I would suggest you to use the PyMol open Source version for Research
Publications.
https://github.com/schrodinger/pymol-open-source
Regards,
Saurabh Gayali
--
*Saurabh Gayali*
Business Analyst [Excelra], Former Research Scientist [IGIB]
saurabh.gay...@gmail.com / +91
Hello, all.
My name is Alex Zatuchney, and I am a full-time high school student that is
looking to use PyMOL to generate renders for both self-study and a possible
research paper for the AP Research program. At some point, I would like to
publish this research. Since I am a full-time student, would
Hi,
I have a few questions regarding selection command for which I am unable to
find the answers:
How to select, say 100th and 120th residue of chain-A and 50th residue of
chain-B?
How to select all the alanine residues of chain-A and glycine residues of
chain-B?
How to count the total number of
Thanks David.
This worked flawlessly... I made one of my .pdb files a favorite in Dropbox
app, set the iPad to airplane mode, so no wifi, back to Dropbox app, tapped the
.pdb file, and selected open in pymol from the actions button. My molecule was
right there with no network connection.
Seem
Hi Steve,
I'll suggest a workaround to having pymol cache the files:
(1) Install the DropBox app
(2) Favorite your PDB files in that app, this will cache those files
locally within the DropBox app for offline access
(3) From the dropbox app, you can open PDB files in Pymol using the
button in the
Greetings,
Minor answer: I usually go to
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/ to search
the list.
Regards,
JP Cartailler
On 11/28/2012 10:48 AM, Steve Williams wrote:
I am a new subscriber to the pymol listserv. I did look around a bit on the
listserv site, but d
Hi Steve.
> I am a new subscriber to the pymol listserv. I did look around a bit on the
> listserv site, but did not find a way to search previous postings and
> responses, so did not find if there is a known answer to my question.
Welcome to the PyMOL community.
> Minor question: is there a
I am a new subscriber to the pymol listserv. I did look around a bit on the
listserv site, but did not find a way to search previous postings and
responses, so did not find if there is a known answer to my question.
Minor question: is there a way to search the pymol message archive, and if so,
Okay, well...
You need to know more about python search paths and importing modules...
You need to define and tell python to search in the directory where the
CEaling script is.
Then you need to import the module in PyMOL.
Then you can use the function.
Basically, you need to learn basic stuff
Have you told PyMOL to import the functions from a module?
What have you written in PyMOL?
/T
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2011/11/24 James Starlight
> Dear PyMol Users!
>
> I've decided to make this topic for all questions wich could be arrise
> during w
Dear PyMol Users!
I've decided to make this topic for all questions wich could be arrise
during working in diffent PyMol plugins.
So My first question about installation of the plugins wich are separate
python modules ( installed not via PyMolf itself)
E.g I have old PyMol wicj lack CEalign plug
sers-boun...@lists.sourceforge.net] On Behalf
> Of Chandra Verma
> Sent: 21. marts 2007 01:58
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] questions
>
> Hi
>
> if i have two structures loaded in pymol with structure 1
> consisting of chains A and chain B of different
Hi
if i have two structures loaded in pymol with structure 1 consisting of
chains A and chain B of different sequences
and similarly structure 2 consisting of chains C and D
is it possible to superpose chain B of structure 1 onto chain C of
structure 2?
thanks
chandra
sage-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Grégori Gerebtzoff
> Sent: Monday, May 30, 2005 6:08 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Questions & comments about CGO objects
&g
Hi list !
I was just building (successfully) my first CGO object, and I have three
questions and two comment:
Questions:
1) what is the difference between LINES, LINE_LOOP, LINE_STRIP. If I
understood correctly, LINES is to build single lines,
LINE_LOOP will connect the first and the last po
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Zach
> Sent: Tuesday, October 05, 2004 9:53 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Questions about ray-tracing
>
> Hello to all,
>
> I am trying to ray trace a picture using pymol and I hav
Hello to all,
I am trying to ray trace a picture using pymol and I have a couple of questions:
a) I am using a cylindrical helix representation. Some of these helices have
side
chains sticking out of them represented as sticks. The connection between the
alpha carbon (within the helix) and the b
Hi, guys:
I have a confusion about PQR file visualization. Since my computer is
Mac G4, I think I may not be able to use the new version of mac pymol
0.97 for the APBS plugin. I converted my pdb file to PQR from the
serve: https://gridport.npaci.edu/apbs/. However, when I want to
visualize the
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> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Qun Wan
> Sent: Tuesday, July 06, 2004 8:30 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [Py
Hi,
I want to show the electrostatics of my protein. However, when I
click electrostatics from the Demo menu, the molecule shown in
electrostatics is not what I want. Does any one know what is wrong?
Meanwhile, I want to show my protein according to its B-factor. When
I label it in color from t
1.When I want to get the exact rotation of my current view, I did as
the following instruction, but Pymol programe says: invalid syntax. I
do not know why that happens. Could you figure it out for me?
Getting the right view in the script:
When creating the script, it is nice to have the view come
Howdy,
I've started writing some more intricate scripts for a movie my prof's
doing _very_ soon.
I have PyMol 0.95 on either a Dual Xeon 3.4 or a Dual Opteron 240 64-Bit
both running Linux 2.6.5. Using 'mencoder' to encode movies.
We've made great progress but would like to mimic a photon by us
Dear Pymolers,
In the on-line help (of `iterate_state'), I found examples that
one can iterate through atoms and obtain their x value.
But I tried on my local installations (both Win and Linux),
an error was there when I tried to access 'x' value, for example.
But I can access other properties lik
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