Thanks Jared. A lot of fantastic tips there. Much appreciated.
Regards.
On Sat, Apr 29, 2017 at 6:03 AM, Jared Sampson
<jared.samp...@columbia.edu> wrote:
> 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 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), 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
>
>
> 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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