Hi Rob,
Assuming that none of the molecular model formats support saving either
general visible annotations or atom labels, and that the solution is to
write an SPT, JMOL or PNGJ, as Rob suggested, that would be perfect if JMol
was the only program other users needed. But, the actual modeling m
Hi Angel,
Thanks for the info. With respect to this:
> > Assuming that none of the molecular model formats support saving
> > either general visible annotations or atom labels, and that the
> > solution is to write an SPT, JMOL or PNGJ, as Rob suggested, that
> > would be perfect if JMol was the
On Wed, May 8, 2013 at 11:23 AM, James Ryley wrote:
> Hi Rob and Angel,
>
> Thank you for clarifying this.
>
>
> and thereby asking if I am misunderstanding something about .pdb. I guess
> these generally are not visual annotations/labels as I am thinking of.
>
All those PDB header records are r
On 8 May 2013 at 12:23, James Ryley wrote:
> and thereby asking if I am misunderstanding something about .pdb. I guess
> these generally are not visual annotations/labels as I am thinking of.
I agree. They are not associated to atoms.
Some of those records, like SITE, are indeed read and used by
Hi Rob and Angel,
Thank you for clarifying this.
To address Rob's question about what functions of the various file formats
are ignored, I'm no expert on the .pdb format, but in reading the .pdb file
spec here:
ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf
it appears
Some additional thoughts:
Jmolis not meant to be a format converter.
Whatever information is in the original file, it remains there
available.
Whatever features were added in Jmol, they are saved into Jmol state
and hence included in both JMOL or PNGJ formats.
So the need to export (Jmol-specif
Hello, James
Precisely!
PDB format has no place for atom labels or annotations, that why Jmol
cannot save that.
You can save to a "JMOL" file which is a file (actually a gzipped set
of files) that holds everything. Of course, that file can only be
opened by Jmol, You can also save to a specia
On Wed, May 8, 2013 at 8:06 AM, James Ryley wrote:
> If you open a .pdb, add a label to one or more atoms, and then “write PDB
> test.pdb”, the resulting file doesn’t seem to have the annotations. I could
> be missing something, like having my default for pdb annotations being
> “off”. But, assum
If you open a .pdb, add a label to one or more atoms, and then "write PDB
test.pdb", the resulting file doesn't seem to have the annotations. I could
be missing something, like having my default for pdb annotations being
"off". But, assuming that is not the case, can one save annotations and
labels
Hi Marius
That looks terrific! A great demonstration of Jmol abilities.
I will let others (Bob) reply to your technical questions.
> - Error handling
Probably by using debug levels and callbacks
http://chemapps.stolaf.edu/jmol/docs/#setdebugging
http://chemapps.stolaf.edu/jmol/docs/#setcallb
Marius,
Welcome! I take it that your art is interactive and kinetic? Very cool.
On Wed, May 8, 2013 at 5:46 AM, Marius Watz wrote:
> Hi,
>
> - Error handling
>
Implement try/catch on your end; but if you are doing things properly, you
should not see errors (ultimately...)
> - Script status
Ah, I see. Sure. I missed that. The Wiki info looks terrific now. Nice use
of JavaScript objects.
On Wed, May 8, 2013 at 4:54 AM, Angel Herráez wrote:
> > It was a bug in JSmol.js Browsers will differ, but at least FF and
> > Chrome will update while you move -- actually 100 ms after you stop
>
Hi,
I'm a new Jmol user working on a semi-complicated project using Jmol to
create some weird and wonderful molecular renderings. (See
http://flic.kr/s/aHsjEXdyUY)
I need the full power of an integrated Java application, so far I have
implemented a functioning rendering framework that controls
> It was a bug in JSmol.js Browsers will differ, but at least FF and
> Chrome will update while you move -- actually 100 ms after you stop
> resizing.
Ok, thanks. That's better, resize now works.
> Then that's a bug. I had that fixed, I'm sure. Don't reload the
> state.
Anyway, I was using "r
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