Dear Thomas,
Even after I installed the Pmw1.3 which should be compatible with python2.7
and reinstalling the pymol, I am still the following error message.
File /Library/Python/2.7/site-packages/pymol/__init__.py, line 450, in
launch_gui
__import__(self.invocation.options.gui)
File
Dear Rhitankar,
I should point out that Schrödinger also sells pre-compiled PyMOL with
easy to use installers. http://pymol.org/academic.html
Open-Source PyMOL was always targeted to power-users who are familiar
with compiling software themselves.
Regarding your question: It will most likely
Dear Thomas,
Thanks for the informations. I think I am able to use port to install the
pymol1.5 version but I would also need to remove the existing 1.6 version.
Can you tell me the command to uninstall the existing version and then do a
fresh installation?
Thanks again
Rhitankar
On Wed,
Hi Rhitankar,
this depends which python you used and which arguments you passed to
setup.py. I assume you used system python and no arguments, then just
remove these:
/Library/Python/2.7/site-packages/pymol
/usr/local/bin/pymol
Cheers,
Thomas
Rhitankar Pal wrote, On 05/08/13 18:46:
Dear
by default, macports installs tcl with the +corefoundation variant (see
http://guide.macports.org/#using.variants )
if you do:
sudo port install tcl -corefoundation
that will solve the problem.
-David
On Mon, May 6, 2013 at 8:26 PM, Rhitankar Pal rhitan...@gmail.com wrote:
Dear Thomas,
Hi David,
I installed tcl without the corefoundation and now while trying to install
pymol I am getting the following error message:
Error: org.macports.archivefetch for port pymol returned: tk must be
installed without +quartz.
How can I install tk without +quartz? Are these issues happening
sudo port install tk -quartz
It has nothing to do with what OS X ships with, it has to do with current
macports defaults, which changed around 18 months ago. You can dig around
the macports bug reports to see discussion of the change.
-David
On Tue, May 7, 2013 at 1:32 PM, Rhitankar Pal
Dear Thomas,
Now I have installed Pmw.1.3 which should be the one compatible with
python2.7 I guess. However I am still getting the same error. I think pymol
is trying to use Pmw2 by default. Is there any way we can ask it to use 1.3
instead?
Thanks for your help
Rhitankar
On Sat, May 4,
Dear Thomas,
One more question. When I tried to install pymol using port [ sudo port
install pymol ] I get the following error message:
Error: org.macports.archivefetch for port pymol returned: tcl must be
installed without +corefoundation.
Do you have any idea why there is this error message?
Hi Rhitankar,
looks like you installed the python3 version of Pmw which is not
compatible with python 2.7.
Cheers,
Thomas
Rhitankar Pal wrote, On 05/03/13 21:16:
Dear Pymol developers,
I have recently installed pymol 1.6.x in MAC OS X 10.8.2 and have the
following error while opening the
Dear Pymol developers,
I have recently installed pymol 1.6.x in MAC OS X 10.8.2 and have the
following error while opening the GUI
Traceback (most recent call last):
File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line 35, in
run
PMGApp(pymol_instance,skin).run(poll)
File
I am having some issues after installing pymol in Mac OS 10.8.2. It
seems
the program is installed but when I try to open in using command line
pymol it doesn't show the 'Molecular Graphics System' window but shows
only the 'Pymol Viewer' window. In the terminal I have the
what method did you use for installation?
--
David Hall
On Wednesday, May 1, 2013 at 11:53 AM, Rhitankar Pal wrote:
I am having some issues after installing pymol in Mac OS 10.8.2. It seems
the program is installed but when I try to open in using command line
pymol it doesn't show the
Dear Pymol users,
I installed Pymol 1.2 on Ubuntu 9.1 but I have the error as the following
for all PDB files.
(Select File - open from the user menu, and select and open that PDB file).
*Error: 1*
*type 'exceptions.UnicodeEncodeError' Exception in Tk callback*
* Function: bound method
Hi Jorgen,
I just tried pair fitting some atoms from your PyMOL session and was
able to reproduce what you found. Pair fitting is done between atoms,
so please show lines or sticks, not just cartoons, when pair fitting.
You can turn off the lines later if you don't need them. In this way,
you
Hello,
I have loaded two PDB files in PyMol to pair fit some of their amino acids.
When using the wizard, I'm getiing the following error. Does anyone has an
idea how to solve this?
_seeker and not _pf_s_*
Editor-Error: Invalid input.
Traceback (most recent call last):
File C:\Program Files
Hi Jorgen,
I cannot reproduce this. Can you please give me the PDBs (or PDB IDs)
and commands to reproduce this error?
Thanks,
-- Jason
On Tue, Oct 5, 2010 at 8:58 AM, Jorgen Ravoet jorgen.rav...@gmail.com wrote:
Hello,
I have loaded two PDB files in PyMol to pair fit some of their amino
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of praba ponraj
Sent: Friday, February 08, 2008 1:46 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] pymol error in linux - does not work
Pymol users on Linux,
I installed the Pymol (pymol-1_or2) on my new Red Hat Enterprise Linux
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