To finish this thread -- Jmol and JSmol can now read (basic) PyMOL 1.8 PSE
files that have
set dump_binary, 1
for faster loading and smaller file sizes. Jmol only implements a small,
basic range of PyMOL functionality, of course.
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.6/Ve
I'll continue this off-list with Bob. Anyone who's interested in following
along please drop me an email :)
On 08 Aug 2016, at 17:38, Robert Hanson wrote:
> Almost have it. Having trouble fitting all that into 120 bytes, though. I'm
> good through bytes 96-99, visrep. Somehow, though I count 1
Almost have it. Having trouble fitting all that into 120 bytes, though. I'm
good through bytes 96-99, visrep. Somehow, though I count 124 bytes total,
not 120 (which is clearly the case in the PSE file). What is
sizeof(AtomInfo_1_8_1) ? I calculate:
...
100-105 (six booleans)
106-111 (six characte
Ah, that is what I needed. For some reason that file is not in the download
I unzipped. Much more sensible!
Bob
On Mon, Aug 8, 2016 at 3:18 PM, Thomas Holder wrote:
> On 08 Aug 2016, at 16:01, Robert Hanson wrote:
>
> > I see this in 1.8.2.1:
> >
> > #define _PyMOL_VERSION "1.8.2.1"
> >
> > an
On 08 Aug 2016, at 16:01, Robert Hanson wrote:
> I see this in 1.8.2.1:
>
> #define _PyMOL_VERSION "1.8.2.1"
>
> and in AtomInfo.h:
>
> #if _PyMOL_VERSION_int < 1770
> #define AtomInfoVERSION 176
> #define BondInfoVERSION 176
> #elif _PyMOL_VERSION_int < 1810
> #define AtomInfoVERSION 177
>
I see this in 1.8.2.1:
#define _PyMOL_VERSION "1.8.2.1"
and in AtomInfo.h:
#if _PyMOL_VERSION_int < 1770
#define AtomInfoVERSION 176
#define BondInfoVERSION 176
#elif _PyMOL_VERSION_int < 1810
#define AtomInfoVERSION 177
#define BondInfoVERSION 177
#else
#define AtomInfoVERSION 181
#define
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),
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 en
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. Ri
