Hi Yeping -
Yes, I can. But there is one additional requirement: to save all the states,
you must add a `state=0` keyword argument to the save command to include all
states. Otherwise, the default is `state=-1`, which includes only the current
state.
http://www.pymolwiki.org/index.php/Save
Dear Jared,I am using Open Source PyMOL 1.6.0.0. If you save the whole virus
structure as a single pdb file, and reload it into pymol and then show it as
cartoon, can you still display the whole structure? As for me, it can display
only one chain shown as cartoon_loop.Best regards.
Yeping Sun
Hi,
When you call cmd.extend(), it does not add the function to pymol.cmd.
Just call it directly:
Change
pymol.cmd.align_all_to_all()
to
align_all_to_all()
You may need to import it if you haven't already (and make sure it is in
the PYTHONPATH).
HTH,
Matt Baumgartner
On 09/02/2014 10:38 AM
Dear Pymol mailing list,
I am facing a problem with some python scripting involving pymol...
I have a python script which adds a new function to pymol
(align_all_to_all.py that I found on pymolwiki).
I added some features to it so that it can load pdbs and thus automate
the calculations.
Whene
Hi Yeping -
I’m unable to reproduce the behavior you’re seeing—using your commands in Open
Source PyMOL 1.7.2.0, I get the whole capsid displayed properly as a cartoon.
What version of PyMOL are you using?
You could also try using the `all_states` setting instead:
fetch 3j2v, type=pdb1, async
Hi Peter,
we haven't seen this problem before, can you give us some details about your
setup? Is this on Windows 8?
Thanks,
Thomas
On 29 Aug 2014, at 14:11, Peter Kahn wrote:
> Dear All:
>
> Help!
> Re-installing Pymol 1.7.0.5 after uninstalling failed with the following
> error:
> "Pymol
Dear all
I want to display structures which contains numerous chains such as viruses in
pymol. I find these sturctures can be displayed normally as line
representation. However, when I show them as cartoon, usually only one chain
can be displayed, and usually it is cartoon loop rather than the n
I have a protein which contains 32 chains. By using A-Z can only name 26
chains. Can I use expression containing two character such as A1, AB, etc. to
as chain id? Will this change the format of the pdb files?
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
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