Dear PyMol Users
While working with a ligand in a pdb file, which I saved in .mol2 file
format, I used following command:
get_bond stick_transparency, *
I observed following outcome in Pymol.
Getting: stick_transparency for 63 bonds in
object "testing".
Dear PyMol Users,
I found an easy way to count total number of bonds in a molecule,
which has been loaded in PyMol viewer:
from chempy import stored, Bond
m = cmd.get_model()
print “number of total bonds:”, len(m.bond)
I hope it will be useful.
Cheers
Vijay
On 3/22/16, Vijay Masand wrote
Dear PyMOL Users,
I am using PyMOL 1.8.6 on Windows 10 (64 bit) with Python 2.7.12. I
was working with small molecule
(ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)F)CCN).
When I tried to select all Nitrogen atoms which are exclusively in the
ring only, I tried following command:
abc=cmd.select('byring
gt; get only nitrogens will yield only those that are members of rings.
>
> Hope it helps,
>
> Tsjerk
>
> On Jun 3, 2017 5:45 AM, "Vijay Masand" wrote:
>
>> Dear PyMOL Users,
>> I am using PyMOL 1.8.6 on Windows 10 (64 bit) with Python 2.7.12. I
>
ogic, which involves deletion of 'not':
abc = cmd.select('elem S and byring elem S w. 4 of elem O')
Sulphur atom present at a distance of 4.8 A from Oxygen atom was not selected.
I hope I will be benefited with better explanation.
Cheers
Vijay
On 6/3/17, Vijay Masand wrote:
&
Dear All,
With the help of internal GUI, we can disable the appearance of an
object,however we can still operate on the representations of objects
that are disabled, even with the commands show and hide. The results
are apparent only when we subsequently enable the object.
Is there any way to enabl
>
> Try something like:
> hide everything object
> show sticks selection
>
> Cheers,
>
> Andreas
>
> On Jun 19, 2017 6:00 AM, "Vijay Masand" wrote:
>
>> Dear All,
>> With the help of internal GUI, we can disable the appearance of an
>&g
Dear PyMOL Users,
It gives me an immense pleasure to inform you that our group has
developed a new plugin to calculate 11,145 molecular descriptors for
small molecules. This is an attempt to add new dimension to PyMOL. The
research article describing 'PyDescriptor' has been published in
Chemometric
Dear PyMOL Users
Today, I installed PyMOL 1.8.7 with Python 3.6 on Windows 10. But,
unfortunatelt facing one issue with Plugin Manager. The error is as
following:
Error: 1
TypeError Exception in Tk callback
Function: .plugin_manager
at 0x019192E818C8> (type: )
Args: ()
Traceback (innermost
Dear Christoph
Thank you for the help. I followed your suggestion, but no success.
However, a new line is appearing now at the bottom of the error
message, here is the complete error message:
Error: 1
TypeError Exception in Tk callback
Function: .plugin_manager
at 0x01B40CB228C8> (type: )
patches/7/>
>
>> On Aug 21, 2017, at 10:32 PM, Vijay Masand wrote:
>>
>> Dear Christoph
>> Thank you for the help. I followed your suggestion, but no success.
>> However, a new line is appearing now at the bottom of the error
>> message, here is the complete erro
Dear PyMOL users
The PyMOL plugin "PyDescriptor' is available on following web-server
with enhanced ability to calculate 16,300 molecular descriptors for a
molecule:
https://ochem.eu/home/show.do
PyDescripto is a platform independent plugin for PyMOL (for Python 2
and 3). It is available free of
Dear PyMOL users,
Today, I used following command to select positively charged ring
carbon atoms, surprisingly, PyMOL 2.0.7 selected negatively charged
ring carbon atoms also. Is it a bug or issue associated with 'Byring'?
carb_pos = cmd.select('e. C and Byring e. C and (pc.>0)')
I am sharing the i
Dear PyMOL Users,
I am using Open source PyMOL 2.1 installed on Windows 10 (Python 3.6). I
found a very interesting ability of PyMOL which is related to SMILES
pattern matching. With the help of following code, I am able to get count
of matches for a specified SMILES pattern. For example, I used
"C
4-5419
>
>
> From: Ali Kusay [akus8...@uni.sydney.edu.au]
> Sent: Sunday, June 21, 2020 7:41 AM
> To: Mooers, Blaine H.M. (HSC); Vijay Masand
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] [EXTERNAL] Valence_Mode issue
>
Hello PyMOL users
I installed open source PyMOL 2.4 (Python 3.7) on Windows 10 (64 bit).
It strated without any problem when the icon was double clicked.But when I
tried to use it from IDLE (PYTHON 3.7- 64bit), it showed following error:
"ImportError: DLL load failed: The specified module could no
l C++ Redistributable for Visual
> Studio 2015, 2017 and 2019
> <
> https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads
> >
>
> Christoph
>
>
> On 10/23/2020 8:11 PM, Dr. Vijay Masand wrote:
> > Hello PyMOL users
> > I
Hello Gerald
I think you are looking for this type of diagram. I drew it using PyMOL
only. I used it in one of the papers (See. Journal of Molecular Structure
1175 (2019) 481-487), in which I used 'PyDescriptor' for QSAR work.
PyDescriptor is a PyMOL plugin.
[image: ring5and7A.png]
With Warm Rega
Dear all
We have successfully developed a new portable version of Python 3.8 (64 bit
only) for windows 7, 10 and 11. It contains fully functional and smoothly
running portable versions of Open Source PyMOL 2.5, RDKit 2022.3.2.1,
Jupyter Notebook, Matplotlib, Sci-Py, Numpy, PyQt5, Pip, Pandas, IPyt
/chatgpt-the-future-of-pymol-automation/
I hope it will be useful for you.
Cheers
from
Vijay Masand
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
Dear Elizabeth
A simple solution is to use DockingApp in Windows. Downliad it from
following site:
http://www.computationalbiology.it/software.html
It is very easy to use it. Contact if you need any help.
From
Dr. Vijay H. Masand
On Mon, 1 Apr, 2024, 8:55 pm Elizabeth Tsakelidou,
wrote:
>
> Hey
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