Hi Daniel,
the "bymol" (long: bymolecule, short: bm.) operator expands the
selection to complete molecules, so all atoms which are connected by
bonds. This is independant of atomic identifiers, unlike the "byres"
operator.
http://www.pymolwiki.org/index.php/Selection_Algebra
The ID rolling probl
Hey Thomas,
could you elaborate on the "bymol" flag? E.g. the given example of
selecting molecules when you got > waters? Is there an easy
workaround for the ID rolling?
Regards,
Daniel
Am 01.07.13 21:38, schrieb Thomas Holder:
> Matthew Baumgartner wrote, On 07/01/13 21:34:
>> I remo
Matthew Baumgartner wrote, On 07/01/13 21:34:
> I removed the byres command because I have more then 1 water
> molecules in my system and the residue ID's were rolling over and waters
> far from the residue of interest were being selected.
> If anyone has a suggestion on this, please let me k
Yes, sorry, the frames are mapped to states. Ah, yes, that is what I
needed, that 'state' keyword argument was not listed in the wiki page.
For posterity's sake, a couple of minor modifications were required in
the code you provided.
python
for i in range(1,41):
cmd.select("wat_" + str(i),
I know you have asked for frames, but I assume that each frame is mapped to a
state. The selection logic allows for you to specify the state.
So if the waters of interest are in state 1,40:
python
for i in range(1,41):
cmd.select("wat_"+i,"byres in within 6 of
",state=i)
python end
J
> 'sel
Hi,
Is it possible to force a selection to only apply to the specific frame
rather then across frames?
I'm running in to a problem where I have some (~40) frames from an
explicit solvent MD that I want to look at. What I want to do is look at
water molecules around a specific residue at each fra
