Dear everyone,
when I run a script in pymol1.4.1 on the command line: pymol -rqkc
script.py.
Then a lot of messages ObjectMoleculeGuessValences(1,1): Unreasonable
connectivity in heteroatom,
unsuccessful in guessing valences. will be printed out on the screen
in addition to the script
Hi Zhijian,
In PyMOL v1.4 and PyMOL v1.4.1 this message will be emitted. We have
changed this warning message for later versions to be released in a
few months' time. If you're using the open-source code, then a
rebuild from source should fix this for you. I just pushed the change
to the
Dear Jason,
Thanks very much for the prompt reply.
Yes, I compiled pymol by hand from source under Linux and I will rebuild it.
Best Regards,
Zhijian Xu
Jason Vertrees wrote:
Hi Zhijian,
In PyMOL v1.4 and PyMOL v1.4.1 this message will be emitted. We have
changed this warning message for
Dear Jason,
I am afraid the change did not work for me. Is there anything wrong in
my rebuild process?
(1) I download the source code with the command: svn co
https://pymol.svn.sourceforge.net/svnroot/pymol pymol
(2) go to pymol/trunk/pymol, and see the ChangeLog: 2011-06-16 Jason
Vertrees
Hi Zhijian,
I recompiled from SVN to test this and the message is no longer
emitted (with default feedback settings). If you have raised the
internal feedback of object molecule to blather then you'll see this
message.
Please try pulling again (ensuring you have commit 3955) and
rebuilding. I
Dear Jason,
I will try again. Thanks for the advice.
Best Regards,
Zhijian Xu
Jason Vertrees wrote:
Hi Zhijian,
I recompiled from SVN to test this and the message is no longer
emitted (with default feedback settings). If you have raised the
internal feedback of object molecule to blather
On 06/16/2011 04:24 PM, zjxu wrote:
(3) In pymol/trunk/pymol:
python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/
python setup2.py install
./pymol
However, when I load a pdb, the warning comes again. pymol -rkqc
script.py complains again.
have you set PYTHONPATH before running
Dear Thomas,
It works now after taking your advice.
Thanks very much.
Best Regards,
Zhijian Xu
Thomas Holder wrote:
On 06/16/2011 04:24 PM, zjxu wrote:
(3) In pymol/trunk/pymol:
python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/
python setup2.py install
./pymol
However, when
