Great!!
Thanks to all !!.. and specially Takanori!!
Cheers,
Abhi
On Wed, Feb 1, 2012 at 6:09 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Thomas,
alternate locations and multi-state objects should not be an issue, the
script on the PyMOLWiki can handle both! The only
On 01/31/2012 05:03 PM, Jason Vertrees wrote:
Please file a feature request on the open-source bug tracker and we'll
be sure to look at this ASAP.
no need for a duplicate, it's already there:
http://sourceforge.net/tracker/?func=detailaid=3326957group_id=4546atid=354546
Cheers,
Thomas
--
On 02/01/2012 12:01 AM, Takanori Nakane wrote:
Hi Abhinav and Jason,
The underlying C-object for a measurement does not support
iterate/alter. This is rather silly; PyMOL should be able to tell you
what's in the object.
As an ad-hoc hack, I wrote a Python script to access internal C-object
Takanori,
This is a very clever script -- well done! There are some pitfalls,
but in general this should work well.
Cheers,
-- Jason
On Tue, Jan 31, 2012 at 6:01 PM, Takanori Nakane
t.nak...@mail.mfour.med.kyoto-u.ac.jp wrote:
Hi Abhinav and Jason,
The underlying C-object for a measurement
Dear Thomas,
Takanori, Looks like you've studied the output of cmd.get_session quite
well. Would you mind to share some of your insights by putting
documentation on http://pymolwiki.org/index.php/Get_session ?
I have a plan to write some documentation of Pymol's internal
data structure and
Jason, what pitfalls? Are they still present in this script?
http://pymolwiki.org/index.php/Get_raw_distances
Cheers,
Thomas
On 02/01/2012 04:01 PM, Jason Vertrees wrote:
Takanori,
This is a very clever script -- well done! There are some pitfalls,
but in general this should work well.
Thomas,
When you hash by coordinates you could get odd results from alternate
locations and multi-state objects. I like how Takanori solved the
problem, but it's not a strictly perfect solution. What I need to do
is provide access to the C-object for real. We plan to provide
something for this
Hi Thomas,
alternate locations and multi-state objects should not be an issue, the
script on the PyMOLWiki can handle both! The only issue would be altering
coordinates after distance objects have been created (and having
dynamic_measures = off).
I just read over your change to Takanori's
Hi thanks,
still it is not the same.. But thanks..
I wish Jason can reply if there is any way to get the list from the apply
command.
thanks,
Abhi
On Mon, Jan 30, 2012 at 5:53 PM, Thomas Evangelidis teva...@gmail.comwrote:
I think you can reproduce the results from apply-find-polar contacts
Hi Abhinav,
The underlying C-object for a measurement does not support
iterate/alter. This is rather silly; PyMOL should be able to tell you
what's in the object.
Please file a feature request on the open-source bug tracker and we'll
be sure to look at this ASAP.
Cheers,
-- Jason
On Tue, Jan
Hi Abhinav and Jason,
The underlying C-object for a measurement does not support
iterate/alter. This is rather silly; PyMOL should be able to tell you
what's in the object.
As an ad-hoc hack, I wrote a Python script to access internal C-object
of distance representation and convert it to atom
Hi,
I am trying to get the list of hbonds formed using
Apply-find-polarcontacts.
I searched and found some scripts, but they never give me the same result
as the one by default pymol.
Any ideas how I can get the hbonds as a list.
Thanks,
Abhinav
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