I do like the compactness of that and the quicker loading, but I do see how
this could be a nightmare. I'm looking at a file that lists the dump
version as 1.8.1, but I don't even see how that would ever work, since in
that AtomInfo structure the ANISOU data is just a 64-bit pointer. That
would end up just a useless reference, wouldn't it?
On Mon, Aug 8, 2016 at 10:05 AM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:
> Hi Bob,
>
> I assume those are PSE files with setting "pse_binary_dump=on". This is
> not the default. You can load such files into PyMOL, set
> pse_binary_dump=off and save it as a regular serialized PSE. I definitely
> recommend the conversion step over reimplementing the "pse_binary_dump"
> decoding. Right now there are 3 binary atom layouts (for 1.7.6, 1.8.0 and
> 1.8.2). Grep the PyMOL code for "AtomInfoTypeConverter" if you're
> interested in the details.
>
> The default (in 1.8.2) is to save PyMOL 1.7.6 compatible PSE files, and
> with the "pse_export_version" setting you can also export for older PyMOL
> versions.
>
> Cheers,
> Thomas
>
> On 08 Aug 2016, at 07:57, Robert Hanson <hans...@stolaf.edu> wrote:
>
> > Thomas,
> >
> > In reading PyMOL PSE files into Jmol I have recently run into the
> problem with some of these files (version 1.8.2.3). Jmol has no problem
> reading the standard Pickle format, but there seems to be an option in
> PyMOL to serialize binary data structures as BINSTRING or SHORT_BINSTRING
> format along with other standard strings. This sounds like a great idea; I
> have no doubt that this will lead to considerably smaller PSE files and
> also faster loading. However, I'm struggling with atom information
> deserialization.
> >
> > Q: Is this the default format now for saving PyMOL PSE files?
> >
> > Q: Is there a way to turn that off?
> >
> > Q: In order to do this properly, how many versions of the atom info data
> structure do I need to be able to process?
> >
> > Bob
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
