RE: [PyMOL] PyMOL tutorial

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

Gareth,

	Thank you for preparing this tutorial and sharing it with the
PyMOL user community!  I am sure it will be helpful to new and existing
PyMOL users.  Your examples section is particularly impressive.

	Note that there were some changes in the preferred atom
selection syntax and terminology which everyone should become aware of.
It would be nice to update web-accessible training materials with the
new syntax at some point, but no hurry -- the older conventions are fine
too.

Key points:

A.   Semicolon abbreviations have been deprecated, with
period-plus-a-space now being the preferred terminator for
selection-operator short-forms.  This gives a cleaner and less
context-dependent syntax, and the semicolon can then just be a command
separator.  However, semicolon-based short-forms still work and will
continue to do so through the 1.x series. 

Deprecated, but allowed:

   color red, ( i;130 ); color green, ( c;A & r;phe )

Preferred:

   color red, ( i. 130 ); color green, ( c. A & r. phe )

B.   Parentheses are now optional around Logical Atom Selections
(formerly "Algebraic Atom selections") that do not contain semicolons.

   color red, i. 130; color green, c. A & r. phe

C.   Selection Macros (formerly referred to as "Hierarchical
Selections") remain the most concise option:

   color red, 130/; color green, A/phe/

D.   Selection Macros can be used anywhere within a
Selection-Expression:

   show sticks, C// or byres 130/ expand 5 

These changes are described in "Command Syntax and Atom Selections"

http://pymol.sourceforge.net/newman/user/S0220commands.html 

from the current manual.

ALL PYMOL USERS, both new and experienced, should at least glance at
this rewritten chapter at some point, since it represents the official
(but not infallible) doctrine.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Gareth Stockwell
> Sent: Tuesday, July 15, 2003 2:47 AM
> To: pymol-users
> Subject: [PyMOL] PyMOL tutorial
> 
> Dear PyMOL-ers,
> 
> I have made a couple of PyMOL resources available on my website which
> may be of interest:
> 
> 1. A tutorial, aimed at beginner to intermediate users (I wrote it to
> advertise PyMOL to my research group).
> This is browsable on the web, or downloadable as a PDF file.  You can
> also download an archive (tar-gzip for Unix, or zipped for Windows)
> which contains some example scripts and the data files they require.
> 
> 2. (Unix users only)  A shell script which generates an MPEG movie,
> given a set of PyMOL-generated frames (i.e. PNG files).  The MPEG is
> built using the Berkeley MPEG encoder.
> 
> You can find both of them at
> 
>   http://www.ebi.ac.uk/~gareth/work/pymol
> 
> Gareth
> 
> --
>
------------------------------------------------------------------------
--
> -----
>  Gareth Stockwell
>  EMBL - European Bioinformatics Institute
>  Wellcome Trust Genome Campus
>  Hinxton
>  Cambridge CB10 1SD
> ga...@eb...
>  Tel 01223 492548
> http://www.ebi.ac.uk/~gareth
> 
> 
> 
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