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
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
