look here: https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/AtomInfoHistory.h
The AtomInfoType_1_8_1 version (used in 1.8.2) stores ANISOU as shorts (PDB precision). The AtomInfoType_1_7_7 version (used in 1.8.0) doesn't support ANISOU (will indeed write an unused NULL pointer), at the time it was work in progress for a specific use case which didn't require ANISOU. Cheers, Thomas On 08 Aug 2016, at 11:32, Robert Hanson <hans...@stolaf.edu> wrote: > 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. ------------------------------------------------------------------------------ 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
