Hi James,
set pdb_use_ter_records, 0
This will not use TER records at all.
Cheers,
Thomas
On 03/20/2012 08:07 AM, James Starlight wrote:
Dear PyMol users!
After editing of my pdb files by means of PyMol I've noticed that some
of my structures contain of wrong TER enties in the body of
BSD
Dear All,
Can anybody confirm that they have a
Mac Pro + Quadro 4000 + OSX 10.7.x + Nvidia 3D Vision glasses + compatible
(non-Zalman) 120 Hz LCD screen
working with quad buffered stereo?
Thanks
Harry
-
Harry M.
Dear PyMOL users,
I put a new python module on the PyMOLWiki which is a comprehensive
collection of scripts. It's basically my in-house setup of PyMOL
scripts, where all good stuff which I need regularly got incorporated.
http://pymolwiki.org/index.php/Psico
Cheers,
Thomas
--
Thomas
Hi James,
In addition to Thomas' answer... What is _wrong_ about the TER
statement? Your chain is broken, indicated by the nonconsecutive
numbers. That means you have two distinct molecules, and they are
separated by a TER statement. Doesn't seem wrong. Yeah, they might be
the same chain, but
Dear Thomas,
Wonderful work. I will have a try.
Cheers,
Zhijian Xu
Thomas Holder wrote:
Dear PyMOL users,
I put a new python module on the PyMOLWiki which is a comprehensive
collection of scripts. It's basically my in-house setup of PyMOL
scripts, where all good stuff which I need
Thomas,
Nice work. We'll be sure to look at making some of those changes standard.
Cheers,
-- Jason
On Tue, Mar 20, 2012 at 5:55 AM, Thomas Holder
spel...@users.sourceforge.net wrote:
Dear PyMOL users,
I put a new python module on the PyMOLWiki which is a comprehensive
collection of
On 03/20/2012 11:35 AM, Tsjerk Wassenaar wrote:
In addition to Thomas' answer... What is _wrong_ about the TER
statement? Your chain is broken, indicated by the nonconsecutive
numbers. That means you have two distinct molecules, and they are
separated by a TER statement. Doesn't seem wrong.
Harry,
I have not seen any evidence of the NVidia 3D NVision system working
on a modern Mac OS X system. For the Mac, you'll have to use something
passive like Zalman (or maybe the new anaglyph).
Cheers,
-- Jason
On Tue, Mar 20, 2012 at 3:59 AM, Harry Mark Greenblatt
Hello I know the plugin mentioned above (in the Subject) will work if I go to
Plugin Manage Plugins Install contact_map_visualizer I get that. But
nothing happens if I run the plugin if I go to File Run
contact_map_visualizer.py I do this because I need it for my project,
preferably
Hi Thomas,
'Wrong', certainly in the context it was given in, is a statement of
judgment. It suggest that there is a failure in the functioning, and
is a criticism to the developer, becoming a wrongdoer. My argument is,
that the answer given (with TER statements) is not wrong, but from a
chemical
Hani,
You can these GUI commands:
A (Action)---preset---ligand sites or
A---find---polar contacts
Hope this helps you!
Peter
syed.abidi skrev 2012-03-19 12:19:
Dear All,
I have a small query regarding PyMol and I would appreciate if you can help
me with it. My query is:
How do I
Shucks! So much for trying to keep the developer out of the wind. But
he's a wrongdoer by PDB definitions anyway! So it would be best to
modify the behaviour concerning writing of TER records. Feel free to
file it as suggestion.
Gotta love polemics! -- Next time I'll manage, David. Next time...
On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Thomas,
'Wrong', certainly in the context it was given in, is a statement of
judgment. It suggest that there is a failure in the functioning, and
is a criticism to the developer, becoming a wrongdoer. My argument
Hi All,
We have different versions of Pymol (1.4 and 1.5.0.3) on different computers,
mainly due to some low end intel graphic chipset not able to support 1.5
version. I would like to know if there is an option to open in pymol 1.4 the
pse files that were saved in pymol 1.5. It is generally
Please remove me from the mailing list. I don't know how to unsubscribe
from this mail.
Thanks a lot.
--
Purushottam Shivaji Narute, BVSc AH./DVM, MVSc (Biotechnology), PhD.
Phone(C): 412-417-1591
Hello,
What I want to do seems so simple, I just can't find the documentation. Would
anyone know how to just change the colors of only certain states when they are
appended to the same object?
For instance I have a simulation that shows atoms moving all over the place for
states 1-300 and a
Hi Jordan,
Please see http://www.pymolwiki.org/index.php/Spectrum_states.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Hi Suheila,
What were the exact commands you used, and what error did it come up with?
Just saying you tried mogrify and convert and the error was still there
isn't very informative to us.
Cheers,
Tsjerk
On Mar 18, 2012 2:39 PM, Suhaila Haji Mohd Hussin
bell_beaut...@hotmail.com wrote:
I
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