Thanks for the prompt responses, Warren and Joe! Works like a charm!
Now, I just wish that my Kensington Expert Mouse could function as a
true three button mouse...is there a keystroke that mimics the third
mouse button?
Thanks again,
james
Hi James,
Sounds like you want a homology model type set up, ie generate
coordinates based on a template. Modeller can do this and an easier way
is via the swissmodel
http://swissmodel.expasy.org//SWISS-MODEL.html
If however you want a relatively random structure then pymol _can_ do
this.
James,
> PyMol would allow one to enter a peptide sequence (generally short in
> length) to create a template structure that can then be used
Just hold down ALT/OPTION and type in the peptide sequence. The
numbering will be arbitrary, but at least you'll have something to work
with.
Hello,
This may be slightly off-topic, but I was wondering whether PyMol
would allow one to enter a peptide sequence (generally short in
length) to create a template structure that can then be used for
structural refinements (minimizations, etc.) elsewhere.
If PyMol cannot do this, is any
> I have been trying to coax Pymol to raytrace or output to pov
> (make_pov.py) some very large surfaces and I am unable to. It works for
> ~33,000 atoms, but chokes on ~61,000. I would like to get up to >100,000.
>
> Anybody have some good tips? I have tried adjusting hash_max, but I
> think this
Dan,
Sorry, that is not currently possible. In order to get individual
distances, you need to create them one by one using a nested loop.
Something like:
for at1 in cmd.index("resi 10"): \
for at2 in cmd.index("resi 11"): \
cmd.dist(None, "%s`%d"%at1, "%s`%d"%at2)
Cheers,
Warren
--
W
> The question is: how can I then delete the created MyColor
> object? I tried the cmd.delete command, it does not generate
> an error but apparently the color is still defined... Any idea?!
Colors can't be undefined, and that would especially be true if an object is
still using a given color,
Hi Daniel,
This problem has been tackled several times, maybe have a look at the
following URLs, it might help you getting started:
http://www.rubor.de/bioinf/tips_python.html#msdist
http://sourceforge.net/mailarchive/message.php?msg_id=2914266
And also dont forget the search feature o
