Re: [PyMOL] Question about Iterate and Edit-Mode

[Jason V. <jas...@sc...>]

Hi Martin,

You could think of it as what Tsjerk purported:


# pseudocode for iterate

def iterate(sel,cmd):
  for x in selection:
    return cmd(x)

where each 'function' cmd would return a value per atom.

For example,

# pseucode for an instance of iterate

def iterate(organic, 'print b')
  for x in organic:
    print_b(organic)


> The second question is related to the Edit-Mode of PyMOL. When I switch
> to Edit-Mode and click on a atom, a couple of states/objects (?) appear
> in the object list: pk1, pkmol, pkresi, pkchain, pkobject.
> What do these objects mean? What are they useful for? I'm sure there is
> a reason for them, but I cant figure it out.

PyMOL has a fully functioning molecular editor, but it's clunky and
not well-understood.  In Selection Mode you 'select,' whereas in Edit
Mode, you 'pick'.  In Edit Mode, (pk1) is the first atom you 'pick'
with the mouse.   Common operations can be completed when you pick the
atoms on which you want to operate.  For example, in edit mode, pick
two atoms and type the word "dist" at the command line.  PyMOL will
measure the distance between those two atoms.  Pick three and you can
calculate an angle.  PyMOL supports pk1 up to pk4.  pkmol is the
molecular object associated with your picks; pkresi is the residue.
The builder has lots of interesting things built into it.  Pick the
correct three atoms and you can 'invert' the stereochemistry by
flipping the liganded groups.

Cheers,

-- Jason

On Sun, Oct 24, 2010 at 8:12 AM, Martin Hediger <ma...@bl...> wrote:
> Dear All
> I am trying to get behind the way 'iterate' works, since I see it quite
> frequently in PyMOL scripts.
> The example in the help page is a bit limited in the sense that I cant
> explain to myself what actually is happening.
>
> Say, if I were to write the functionality of 'iterate' using a for-loop,
> how would this for-loop look like?
> Something like this maybe?
>
> for i in selection:
>     i.expression()
>
> I'm a bit confused about what can go into 'expression'.
>
> The second question is related to the Edit-Mode of PyMOL. When I switch
> to Edit-Mode and click on a atom, a couple of states/objects (?) appear
> in the object list: pk1, pkmol, pkresi, pkchain, pkobject.
> What do these objects mean? What are they useful for? I'm sure there is
> a reason for them, but I cant figure it out.
>
> Thanks a lot for your help guys.
>
> Martin
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120