bash
> script operating with the command lines of the pymol it produces
> correctly pse session with the surfaces. BUT if I save an image using
> png, the surface is totally absent. Here are my commands directly from
> the shell script:
>
> $pymol -c -d "
> from pymol import cmd
> cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
> cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
> and not polymer' )
> cmd.set( 'transparency', '0.5' )
> cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
>
> cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
> "
> As the result of this workflow, the surface is present in the PSE
> file but not in the png image. Otherwise when I save png directly from
> the pymol's GUI the surface is well captured on the png as well. What
> should I include in my script ?
>
> пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay :
> >
> > Hi Enrico,
> >
> > You can carve the protein surface around the ligand, i.e. show only the
> surface behind the ligand, see this guide:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_1Of6CNLJyQU0W9yVofmRSV0-3Fdomain-3Dpymol.org=DwIGaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh=eU60ct3XrRn6e7JdG6JrHLyikGkuUbzJY35JQFXvTv8=
> >
> > You can also try and made the surface more transparent, but this
> doesn't always give the best results, see:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_vdsUCOMKzVTp8wQ53fvOudq-3Fdomain-3Dpymolwiki.org=DwIGaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh=pOFWGOP750OszaW7BCL8qGLr_VvBCCumHmvodMSYBeo=
> , i.e.:
> >
> > set
Re: [PyMOL] surface representation of the protein-ligand interactions
Thank you very much,Ali!
just one question: when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
the shell script:
$pymol -c -d "
from pymol import cmd
cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
and not polymer' )
cmd.set( 'transparency', '0.5' )
cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
"
As the result of this workflow, the surface is present in the PSE
file but not in the png image. Otherwise when I save png directly from
the pymol's GUI the surface is well captured on the png as well. What
should I include in my script ?
пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay :
>
> Hi Enrico,
>
> You can carve the protein surface around the ligand, i.e. show only the
> surface behind the ligand, see this guide:
> https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces
>
> You can also try and made the surface more transparent, but this doesn't
> always give the best results, see:
> https://pymolwiki.org/index.php/Transparency, i.e.:
>
> set transparency, 0.5
>
> It would help to see an image of what you are working with atm
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 10/1/22, 10:10 pm, "Enrico Martinez" wrote:
>
> Dear Pymol users!
> Working on the vizualisation of the protein-ligand interactions I
> would like to switch from cartoon to the surface representation of the
> protein, while still being capable to see the ligand-binding cavity
> (as well as non-covalent interactions)
>
> Could you suggest me some combination of the options which could helps
> me with such vizualisaiton?
> I have alread tried
> show surface, all within 5 of my_pdb and not polymer
> set surface_smooth_edges, onset surface_smooth_edges, on
> where my_pdb and not polymer corresponds to the selection of the ligand
>
> Eventualy this create cool surface representation of the protein and
> but completely hides the ligand-binding cavity
> Many thanks in advance!
> Enrico
>
>
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[PyMOL] surface representation of the protein-ligand interactions
Dear Pymol users! Working on the vizualisation of the protein-ligand interactions I would like to switch from cartoon to the surface representation of the protein, while still being capable to see the ligand-binding cavity (as well as non-covalent interactions) Could you suggest me some combination of the options which could helps me with such vizualisaiton? I have alread tried show surface, all within 5 of my_pdb and not polymer set surface_smooth_edges, onset surface_smooth_edges, on where my_pdb and not polymer corresponds to the selection of the ligand Eventualy this create cool surface representation of the protein and but completely hides the ligand-binding cavity Many thanks in advance! Enrico ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] how to create multi-model pdb for protein-ligand complex?
try this man!
awk 'NR==FNR {s = s $0 ORS; next} $0 == "ENDMDL" {$0 = s $0} 1'
./receptor.pdb ./docking.pdb >> together.pdb
пт, 7 янв. 2022 г. в 18:10, Saurabh Gayali :
> I guess we need to split the docking poses first and then merge them
> together.
> Hope I come up with a python script or anyone else does.
>
> On Fri, 7 Jan, 2022, 18:47 Enrico Martinez,
> wrote:
>
>> In the case of
>> cmd.save("together.pdb", "all", "0", "pdb")
>> it saves everything in one pdb when the protein is present only in the
>> first model, while I need to obtain its representation in all models
>> Cheers
>> E.
>>
>> пт, 7 янв. 2022 г. в 13:14, Saurabh Gayali :
>>
>>> Have you tried the save command after opening both files?
>>> https://pymol.org/dokuwiki/doku.php?id=command:save
>>> Though not sure how the different poses will merge.
>>> Also looking for a solution for a similar problem.
>>>
>>> --
>>>
>>> *Saurabh Gayali* / Post Doctoral Fellow
>>> saurabh.gay...@gmail.com / +91 8800412916
>>>
>>> *CSIR-IGIB*
>>> <http://example.com/>New Delhi, India
>>>
>>>
>>> [image: Mailtrack]
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>> Sender
>>> notified by
>>> Mailtrack
>>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
>>> 07/01/22,
>>> 05:43:49 pm
>>>
>>> On Fri, Jan 7, 2022 at 3:43 PM Enrico Martinez
>>> wrote:
>>>
>>>> Dear Autodock Users!
>>>> I am dealing with the structural analysis of the protein-ligand
>>>> interactions observed in the protein-ligand docking using VINA.
>>>> Basically operating with the outputs I have two different pdb files:
>>>> 1) for docking receptor (1 protein model) as well as for 2) docking
>>>> sollutions (100 solutions). So I use pymol to open the both filles and
>>>> visualize them
>>>>
>>>> pymol sollutions.pdb receptor.pdb
>>>>
>>>> May you suggest me some pymol command to merge the both in the pymol
>>>> to. create multi-model PDB consisted of the both receptor and ligand
>>>> poses in order then I could perform some structural analysis of this
>>>> combined complex?
>>>> Many thanks in advance
>>>> Enrico
>>>>
>>>>
>>>> ___
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>>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>>
>>>
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Re: [PyMOL] how to create multi-model pdb for protein-ligand complex?
In the case of
cmd.save("together.pdb", "all", "0", "pdb")
it saves everything in one pdb when the protein is present only in the
first model, while I need to obtain its representation in all models
Cheers
E.
пт, 7 янв. 2022 г. в 13:14, Saurabh Gayali :
> Have you tried the save command after opening both files?
> https://pymol.org/dokuwiki/doku.php?id=command:save
> Though not sure how the different poses will merge.
> Also looking for a solution for a similar problem.
>
> --
>
> *Saurabh Gayali* / Post Doctoral Fellow
> saurabh.gay...@gmail.com / +91 8800412916
>
> *CSIR-IGIB*
> <http://example.com/>New Delhi, India
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
> Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;>
> 07/01/22,
> 05:43:49 pm
>
> On Fri, Jan 7, 2022 at 3:43 PM Enrico Martinez
> wrote:
>
>> Dear Autodock Users!
>> I am dealing with the structural analysis of the protein-ligand
>> interactions observed in the protein-ligand docking using VINA.
>> Basically operating with the outputs I have two different pdb files:
>> 1) for docking receptor (1 protein model) as well as for 2) docking
>> sollutions (100 solutions). So I use pymol to open the both filles and
>> visualize them
>>
>> pymol sollutions.pdb receptor.pdb
>>
>> May you suggest me some pymol command to merge the both in the pymol
>> to. create multi-model PDB consisted of the both receptor and ligand
>> poses in order then I could perform some structural analysis of this
>> combined complex?
>> Many thanks in advance
>> Enrico
>>
>>
>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>
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[PyMOL] how to create multi-model pdb for protein-ligand complex?
Dear Autodock Users! I am dealing with the structural analysis of the protein-ligand interactions observed in the protein-ligand docking using VINA. Basically operating with the outputs I have two different pdb files: 1) for docking receptor (1 protein model) as well as for 2) docking sollutions (100 solutions). So I use pymol to open the both filles and visualize them pymol sollutions.pdb receptor.pdb May you suggest me some pymol command to merge the both in the pymol to. create multi-model PDB consisted of the both receptor and ligand poses in order then I could perform some structural analysis of this combined complex? Many thanks in advance Enrico ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Analysis of protein-ligand interactions
Dear Pymol users! I am performing analysis of protein-ligand interactions for the ligand pose established in protein-docking and comparing it with the pattern observed in the X-ray structure for the same complex. Is it possible to use some Pymol command in the pymol's command line to save (in the text log) all of the non-bonded interactions established between ligand and all of the surrounded groups of the receptor for two different selections: (1) between the conformation used for docking and the best docking pose (2) between the X-ray structure + it's (native) ligand pose assuming that ((1): two different objects for receptor.pdb and the ensemble of docking conformations) and ((2): one object consisting of ligand and receptor together) are loaded in Pymol. Many thanks in advance! Cheers Enrico ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
