Re: [Jmol-users] Jmol-14.6.4

[Scalfani, Vincent]

This is an awesome addition to Jmol. Thanks again Bob!

I’m curious if there is any advantage to using STL ASCII over STL Binary? I 
have not found a difference with processing these formats in our 3D Printer 
software applications.

Vin


—
Vincent F. Scalfani, Ph.D.
Science and Engineering Librarian
University Libraries
The University of Alabama
109 Rodgers Library
Box 870266
Tuscaloosa, AL 35487
Phone 205-348-5806
vfscalf...@ua.edu | 
-0002-7363-531X





From: Mike Casey [mailto:mike.ca...@ucd.ie]
Sent: Monday, October 03, 2016 2:52 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol-14.6.4

Many thanks Bob, that's another very useful addition to what is already an 
enormous feature set.
Mike


Dr Mike Casey
School of Chemistry
UCD
Dublin
01 716 2420

On 3 October 2016 at 06:14, Robert Hanson 
> wrote:
Jmol users,

I finally took a look at how 3D printer formats WRL and STL work and what it 
would take to get them working in Jmol. It turns out, not too much! The key 
with WRL is to not use high-level objects such as built-in standard VRML 2.0 
Cone, Cylinder, and Sphere nodes. Once those were dispensed with, it was simple 
enough to implement both STL binary (Jmol default) and STL ASCII (set debug 
TRUE) options. So, Jmol now can be used to produce color (WRL) or monochrome 
(STL) 3D printer input files.
(Note that write xxx.STL is only implement in the Java version of Jmol in this 
release. The next release will also implement it in JSmol/HTML5, but I'm not 
sure that would be recommended anyway; these files can get very very large, and 
it is not clear that that they can be successfully delivered in JavaScript.)

A few additional bug fixes, and it seemed appropriate to go to a new 
subversion, 14.6.4.

Bob

new feature: 3DPrinter-compatible VRML and STL writing.
  -- mesh only; does not use high-level objects Cone, Cylinder, Sphere
  -- extensive use of D EF and USE for small-footprint VMRL files
  -- STL is binary generally, but will be ASCII using SET DEBUG TRUE
  -- write t.wrl
  -- write t.stl

bug fix: COD CIF files have mixed-lower case atom labels (H5a) in bonds def, 
causing Jmol to miss bonds.
bug fix: rogue System.out.println for text rendering.
bug fix: print compare({1.1}, {2.1}, "MAP", "H") broken in 14.6.0_2016.06.14
bug fix: Google Closure Compiler not set up for UTF-8 encoded language class, 
used in pop-up menu.


--
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

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
Check out the vibrant tech community on one of the world's most 
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] JSmol in Institutional Repositories?

[Scalfani, Vincent]

Hello,

I have seen many great incorporations of JSmol in chemical databases and web 
pages. However, I am curious if anyone has incorporated JSmol into an 
Institutional Repository (e.g. Dspace)?

Thanks!

Vin



Vincent F. Scalfani, Ph.D.
Science and Engineering Librarian, University Libraries
The University of Alabama
109 Rodgers Library
Box 870266
Tuscaloosa, AL 35487
Office 205-348-5806
vfscalf...@ua.edu | 
http://lib.ua.edu
[The University of Alabama]

--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] exporting x3d files with specifications

[Scalfani, Vincent]

Dear Christian:

I use the set exportScale. Somewhere in the 10-20 range seems to work well for 
3D printing sizes. Not sure if you can set exact dimensions.

Example:

set exportScale (10.0)


-
Vincent F. Scalfani, Ph.D.
Assistant Professor
Science and Engineering Librarian
The University of Alabama
(205) 348-5806
@vfscalfani



From: Christian Baerlocher [mailto:christian.baerloc...@mat.ethz.ch]
Sent: Tuesday, September 30, 2014 10:11 AM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] exporting x3d files with specifications

Dear Bob,

One of my users wants to export x3d files for 3d printing. It works, but he has 
a question. He writes:

Our 3-D printer expert would like the X3D file with mm units and scaled so the 
longest side is under 200 mm?  Is that possible?

Can I specify this somehow?

Thanks for your help

Christian






--
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Using Jmol to convert crystals into 3D Printable files

[Scalfani, Vincent]

Thanks Bob,

We did include Jmol briefly in Scheme 1 and the supporting info. ☺ Actually now 
I see a mistake in Scheme 1, it should also have .cif to .wrl with Jmol, not 
just .pdb to .wrl.

That work was actually done a year ago (J. Chem. Ed is very slow….) before we 
discovered Jmol as a great route and that is really unfortunate, because by far 
the easiest way is to use Jmol.

I was actually just going to send you a note, that we should write up an update 
with using Jmol and the RSC repository. Especially since now we are exclusively 
using Jmol.

Cheers,

Vin

P.S. An STL writer in Jmol would be AWESOME!













From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Thursday, September 04, 2014 6:57 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Using Jmol to convert crystals into 3D Printable files

... and don't forget to check out the cover article:

http://pubs.acs.org/action/showLargeCover?jcode=jceda8vol=91issue=8
Bummer that you didn't indicate the possibility of

Jmol -- WRL
there. Seems to me that would be at least as good as using Diamond or Mercury. 
Any particular reason for that, Vincent?

I guess we should get an STL writer set up in Jmol.
Bob
​
--
Slashdot TV.  
Video for Nerds.  Stuff that matters.
http://tv.slashdot.org/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Using Jmol to convert crystals into 3D Printable files

[Scalfani, Vincent]

Yes, I think they are always only triangles?? Though many small triangles can 
make a nice sphere…

There are typically some holes in the surface where the bonds meet the atoms, 
and we are able to correct this with Netfabb.



From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Friday, September 05, 2014 9:53 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Using Jmol to convert crystals into 3D Printable files

It's not a great format, but we do that for other formats as well.

On Fri, Sep 5, 2014 at 9:35 AM, Angel Herráez 
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote:
5 Sep 2014, 9:12, Robert Hanson wrote:

 On Fri, Sep 5, 2014 at 8:29 AM, Scalfani, Vincent 
 vfscalf...@ua.edumailto:vfscalf...@ua.edu
  wrote:

 P.S. An STL writer in Jmol would be AWESOME!

 show me the spec.

The info I see for STL in Wikipedia speaks only of triangles. We'd
need cylinders and spheres too for a good rendering, right?



--
Slashdot TV.
Video for Nerds.  Stuff that matters.
http://tv.slashdot.org/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users



--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
--
Slashdot TV.  
Video for Nerds.  Stuff that matters.
http://tv.slashdot.org/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Using Jmol to convert crystals into 3D Printable files

[Scalfani, Vincent]

Hello,

Bob's recent Jmol update email reminded me that many of you may be interested 
in our little project of using Jmol to batch convert crystal structures from 
the COD into 3D printable files (.wrl and .stl). We are working with the RSC to 
develop an online repository for these files.

Here is my recent talk at ACS in San Francisco:

http://www.slideshare.net/AntonyWilliams/accessing-3d-printable-structures-online

And here is the beta RSC repository direct link (UI coming soon):

http://api.beta.rsc-us.org/Crystals/v1/cod/


Many thanks to Bob, Antony Williams, Valery Tkachenko, and everyone else for 
making this possible.

Enjoy!

Vin


-
Vincent F. Scalfani, Ph.D.
Science and Engineering Librarian
The University of Alabama
(205) 348-5806

--
Slashdot TV.  
Video for Nerds.  Stuff that matters.
http://tv.slashdot.org/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users