Hi Ahmad -
Here are a few suggestions:
> I'm still a bit new to the API so I'm not sure which commands to use.
> At least I know I will start with cmd.select(string name, string
> selection).
>
> How can I tell Pymol to:
>
> 1) look within a certain radius distance, and return resi's within
> that distacne.
cmd.select('mysele', 'byres all within 5 of sele')
See https://pymolwiki.org/index.php/Selection_Algebra
<https://pymolwiki.org/index.php/Selection_Algebra> for more handy operators
(`beyond`, `around`, `expand`, etc.)
> 2) find all polar interactions within a distance,
You can use cmd.distance (https://pymolwiki.org/index.php/Distance
<https://pymolwiki.org/index.php/Distance>), e.g. (as done in the GUI by [A] >
find > polar contacts...)
cmd.dist("mysele_polar_conts","mysele","all within 5 of
mysele",quiet=1,mode=2,label=0,reset=1)
or for a list of atoms, check out https://pymolwiki.org/index.php/Polarpairs
<https://pymolwiki.org/index.php/Polarpairs>
> use sticks,
cmd.show('sticks', 'mysele')
or to hide all other representations,
cmd.show_as('sticks', 'mysele')
> color by atom
util.cnc('mysele')
I use this one all the time ("cnc" == color non-carbon). There is also
`util.cbc` == color by chain.
> hide everything else
cmd.hide('everything', 'all and not mysele')
> and output an image of the selections and interactions around it.
cmd.zoom('mysele', 5)
cmd.png('mysele.png', ray=1)
> Please feel free to throw in any useful commands that can you might think is
> helpful.
One useful trick to learn new commands is to open a log file (via `log_open
log.pml` or the File menu) and then perform the desired action in the GUI. The
log file will show the API commands that are called from the GUI. It doesn't
work for everything (e.g. wizards), but for most basic actions, it should be
helpful. At least it will give you the right command to look up on the PyMOL
wiki!
Hope that helps.
Cheers,
Jared
>
> Your help is greatly appreciated.
>
> Regards.
>
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