Hi,
http://www.pymolwiki.org/index.php/Label would help.
Zhijian Xu
On 09/26/2013 10:40 AM, xfc_2013 wrote:
Dear everybody,
I'm a new user of pymol and have come with some questions about label. The two
main progroms are as following:
1. I have labeled residue names of a receptor protein
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
Dear,
I compiled PyMOL 1.5.0.1 from SVN revision 3979 on Centos 5 with python
2.7.1. and found splash screen 1.3.x too.
Best,
Zhijian Xu
Troels Emtekær Linnet wrote:
Hi.
I can confirm that you can compile pymol 1.5.0.1 on RHEL 6, with
python 2.6.6 from the RHEL repositories.
Dear Masataka,
Will you try update python 2.4.3 to python 2.6 or later?
Pymol 1.4.1 works well on my centos5.4.
In my case, I both have python 2.7.1 and pytnon 2.4 in the system, and
use python 2.7.1 to compile pymol.
In addition, the gcc version is 4.1.2.
Hope it helps,
Zhijian Xu
Dear Suda,
cealign can be used to do structure based superposition
PyMOL cealign target, mobile
However, it's a pair-wise based alignment. You have to align two
structures each time.
Hope this helps.
Zhijian Xu
Suda Ravindran wrote:
Hi,
I would like to know how to do structure based
Dear leila,
Check this: http://www.pymolwiki.org/index.php/Label
enter edit_mode
http://www.pymolwiki.org/index.php?title=Edit_modeaction=editredlink=1
and *ctrl-middle-click* to drag labels around. In this way, you can
change the position of one of labels while position of others be fixed.
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
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 open-source project a few moments ago.
Cheers,
-- Jason
On Thu, Jun 16, 2011 at 8:52 AM, zjxu z
.
Best Regards,
Zhijian Xu
zjxu wrote:
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
then you'll see this
message.
Please try pulling again (ensuring you have commit 3955) and
rebuilding. I also suggest cleaning the last version before
installing.
Cheers,
-- Jason
On Thu, Jun 16, 2011 at 10:24 AM, zjxu z...@mail.shcnc.ac.cn wrote:
Dear Jason,
I am afraid the change
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
Dear Joyce,
It sounds like a question related to homology modeling. You could try
http://salilab.org/modeller/download_installation.html or
http://swissmodel.expasy.org/.
In pymol, this may be a rough way: (1) align B to A, (2) create
A_complete, A or ( the missing residues from B), (3) Now
Dear Maia,
Would you like to try this:
select bridge, (c. a and i. 160+356+505+507+508) or (c. c and i.
275+355+128)
Best Regards,
Zhijian Xu
Maia Cherney wrote:
Hi Jason,
I keep sending my e-mail from a wrong address that the pymol mailing
list does nor recognize.
I need a command that
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