Hello there.
I am dealing with the extraction of ligand coordinates (in PDB) from
the typical autodock output file (DLG). Using simple shell routine I
can do it in just few steps:
# convert DLG to PDBQT
grep '^DOCKED' test.dlg | cut -c9- > ${output}/test.pdbqt
# convert PDBQT to PDB
Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
>
> From: Jeff Saxon [jmsstarli...@gmail.com]
> Sent: Thursday, October 15, 2020 2:34 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Protein-ligand multi-mode
Dear PyMol users,
I would like to integrate pymol in my scripting workflow in order to
save images/pymol sessions of different protein-ligand complexes.
Notably I have a typical autodock output in multi-model format of 20
ligand poses and 1 snapshot of the protein. I need to execute from the
termi
hello,
I am using educational version of Pymol to generate png image of
protein-ligand complex
First, there are no problems in the case of PNG command from pymol's
GUI. However if I run the same from script from terminal:
MacPyMOL -c -d "
from pymol import cmd
cmd.load('${pdb}')
cmd.png('
nt of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
>
>
Hello,
I am trying to install Open source version of Pymol on my mac using
recommended method. Although I've never had problems with brew, here I
got the following error message:
brew install brewsci/bio/pymol
touch: /usr/local/Homebrew/.git/FETCH_HEAD: Permission denied
touch: /usr/local/Home
Rickhaus :
>
> Have you tried running it with sudo?
>
> Cheers
> Michel
>
> On Tue, 20 Oct 2020 at 12:53, Jeff Saxon wrote:
>>
>> Hello,
>>
>> I am trying to install Open source version of Pymol on my mac using
>> recommended method. Although I
Dear Pymol Users,
I am dealing with the analysis of protein-ligand binding predicted by
Auto-Dock, mainly focusing on the visualization of ligand clusters on
the surface of the receptor.
Assuming that I have in current pymol session several distinct
clusters of ligand, would it be possible to col
> >
> > Blaine
> >
> > Blaine Mooers, Ph.D.
> > Associate Professor
> > Department of Biochemistry and Molecular Biology
> > College of Medicine
> > University of Oklahoma Health Sciences Center
> > S.L. Young Biomedical Research Center (BRC
Dear PyMol users,
I am generating png images of protein-ligand complex using png command
of pymol. This is the syntax that I am using from my bash script:
image=800
pdb='my.pdb'
# load pdb, split states, make image
MacPyMOL -c -d "
from pymol import cmd
cmd.load('${pdb}')
cmd.split_states(
iology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
>
> From: Jeff Saxon [jmsstarli...@gmail.co
. = 186.9 frames/hour (19.26 sec. accum.).
My hardware is iMAC 3.4 ghz Core i7, 16Go 13000 DDR3
I am using pymol 2.4.1 (full version)
ср, 21 окт. 2020 г. в 14:59, Jeff Saxon :
>
> thank you, Blaine!
> actually this problem only exists for the saving image of the system
> consisted of many m
just left my Mac during the night to generate images:
new benchmark record:
PyMOL>
cmd.draw(800,800);cmd.png('/img/cne_998.png',width=800,height=800,dpi=50,ray=1)
Ray: render time: 18259.74 sec. = 0.2 frames/hour (18259.74 sec. accum.).
:-)
ср, 21 окт. 2020 г. в 15:31, Jeff Sax
Dear all,
probably it is not a very pymol-oriented question, but otherwise I am
looking for people who worked with autodock tools, or maybe who dealt
with some pymol plugins suitable to handle DLG filles of AT runs?
Particularly, I am looking for some methods for
combining/reclusterization of autod
Dear Pymol Users,
I am using the Centre of mass python script found in PymolWIKI with
the aim to calculate the centre of mass of the loaded ligand
structure. Could you tell me if it would be possible to apply this
script on the multi_model pdb loaded in pymol in the similar way and
to obtain XYZ co
ormat, but
is it possible rather to modify the python script, automatically
loading all pdbs located from the current directory and save the
output automatically in the list format indicated in my first message?
сб, 7 нояб. 2020 г. в 14:16, Jeff Saxon :
>
> Dear Pymol Users,
> I am using
ofessor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
>
Sorry Blaine, I misspelled your name!
Cheers,
J.
сб, 7 нояб. 2020 г. в 16:18, Jeff Saxon :
>
> Hi Blame,
> I was talking about this pymol script (it can be downloaded directly
> from the page below)
> https://pymolwiki.org/index.php/Center_of_mass
>
> I used all of the pos
Dear Pymol Users,
I am looking for a possibility to display names of the objects in the
pymol session. For example I loaded 4 objects corresponded to 2
different positions of the same ligand as well as 2 positions of its
centres of masses. How would it be possible to display the names of
each of t
acist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
> On 22/2/21, 10:47 pm, "Jeff Saxon" wrote:
>
> Dear Pymol Users,
>
> I am looking for a possibility
the labels produced using cmd.label('sele', 'model') ? Or
alternatively I ought to rename the both objects before their
labelling? What are the other possible solutions ?
пн, 22 февр. 2021 г. в 15:07, Jeff Saxon :
>
> Right, this is what I was looking for!
> Thank yo
27;)
>
> Another way to do this is lets say you select an object beginning with
> COG_, you can slice away the first 4 characters to get rid of COG_
> label sele, model[4:]
>
> Cheers,
>
> Ali
>
> On 23/2/21, 1:32 am, "Jeff Saxon" wrote
ol the sphere sizes consistently using:
> set sphere_scale, 1.5 # or what ever size you need
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and
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