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
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
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')
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:
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
> d
ng 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 r
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
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)
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
, 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
&
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
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
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:
&
')
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 :
>
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,
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
ia
>
>
> [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;>
> 21/01/22,
> 10:10:
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:
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)
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)
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
ti, 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
>> (w
' 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 Ma
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 vis
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')
k 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 (
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
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
ral 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:
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 p
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
e 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 onl
fied 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
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
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
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