Not sure who on the forum would know the answer to this question but I am sure
someone will. I used many of the python scripts in pymol for my MS thesis,
including the get_distance script that I also made modifications to. I
mentioned all these scritps in my thesis and of course cited the PyMol
I am running this script with my structure, and the result I get is states how
many polar pairs I have but not the location, which I thought the script was
supposed to do. Here is the printout I get when running the script in pymol:
Settings: cutoff=4.0angstrom angle=63.0degree
Found 2 polar con
Under the Action (A) popup menu there is the option modify and you can do
residues or atoms within a certain Angstrom range. So when you do this, at
least in my hands, the answer/output becomes highlighted, but a selection of
this result is not created. Is this what is supposed to happen. Guess
Great! Thank you Microlytic! I assume that the PyMol wiki site will still have
the same web address?
From: Jason Vertrees [jason.vertr...@gmail.com]
Sent: Friday, June 20, 2014 8:00 AM
To: pymol-users
Cc: Melanie Adams-Cioaba
Subject: [PyMOL] PyMOLWiki Update
Gree
Sent: Tuesday, June 17, 2014 5:54 PM
To: Lapolla, Suzanne M (HSC)
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file
Hi Suzanne - The reason you have been getting only one distance in your output
file is that your script is openin
Ah I see--I will try and let you know how it works. Thanks again!
From: Andreas Warnecke [4ndreas.warne...@gmail.com]
Sent: Tuesday, June 17, 2014 2:18 PM
To: Lapolla, Suzanne M (HSC)
Cc: Robert Campbell; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL
to the external window.
>
> https://urldefense.proofpoint.com/v1/url?u=http://pymolwiki.org/index.php/Get_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=921f4dfed39cd38f4ae7a70dfb9
oVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
>
> Cheers,
> Thomas
>
> On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
> wrote:
>
> > Fellow Pymol Users:
> > I may have asked this question before...but if so have forgot
Fellow Pymol Users:
I may have asked this question before...but if so have forgotten. I am
measuring distances between 2 atoms in 2 different objects using the distance
command, and it is working perfectly, but I wonder if there is a command I can
use/add so that those distances can be printed i
I have been able to use this script successfully in the past but now for some
reason I cannot. I load my structure and in the command line type
run show_bumps.py
show_bumps (selection of what I want to show bumps for), showbumps
and while I get a vanderwaal strain printed out on the command line,
Fellow Pymol users:
Have a question about moving a selection of my protein. I would like to rotate
a particular helix of my protein so that it rotates "into" the screen (x axis?)
, changing the side of the helix that is shown. I know how to select the helix,
deprotect it, protect the other regio
.
From: Lapolla, Suzanne M (HSC)
Sent: Friday, April 04, 2014 5:11 PM
To: Thomas Holder
Subject: RE: [PyMOL] manual superposition with pymol
Thank you! I will try this and get back to you.
From: Thomas Holder [thomas.hol
I am using pymol 1.3 and having trouble with doing manual superposition with my
structures. I am able to download my structures, select the portion I want to
move manually and, after deprotecting it using the action menu move it using
the shift-mouse editing command. When I do this with my selec
I have several .pse files I made on pymol 1.3 version--that may or may not be
of significant to what is going on--but when I open the file and try to use the
measurement wizard on them, I am prompted to "click on the first atom", and
when I do so, nothing happens (nothing gets selected and no er
Just wanted to say that your fix did solve my problem. Thanks again!
From: David Hall [li...@cowsandmilk.net]
Sent: Monday, January 20, 2014 8:34 AM
To: Lapolla, Suzanne M (HSC)
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Still need help
Thank you thank you! I will try that later today--I do appreciate the help. Did
I say thank you yet? Suzanne
From: David Hall [li...@cowsandmilk.net]
Sent: Monday, January 20, 2014 8:34 AM
To: Lapolla, Suzanne M (HSC)
Cc: pymol-users@lists.sourceforge.net
Subject
So, an update to my prev post/question--my computer husband was able to look at
the error msg I get when trying to "fetch" with pymol 1.7. He says the error is
with the python2.7 code, specifically in a library that handles unicode
characters--but according to the comment made in the code, this
I am posting this again as I have still not figured out why I am unable to
fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted the
error msg I get below. I have tried uninstalling and reinstalling python 2.7.6
as well as python 1.7 (I have windows 64 bit --so I tried the 6
I have just downloaded pymol 1.7 along with python 2.7.6. (I previously had
pymol 1.3). I am able to open existing .pdb and .pse files I have saved, but if
I try to fetch them from the PBD I get a huge error message (see below). I feel
like this question has been asked before but cannot find it
ferent names. You will also be able to open your old pse files.
>
> Cheers,
> Marcelo
>
> On Jan 14, 2014, at 12:18 PM, Lapolla, Suzanne M (HSC)
> wrote:
>
>> I would like to upgrade to Pymol 1.6 on my windows 7 64 bit laptop. Right
>> now I have Pymol 1.3 opensour
I would like to upgrade to Pymol 1.6 on my windows 7 64 bit laptop. Right now I
have Pymol 1.3 opensource. I have a many session files (.pse) that I have made
on PyMol 1.3, and want to make sure that upgrading will not be a problem. Can
I uninstall Pymol 1.3, then install Python 2.7 and Pymol 1
I noticed my question was truncated when I submitted it so will try again.
When I run showbumps.py on Pymol I get a vanderwaal value of about 163.
I need a good ref point as to what that number represents.
Thanks, Suzanne
-
New to the forum but have been uisng Pymol for about a year. I have a ? Re
using the showbumps.py script and the vanderwaal strain number given after the
run. The vanderwaal strain number that pymol gives after you run showbumps, is
that in J/mol? kJ/mol? I am trying to get a handle on how dest
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