Dear Bob
I have been trying out your new .pmesh feature. It works well for me, both in
JSmol and in Jmol_S.
Thanks very much: that solves my timing problems with orbital contour plots
in a plane, and I will work
on converting the web pages concerned to read in pre-saved isosurfaces instead
of calculating them
from the orbital data. I will read contours from .pmesh files and orbital
surfaces from .jvxl files.
The only thing I noticed was that the .pmesh files were rather large at half a
megabyte each, for pretty small
orbitals with only 21 contours, extending over about 5 Angstroms each. I found
that these could be
compressed using gzip to about 140 kB, and Jmol_S or JSmol would still read
them without obviously more
delay.
I just wonder whether all that precision is necessary, for models which are
only going to be assessed by eye,
relatively quickly. I don’t know how easy it is to control numeric output
format in the languages you are
using, or whether lower precision would be compatible with existing routines
for reading .pmesh files.
It just occurred to me that if one was going to use this method a lot, it would
save server file space
and users’ downloads if the files could be a bit smaller.
Thanks again
Bruce
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 20 April 2017 16:47
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.14.1
OK - this is better: Looking for the latest version? Download
Jmol-14.14.1-binary.zip (69.7 MB)
<https://sourceforge.net/projects/jmol/files/latest/download?source=files>
On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
hmm. something is missing there. I had to delete that and will upload again.
On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
Jmol.___JmolVersion="14.14.1" // released 4/19/17
new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
-- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file format)
-- relatively compact format
-- can speed up loading of meshes and contours
-- for filled surfaces, use .jvxl instead
-- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
-- note that binary files are NOT RECOMMENDED for JSmol because some
platforms cannot read them locally
-- example:
load $methane
isosurface plane {0 0 0 1} map vdw contours 20
write ISOSURFACE contour.pmb
isosurface contour.pmb
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