The WRITE command writes pixel for pixel exactly what is on the screen,
provided you are using
set antialiasDisplay
so perhaps it's an issue with that. You could always use
zoom 80
zoom 90
(as in percent) to get a bit more margin before issuing the WRITE command.
Bob
On Sun, Aug 18, 2013 at 11:18 PM, James <[email protected]> wrote:
> Works great! I had forgotten about backticks because I was using "system."
> I had some awful syntax issues (I'm on windows - my double quotes versus
> single quotes seem to work backwards form what your code uses sometimes -
> I'm on windows, wonder if that matters), but got it working, which I would
> not have without your code to make me believe it actually did work given
> all the ways I wrote it that did not work (just due to syntax uggghhh!).
> Thanks!
>
> One largely-unrelated question: When outputting an image file, if you are
> looking at the bound box straight on and then export, Jmol runs the edge of
> the image RIGHT up to the bound box. Not only does this not give any margin
> space, but I think it actually cuts off half of the outermost atoms
> (presumably because if you display in sticks and balls, atoms have width,
> but I'm guessing that bound box goes through the center of the atoms). Is
> there any way to ask the bound box, or the "write" routine, to provide some
> margin space?
>
> Sincerely,
> James Ryley, PhD, Patent Agent
> SumoBrain: Intellectual Property Solutions & Data
> AcclaimIP <https://www.acclaimip.com/> |
> FreePatentsOnline.com<http://www.freepatentsonline.com/>|
> SumoBrain.com <http://www.sumobrain.com/> |
> BioMedSearch.com<http://www.biomedsearch.com/>
>
> This communication is confidential and may be subject to legal privilege.
> Nothing contained herein should be construed as legal or patenting advice.
>
>
> On Sun, Aug 18, 2013 at 3:03 PM, Rolf Huehne <[email protected]>wrote:
>
>> Am 18.08.2013 20:09, schrieb Rolf Huehne:
>> > In Perl it could look like this (not tested):
>> >
>> > --------------
>> > chdir("my_jmol_path");
>> > my @jmol_output = `java -jar JmolData.jar -n -J 'function
>> > my_print(value) {for (var z in value.lines) { print "DATA:\t" + z; }}
>> > my_print("Hello from Jmol"); load =1deh; my_print(script("show
>> > orientation"));'`;
>> >
>> > foreach my $jmol_output_line(@jmol_output) {
>> > my $data = substr($jmol_output_line, 5);
>> > print $data;
>> > }
>> > --------------
>> >
>> Sorry, I forgot the test for "DATA: " at the beginning of the output loop:
>>
>> if (substr($jmol_output_line, 0, 5) eq "DATA: ") {
>> ...
>> }
>>
>> Regards,
>> Rolf
>>
>>
>> --
>>
>> Rolf Huehne
>> Postdoc
>>
>> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
>> Beutenbergstrasse 11
>> 07745 Jena, Germany
>>
>> Phone: +49 3641 65 6205
>> Fax: +49 3641 65 6210
>> E-Mail: [email protected]
>> Website: http://www.fli-leibniz.de
>>
>> Scientific Director: Prof. Dr. K. Lenhard Rudolph
>> Head of Administration: Dr. Daniele Barthel
>> Chairman of Board of Trustees: Dennys Klein
>>
>> VAT No: DE 153 925 464
>> Register of Associations: No. 296, Amtsgericht Jena
>> Tax Number: 162/141/08228
>>
>>
>>
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>
>
>
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--
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
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