Re: [Jmol-users] how export in fractional coordinates

apparently is the 2nd option a Jmol bug because by typing : print {1.1}.length = 10 print {1.2}.length = 20 print {1.1 and 1.2}.length = 10 I sent you the file too. Thanks, Piero Bob, I sent the file to you -- Please consider the environment before printing this e-mail. Pieremanuele Cane

Re: [Jmol-users] Jmol and crystallography: the paper

Excellent - lots of beautiful examples showing why Jmol is a "killer" app! Dean On Thu, Sep 2, 2010 at 3:21 PM, Robert Hanson wrote: > *This just in! > * > > *J. Appl. Cryst.* (2010). *43* [ > doi:10.1107/S0021889810030256] > *Jmol* - a paradigm sh

Re: [Jmol-users] how export in fractional coordinates

Piero wrote: > 2) I cannot find in the script guide how to get the number of atoms of a certain frame. For instance I have a MgO cell with 4Mg and 4O atoms how can I know that the structure has 4 Mg and 4O? Maybe {1.1 and _O}.length or is it .size ? --

Re: [Jmol-users] camera dependent slab setting

Hi Bob, I set up a web page to clarify what I mean: http://weirdbyte.de/jmol-test/html/nav.html There are three applet, showing a protein in the same orientation. The first applet shows the protein in the normal - non navigation - mode and has some atom obscuring most of the rest. The second a

Re: [Jmol-users] how export in fractional coordinates

I found it. THIRD possibility: It was file reading bug that only affected the CrystalReader, but not a CrystalReader bug. Bob 2010/9/3 Angel Herráez > Piero wrote: > > > 2) I cannot find in the script guide how to get the number of atoms > of a > certain frame. For instance I have a MgO cell wi

Re: [Jmol-users] camera dependent slab setting

It seems to me that is what the standard SLAB command is for. Right? If you use slab on slab 60 # or whatever set slabByAtom it might be very close to what you are talking about. Bob On Fri, Sep 3, 2010 at 9:36 AM, Alexander Rose wrote: > Hi Bob, > > I set up a web page to clarify what I me

Re: [Jmol-users] More on NIH Resolver

Ho, ho, HO! No kidding! Wow... 3D to 2D! I suppose you want this as a built-in Jmol option now... On Thu, Sep 2, 2010 at 9:24 PM, Otis Rothenberger wrote: > The NIH Resolver will generate a gif image of the Lewis line structure > of a submitted SMILES. I ignored this feature because I thought it

Re: [Jmol-users] Find SMILES problem

got it -- a SMILES generator bug. On Thu, Sep 2, 2010 at 2:50 PM, Otis Rothenberger wrote: > Bob, > > The ring is flat, but it has two sp3 carbons (CH2's). To make sure this was > not associated with my post model change processing, I reproduced the effect > by building benzene from methane foll

Re: [Jmol-users] odd results (12.0.11 and 12.1.9)

When you have multiple layers of translucent objects, it is possible to get some odd effects. On Thu, Sep 2, 2010 at 8:01 AM, Pshemak Maslak wrote: > A case of odd outcome. > > I have run the following in 12.0.11 and 12.1.9 (and compared to 12.0,8 > which I happen to have on my website):: > >

Re: [Jmol-users] More on NIH Resolver

Bob, Yeah, it's amazing how fast this is done. It's not a database look-up. It's being done on the fly from SMILES. But here's the big thing. The Resolver molfile has stereo information. I checked this out because on the Web site their embedded JME will translate the word taxol (or any SMIL

Re: [Jmol-users] More on NIH Resolver

Oh my, it's this simple! http://cactus.nci.nih.gov/chemical/structure/CCC%28C%29CC/file?format=jme OR http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=jme Otis Otis Rothenberger chemagic.com On 9/3/2010 11:26 AM, Otis Rothenberger wrote: Bob, Yeah, it's amazing how fast

Re: [Jmol-users] camera dependent slab setting

Hi, - Ursprüngliche Mail - > Von: "Robert Hanson" > An: jmol-users@lists.sourceforge.net > Gesendet: Freitag, 3. September 2010 16:46:50 > Betreff: Re: [Jmol-users] camera dependent slab setting > It seems to me that is what the standard SLAB command is for. Right? > In a way, but it's

Re: [Jmol-users] odd results (12.0.11 and 12.1.9)

On 9/3/2010 11:06 AM, Robert Hanson wrote: When you have multiple layers of translucent objects, it is possible to get some odd effects. I am not surprised by that, but by the fact that they are different in the three Jmol versions. PM PS. Congrats on your crystallography paper. I have to

Re: [Jmol-users] camera dependent slab setting

So I think we could set some slab option to be dependent upon zoom. For example: slab 5.0 a decimal here would indicate that at whatever zoom level you are at, the slab would be set to be wherever the visual range is 5.0 Angstroms. Something like that? On Fri, Sep 3, 2010 at 11:10 AM, Alexande

[Jmol-users] True Jmol Depict Jmol to JME

This is an outgrowth of the gif image note, but its a new subject. So new chain... Here's a true Jmol depict - i.e. Jmol model kit mode 3D --> JME stereo 2D http://chemagic.com/web_molecules/script_page_large.aspx Click The Molecular Editor link; Click the Draw link. Click the Depict link; T

Re: [Jmol-users] how export in fractional coordinates

ok Thanks a lot huh! -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@kent.ac.uk mobile: +44 (0) 7772-975