RE: Question about commandline -d option (was RE: [PyMOL] displaying protein with propeptide)

[Warren D. <wa...@de...>]

> This is awesome.  It looks like this has been a valid setting=20
> for a *long* time, but I've never seen it.  I look at a lot=20
> of MCSS-type structures, and I have some really painful=20
> scripts that get the bonds right once the structure is loaded=20
> in PyMOL.  Now, I can just stamp the CONECT records at the=20
> end of the file and load things up in connect_mode=3D1 world=20
> and everything works.  Speaking of which, I made a little=20
> bash shell script to launch PyMOL this way:
>=20
> pymol -d "cmd.set('connect_mode',1)" $@
>=20
> It took me a couple of tries to get that right.  The=20
> documentation for command-line options says
>=20
>    -d <string> Run pymol command string upon startup.
>=20
> so I first tried
>=20
> pymol -d "set connect_mode,1" $@
>=20
> but that doesn't work.  Is this a documentation typo?  I=20
> thought a PyMOL command string was anything you could type at=20
> the PyMOL command prompt.

Michael,

The issue here is that spaces in the command used to cause trouble in
the launch process.  This has now been fixed in the current
pymol.com.template, but for now substitute a percent sign for spaces in
-d command arguments:

pymol -d "set%connect_mode,1" $@

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20