Re: [Jmol-users] R/S asymmetric carbon

On Thu, January 12, 2012 4:29 pm, FyD wrote: > Dear All, > > Is it possible to report R/S asymmetric carbons with Jmol? > > thanks, regards, Francois No, Jmol can't, in general, provide this information. RIch -- RSA(R)

Re: [Jmol-users] Molecular view (CIF)

On Mon, July 18, 2011 11:34 am, Robert Hanson wrote: > You should be able to get the correct molecular view even without any {xxx > xxx xxx}, but maybe only if you use the latest build. Would you please > try > that? http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip > Bob, Would it ma

Re: [Jmol-users] Molecular view (CIF)

On Fri, July 15, 2011 1:02 pm, r...@ellerbach.com wrote: > On Fri, July 15, 2011 12:52 pm, s...@publcif.co.uk wrote: > [snip] >>> >>> So what is the generic command that'll load a molecule and display all >>> of >>> those (complete) molecules that have an atom within a unit cell? >>> >>> Rich >>> >

Re: [Jmol-users] Molecular view (CIF)

On Fri, July 15, 2011 12:52 pm, s...@publcif.co.uk wrote: [snip] >> >> So what is the generic command that'll load a molecule and display all >> of >> those (complete) molecules that have an atom within a unit cell? >> >> Rich >> >> > load "" {444 666 1}; display within(molecule, cell=555) > might

Re: [Jmol-users] Molecular view (CIF)

On [2011-Jul-14] Robert Hanson wrote: > OK, I got it. In generating models, Jmol was not establishing this connection: > > C4 C6 2_855 1.393(3) > [snip] > I'll take a look at this and get back to you. I'm a bit surprised that Jmol can't handle it directly, but here's how you do it: > > load

Re: [Jmol-users] Java 1.5 vs 1.6 on Macs?

On Tue, April 26, 2011 4:13 pm, Eric Martz wrote: > I recently noticed that a colleague, using a Mac with Snow Leopard OS > 10.6, has Java 1.6.0_24. In contrast, the java running Jmol on my Mac > with (plain old) Leopard OS 10.5 is version 1.5.0_28, despite my > having run all Apple Updates. > > If

Re: [Jmol-users] writing .mol files

Yeah, I know. I was sure you'd say that. :-) Unfortunately it isn't a machine I have any control over. But I will send the suggestion. Rich On Fri, April 15, 2011 9:02 am, Robert Hanson wrote: > Yeiks! 11.2! upgrade! > > On Fri, Apr 15, 2011 at 7:40 AM, wrote: > >> Thanks Bob. >> >> I brought t

Re: [Jmol-users] writing .mol files

Thanks Bob. I brought the Jmol screen back up this morning, opened the Jmol Script console and entered: print write("coord", "mol") and got back: print write("coord","mol") pending script compiler ERROR: command expected print write("coord", "mol") This is for Jmol 11.2.

[Jmol-users] writing .mol files

If I have selected just the "good" atoms of an interesting molecule in a binding pocket will "write file.mol" or "write coords file.mol" give me just those atoms in the file? I can't actually test this since the server, at the moment, has neither a current version of Jmol nor the signed applet on

Re: [Jmol-users] obj surface files exported from pymol

On Wed, November 24, 2010 10:17 am, Alexander Rose wrote: > Manipulating the pdb file before creating the surface with PyMOL does not > work because the PyMOL obj has no relation to the pdb coordinates. Isn't this something pymol should do? Maybe suggest a bug-fix/enhancement on the pymol list? R

Re: [Jmol-users] Possible problem with the representation of a double bond

Understood Bob. I think having a parameter for it would be good and I think the default should be: multipleBondSpacing = 0.35 multipleBondCylinderThickness = 0.75 (or however you want to code it) Rich On [2010-Sep-10] Robert Hanson wrote: > This isn't thickness, it's distance apart. We could a

Re: [Jmol-users] Possible problem with the representation of a double bond

On Fri, September 10, 2010 9:19 am, Robert Hanson wrote: > that can be experimented with at > http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?topic=11 > > I think this could be a new default. Let's talk about it. > > On Fri, Sep 10, 2010 at 7:31 AM, Robert Hanson wrote: > >> Uploading now

[Jmol-users] bug in app 12.1.10?

Jmol Application 12.1.10 on MacOSX 10.5.8 with FF 3.6.7 or X11 If I'm rotating a molecule in Jmol and switch over to FF or X11 and type text or scroll the page and then click back into Jmol the leftmouse button no longer rotates the molecule but either translates it or zooms it. It appears that Jm

Re: [Jmol-users] Possible problem with the representation of a double bond

Bob, My choice of words is leading to some confusion. In the current implememtation as the model is rotated the double bond rotates so the user sees two sticks in almost all orientations. This requires rotating the bond cylinders as the molecule rotates. Sometimes the aliasing of edges of the cyl

Re: [Jmol-users] Possible problem with the representation of a double bond

Something else to consider is the intent of the display. Sitting at the screen rotating a molecule by hand to get to a particular view of the molecule is one thing. Creating a movie which is is presumably intended to illustrate something about the molecule is another. In the former having things j

Re: [Jmol-users] Jmol 12.0 release -- feature check

Why is Jmol 12.0 called Jmol-11.zip? Rich > > > Uploaded version is at > http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip > -- This SF.net email is sponsored by Sprint What will you do first with EVO,

Re: [Jmol-users] faulty output of write('PDB')

Robert Hanson wrote: > Jmol is not attempting to write a perfect PDB file, especially when > the data are not originally PDB data. I'll look into the occupancy > issue. I think that should be proper if the file has occupancy data. > Since the PDB-format is such a fundamentally broken one it is pr

Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model

Otis Rothenberger wrote: > Bob, > > This is the cat's meow. Thanks for the help. I'm still stuck with a > server side approach (AJAX very frustrating!), but the "Jmol load > completed" approach seems to work. Cholestane is below. What a slick > way to communicate 3D models via email: > > http://

Re: [Jmol-users] Jmol "3D-SCULPT" mode

I agree with Angel. I think Jmol should be a professional-level display tool and there should be an educational-level tool for the molecule manipulation functions. The focus/needs of the two groups are different enough that one program is never going to satisfy the two groups and the compromis

Re: [Jmol-users] ah, this is very, ah, WEIRD

Yep, fixed. Rich Robert Hanson wrote: > Mac-side bug fixed. Please do check this out: > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=135 > > Bob > -- ___

Re: [Jmol-users] ah, this is very, ah, WEIRD

nada Rich Robert Hanson wrote: > so you don't even see a structure? > > On Thu, May 20, 2010 at 7:07 PM, Philip Bays > wrote: > > Bob: > > I click on the red text in the description which transfers the > command to the command area under the applet. Clic

Re: [Jmol-users] RC9-11 nonstarters?

on OSX 10.5.8 Rich Robert Hanson wrote: > http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol.jar > > On Tue, May 18, 2010 at 7:35 PM, rgb <mailto:r...@ellerbach.com>> wrote: > > Robert Hanson wrote: > > Did you try my latest, Rich? > > >

Re: [Jmol-users] RC9-11 nonstarters?

Robert Hanson wrote: > Did you try my latest, Rich? > > http://chemapps.stolaf.edu/jmol-docs/examples-11/Jmol.jar ? > That link gives: The requested URL /jmol-docs/examples-11/Jmol.jar was not found on this server. I can't test with my work version until I'm back in the lab/office. The version

Re: [Jmol-users] RC9-11 nonstarters?

Robert Hanson wrote: > Yes, the issue is definitely the Java version.We changed to 1.5 > recently. Actually, from what I could tell, we were using 1.5 > functionality already for several months. It looks like Eric is > probably using Java 1.4. > > Eric, if that's the case, first thing to do is

Re: [Jmol-users] RC9-11 nonstarters?

Running OSX 10.5.8. Downloaded jmol-12.0.RC12-full.tar.gz and double clicked on the jmol.jar file. Error to console is: Exception in thread "main" May 18 14:57:39 xrayMP [0x0-0x40040].com.apple.JarLauncher[771]: java.lang.UnsupportedClassVersionError: Bad version number in .class file May 18 14:57

Re: [Jmol-users] Jmol Virtual Model Kit

On Fri, April 9, 2010 12:16 pm, Otis Rothenberger wrote: > > Downside: It's a helper application. Upside: ACD generously makes > ChemSketch a free download for private, student, educational use. > Isn't ChemSketch a MSWindows-only product? Rich --

Re: [Jmol-users] Jmol align

On Mon, 15 Mar 2010 14:33:08 -0500, Robert Hanson wrote: > "Spacial" doesn't really describe it. > > The method goes like this: > > --Identify pairs of matched residues (as opposed to atoms). > So not of general use but limited to the special cases of nucleic acids and proteins. Rich ---

Re: [Jmol-users] Jmol align

On Mon, 15 Mar 2010 13:48:19 -0500, Robert Hanson wrote: [snip] > > Be that as it may, I'm also quite happy to change the name to anything > reasonable. Since it's not just doing (at this point) a standard > matrix-based RMSD minimization operation (which is what you want to call a > superpositi

Re: [Jmol-users] Jmol align

On Mon, 15 Mar 2010 11:29:40 -0500, Robert Hanson [snip] > > The operation Jmol is performing is definitely an alignment of sorts; I can > certainly be careful not to claim it is "structural" alignment if that term > is now synonymous with something more involved. "of sorts" It really is a su

Re: [Jmol-users] black-and-white ORTEP diagrams? (was : CCL: Visualizing Software)

On Tue, 9 Mar 2010 17:22:39 +0100, Egon Willighagen wrote: > On Mon, Mar 8, 2010 at 2:57 PM, Robert Hanson wrote: >> That's ridiculous. Sorry, but to try to go retro on this is just too >> strange. > > :) > > I agree; don't shoot the messenger. Especially when there is a free program (Mercury)

Re: [Jmol-users] black-and-white ORTEP diagrams? (was : CCL: Visualizing Software)

I kinda agree with Bob. I certainly wouldn't want Jmol to be able to produce something of the quality of the image in that first link Egon quoted :-) But, if Jmol is to be a tool to produce hard-copy images for publications then an argument could be made for a really good-looking ORTEP style image

Re: [Jmol-users] auto-orientation?

On Tue, 16 Feb 2010 12:04:32 -0800, Thomas Stout wrote: > To follow up on my question from last week concerning "auto-orientation", > Rolf Huehne very graciously pointed me in the direction of a solution that > he had already crafted for JenaLib. He uses the dimensions of the bounding > box, sele

Re: [Jmol-users] Electron Density Map Demo

Robert Hanson wrote: > Keep talking, Rich. I don't quite have it. > > I have a file of numbers. An isosurface is produced not by contouring > but by finding the surface that intersects that cube of numbers at a > specific "cutoff" value. > > > dmin dmax dmean (density min max mean) > > >

Re: [Jmol-users] Electron Density Map Demo

On Tue, 19 Jan 2010 14:03:32 -0600, Robert Hanson wrote: > Is that in the file somewhere? What I have is > > dmin dmax dmean (density min max mean) > > rms > > Now, I DON'T think the "rms" is really "rms" -- I think it's rms deviation, > but I could be wrong about that. What seems to work as a

Re: [Jmol-users] Electron Density Map Demo

The "sigma" is the esd (estimated standard deviation) for the value of the electron density at any grid point. So if the electron density calculations provide an esd of 1.2 electrons per cubic angstrom the 1 sigma contour lines would be at 1.2, the 2 sigma lines at 2.4, 3 sigma at 3.6 etc. Rich O

Re: [Jmol-users] feature suggestions

How do you decide on how pyramidal (or not) to make a N Bob? What about hydroxyl H atoms when there is the potential for intramolecular H-bonding? Rich On Fri, 15 Jan 2010 11:01:22 -0600, Robert Hanson wrote: > OK, that's in. See Jmol 11.9.19 --- > http://chemapps.stolaf.edu/jmol/docs/example

Re: [Jmol-users] multi-touch terminology: swipe

On Thu, 14 Jan 2010 18:54:46 +0100, Angel Herráez wrote: > El 14 Jan 2010 a las 11:24, Robert Hanson escribió: >> A "swipe" means you drag and the motion stops at the exact moment >> that the mouse is released. > > So the key is whether you release the button (swipe) or not (drag). > Thanks >

Re: [Jmol-users] what is Jmol for?

It detracts from the time devoted to the development of Jmol more than anything else. I don't disagree that some things might be of interest down the road but given the limited development resources I think they should be focused on the functionality related to the display of small and large mo

[Jmol-users] what is Jmol for?

As interesting as it is to plot stuff I really don't see the purpose of putting time and effort into making Jmol a generic 3D plotting program. Maybe if its abilities and interface were perfected for plotting molecules (large and small) then there might be some impetus to create Jplot (or something

Re: [Jmol-users] bond order

On Tue, September 22, 2009 3:30 pm, Robert Hanson wrote: > multiple bonds -- I guess this depends upon your definition of "ideally." > Others feel that "ideally" the bonds should rotate so that there is never > a > question as to their order. In addition, this introduces the ambiguity in > cases su

Re: [Jmol-users] moveto transition data

Ralf Stephan wrote: > Hello, > let's say I have two orientations and want to write 50 > intermediate frames as image files: > > ---From: > moveto 0.0 { -142 866 480 107.35} 100.0 0.0 0.0 {61.260506 38.7915 > 44.659} 50.97134 {0.0 0.0 0.0} 8.481314 102.86942 50.0; > ---To: > moveto 2.0 { -46 -870 49

Re: [Jmol-users] How to select atoms with names ending in '?'

This is a good suggestion Chris. For Ian's problem (since it is a well-defined in-house setup) the preprocessing could change the ? of an atom name to "disordered" (no need to stick with one character). Rich On Wed, April 15, 2009 9:05 am, Chris Foley wrote: > Again, this won't solve the "?" prob

Re: [Jmol-users] How to select atoms with names ending in '?'

tho...@ccdc.cam.ac.uk wrote: > Hi Rich, > > >>> My input file is a CIF and the presence >>> of >>> a trailing question mark in the atom name indicates a disordered atom, >>> e.g. 'C33?'. >>> >> Is this construct a legal CIF atom_site_label Ian? As far as I am aware >> the CIF dictionary d

Re: [Jmol-users] How to select atoms with names ending in '?'

On Tue, April 14, 2009 3:02 pm, tho...@ccdc.cam.ac.uk wrote: > Hello, > > I'm sure there's a really easy way to do this but as a new Jmol scripter > I'm struggling to see how! I need to write a Jmol script to select all > atoms with names ending in '?'. My input file is a CIF and the presence of >

[Jmol-users] atom indexes, serial numbers and names

Have the atom names stayed unique through the various remediation cycles of the PDB? If so use the CIF files with the names rather than the .pdb format files. Rich -- ___ Jmol

Re: [Jmol-users] No more CambridgeSoft Chem3DPro for Macs

Fred Ziegler wrote: > Jmol-ers: > > I still use OSX 10.4.11 (Tiger) on my Macs because it has OS9 > (classic) which allows me to use CambridgeSoft's Chem3DPro to create > minimized .mol files for Jmol display. CambridgeSoft no longer makes > Chem3DPro for OSX but it does for Windows. Short of

Re: [Jmol-users] Letting Jmol make a movie between two views

Thanks for the extra information Bob. I'll incorporate it into my scripting. Rich On Wed, December 3, 2008 9:57 am, Robert Hanson wrote: > how excellent! Good job, Rich. Thank you for sharing this. > > Just a couple of comments: > > The default for Jmol is to render a structure with 100% zoom sca

[Jmol-users] Letting Jmol make a movie between two views

With Bob's implementation of quaternions in Jmol it is *extremely* easy to let Jmol create an image sequence between two user-defined views. This sequence can then be converted into a movie using the standard tools. I did this recently (with Bob's help to get the syntax right) using the application

Re: [Jmol-users] Protein Hydrogen Bonds again

On Thu, November 6, 2008 12:01 pm, David Leader wrote: > > However I still might see if there is a student up to integrating the > C code. My colleague tells me that this is quite sophisticated. For > example it calculates the H atoms and deals with the uncertainty in > serines and threonines, by c

Re: [Jmol-users] Protein Hydrogen Bonds again

On Tue, November 4, 2008 3:23 pm, Thomas Stout wrote: >[snip] > here. The basic premise was: if two appropriate heteroatoms are spatially > located within a set range of separations (1.8-3.4A) and disposed to one > another within a certain angular spread (120-180 degrees) relative to the I think

Re: [Jmol-users] defaults for jmol application

On Sun, May 4, 2008 9:30 pm, Bob Hanson wrote: > Rich, the popup menu is entirely cunstomizable. You can save whatever > modifications you want to a file and then modify it to make it do > whatever you want it to do. So it sounds to me like you should perhaps > consider that as an option and then e

Re: [Jmol-users] defaults for jmol application

On Fri, May 2, 2008 1:24 pm, Angel Herráez wrote: > On 1 May 2008 at 16:03, [EMAIL PROTECTED] wrote: > >> >From a usability perspective most of what is in the right-button menu >> should be in the application menus (and sub menus). The pop-up menu >> should >> be limited to those things that are re

Re: [Jmol-users] defaults for jmol application

Thanks Bob. I understand that that there are some builtin settings for the application that you want to rely on for a consistent look&feel so that is the way it is currently set. One of my points is that the available preference settings within the app do not let a user (or a distributor) configu

[Jmol-users] defaults for jmol application

I've had a look at both 11.4.2 and 11.5.33 and I don't think the default setup of the application is appropriate for new/casual users of chemical crystallography information. When fed a CIF the application puts up a unit cell box with one molecule with the center of rotation not coincident with th

Re: [Jmol-users] Thermal ellipsoid plots?

On Thu, April 17, 2008 10:46 am, Bob Hanson wrote: > Note that I am defining temperature as > > (U11 + U22 + U33)/3.0 * 100 > > If this is not correct, please let me know. (I can't find where I read > that, and I don't know if I remember it correctly.) > David Watkin prefers: Uequiv = (U1*U2*U3)*

[Jmol-users] colouring ADP plots (was Re: Thermal ellipsoid plots?

On Wed, April 16, 2008 6:32 am, Brian McMahon wrote: > Bob > snip > > I doubt that it's Jmol's job to distinguish between "main residue" and > "small moiety", so I would suggest allowing an optional colour scheme > that maps ellipsoid colour to maximum/minimum main axis ADP ratio > that runs somet

Re: [Jmol-users] Thermal ellipsoid plots?

On Mon, April 14, 2008 9:28 am, Bob Hanson wrote: > Brian, I would love to get this into Jmol. I think we can do a fabulous > job of it, but I need to understand how thermal ellipsoids are > designated in common file formats and how one would suggest depicting > them (with the quarter-segment left

Re: [Jmol-users] adding hydrogens

On Mon, January 29, 2007 6:16 pm, Francesco Pietra wrote: > Let me say that a package dealing with molecules that > does not place hydrogens correctly is of no use > professionally. If Jmol was a MM program or even a molecular-editor you might have reason to have such a view. But, Jmol is a molecu

Re: [Jmol-users] Selecting molecules in unit cell -Jmol 11

On Tue, October 3, 2006 12:40 pm, Bob Hanson wrote: > Ah, I see. If they do not cross cell boundaries, you could > > select cell=566 and > > for example. Or, if not, and they are all connected as a single organic > molecule, you could: > > select within(molecule,cell=566 and symop = 1) > > "si

Re: [Jmol-users] Jmol's use of ionic radii

Philip, Bob, It is an unfortunate fact of life that some (many?) CIF parsers rely to some degree on an assumed ordering of dataitems in the CIF. Even the cif-checking software that does structure checking at the IUCr breaks in this regard! The only way to not have this problem is if the CIF is par

Re: [Jmol-users] PDB and crystallography

On Fri, September 8, 2006 2:12 pm, G. Jones wrote: > PDB is fine, I don't know the format of cif files but if I did, or if you > know a link where I can find it then that would be fine to. CIF files are very easy to write since they are free-format in a dataname datavalue style with not very many

Re: [Jmol-users] jmol and space groups

On Tue, September 5, 2006 4:35 pm, Bob Hanson wrote: > In response to requests for Jmol to be able to visualize a wider range > of crystallographic data sets, with the help of Peter and Judith > Murray-Rust and Syd Hall, I've made a preliminary implementation of > space group name analysis in Jmol

Re: [Jmol-users] new documentation popup method

On Wed, September 6, 2006 8:32 am, Bob Hanson wrote: > Jmol users: > > Please test the new documentation pop-up examples. Everything seemed to go OK with FF 1.5.0.6 on OSX 10.3.9 Rich - Using Tomcat but need to do more? Need

Re: [Jmol-users] showing h-bonds with jmol

On Tue, August 29, 2006 2:29 pm, Bob Hanson wrote: > must be a different URL Yep, Bull forgot the enclosing directory. See: http://www.people.virginia.edu/~wrp/bioch503/bioch503_l3.html Rich - Using Tomcat but need to do mo

Re: [Jmol-users] Jmol-11 does not accept blank lines in CIF

On Tue, August 29, 2006 11:49 am, Alan Hewat wrote: > > Well a line starting with a hash such as #Jmolscript: will get carried as > a comment by any CIF parser (I hope) so that should be CIF OK. > The problem is that it is up to the individual parser. Parsers are also allowed to rearrange dataitems

Re: [Jmol-users] Jmol-11 does not accept blank lines in CIF files (it should)

On Tue, August 29, 2006 11:18 am, Bob Hanson wrote: > Alan Hewat wrote: > >> It seems that Jmol-11 does not load CIF files containing any blank >> lines. But blank lines are not flagged as errors by ENCIFER >> http://www.ccdc.cam.ac.uk/free_services/encifer/ and should simply be >> ignored by the J

Re: [Jmol-users] Jmol-11 does not accept blank lines in CIF files (it should)

On Tue, August 29, 2006 8:15 am, Alan Hewat wrote: > > > It seems that Jmol-11 does not load CIF files containing any blank lines. > But blank lines are not flagged as errors by ENCIFER > http://www.ccdc.cam.ac.uk/free_services/encifer/"; > eudora="autourl"> > http://www.ccdc.cam.ac.uk/free_servi

Re: [Jmol-users] Use of Jmol 10.2 to display unit cells

On Tue, August 29, 2006 4:47 am, Alan Hewat wrote: [snip] > But otherwise it would indeed be interesting to have a Jmol script to > apply symmetry operations ie: > Select (Basis); > Symmetry (x, 1/2-y, 1/2+z) > Select (Basis) would mean select all atoms if it is a file that does > not contain symm

Re: [Jmol-users] Mac 10.3.9 with new FireFox (1.5.0.4)

On Tue, June 13, 2006 10:58 am, Bob Hanson wrote: >> > Rich, you sure you are looking at the Java console log? (In one of your > Mac directories? "logs" or "log" or something like that?) I checked both the javascript log and the java log. The interesting thing in the java log is what is not there.

Re: [Jmol-users] Mac 10.3.9 with new FireFox (1.5.0.4)

On Tue, June 13, 2006 9:04 am, [EMAIL PROTECTED] wrote: > On Tue, June 13, 2006 8:43 am, Bob Hanson wrote: >> rich, do you know how to get a Java console output? We need to see that >> to see what error is occurring. > > No errors reported Bob. It just sits there with an unfilled space for the > ap

Re: [Jmol-users] Mac 10.3.9 with new FireFox (1.5.0.4)

On Tue, June 13, 2006 8:43 am, Bob Hanson wrote: > rich, do you know how to get a Java console output? We need to see that > to see what error is occurring. No errors reported Bob. It just sits there with an unfilled space for the applet. In the bottom FF window info bar it says: Applet jmolAppl

[Jmol-users] Mac 10.3.9 with new FireFox (1.5.0.4)

This new version of FF doesn't seem to want to display the Jmol applet (v10.00) as reliably as the previous versions did (FF 1.5.0.3 and earlier). Quite often the spot for the applet just stays as an empty block. Multiple reloads will sometimes get it to display. Safari works just fine under the sa

Re: [Jmol-users] jmolappletproto.jar: resolution

On Wed, June 7, 2006 1:54 pm, Steven R. Spilatro wrote: > Angel, > 1) XP with Service pack 2 > 2) no compression file installed, other than that which comes with windows > 3) the extension is .zip, unless .jar is added in the "save as" > window as previously described. What happens if you use Fire

Re: [Jmol-users] question about spinning

On Mon, May 22, 2006 5:36 am, Angel Herraez said: > I would say the spinning could retain its status, at least in respect to > spin x , y , z. I don't see why the spin should be an applet state as opposed to a molecule state. I can see setting some things as an applet (or rendering) state that yo

Re: [Jmol-users] bug or not a bug -- select within()

On Tue, May 9, 2006 4:17 pm, Bob Hanson said: > right, that's my point. It seems unnatural to me as well. That's why I > was surprised and initially thought it was a bug. Personally I can't > imagine it, either, unless Wouldn't it be more natural to have a model specifier? Do "x" to model "n",

Re: [Jmol-users] Jmol and mmCIF

On Mon, April 17, 2006 5:40 am, Egon Willighagen said: > As long as the informat is split up > over several data substructures, and one has to get those bits of > information > together, it does not really matter wether it is PDB, mmCIF or XML syntax. This is true. CIF is an information exchange

[Jmol-users] cif parsing (was: Jmol prerelease 10.00.56

On Tue, April 4, 2006 1:34 pm, Bob Hanson said: >> >> >> Any symbol may be used as the "atom type" and that symbol (case >> included) >> is then forever associated with that atom type defined. So I don't think >> it is a good idea to assume you can change case to make comparisons or >> assignments.

Re: [Jmol-users] Jmol prerelease 10.00.56

On Tue, April 4, 2006 10:58 am, Bob Hanson said: > > I've found one bug in the CIF reader. I believe that if the second > character of the atom.type_symbol field is capitalized, it should be > uncapitalized before checking to see if it is an atom symbol. Any symbol may be used as the "atom type" a

Re: [Jmol-users] Web page with Jmol applet for human hormones

On Tue, March 28, 2006 8:54 am, Miguel said: > > If I recall correctly, I suggested only allowing x/y rotation to one of > these people. If I recall correctly, he responded by saying that even x/y > rotation was flawed, because 2D molecular models were supposed to be > presented in a standard orien

Re: [Jmol-users] Web page with Jmol applet for human hormones

On Tue, March 28, 2006 5:24 am, Miguel said: > Several educators have told me that it is a mistake for Jmol to read 2D > structures ... because of the potential confusion caused by representing > these structures as flat. I'm not sure "mistake" is the right way to characterize it. But it would be

Re: [Jmol-users] getProperty -- synchronous applet interface -- JSON

On Wed, February 8, 2006 8:58 am, Frieda Reichsman said: > > Firefox 1.5 crashed the first time I tried it, after I used several > different links to report info. I will re-test and get back to you > later. I didn't get any crashes using FF1.5 on OSX10.3.9 but I do get a lot of applet-window-flash

[Jmol-users] trim list replies

Whether you top-post or bottom-post please trim the quoted material to *just* what is necessary. Leaving entire multi-person posts intact after a line or two of top-post reply is really quite annoying. Rich --- This SF.net email is sponsored by

Re: [Jmol-users] README.txt file in the distribution

On Thu, February 2, 2006 2:12 pm, [EMAIL PROTECTED] said: > > > De: [EMAIL PROTECTED] >> >>I'd like to see this file expanded to have, even a brief, description of >>each of the files in the distribution. > > Would you be willing to write the descriptions ? Oh, I would have already if I knew what

[Jmol-users] README.txt file in the distribution

I'd like to see this file expanded to have, even a brief, description of each of the files in the distribution. Rich --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX se

wireframe/connect usage (was Re: [Jmol-users] Jmol prerelease 10.00.47

On Thu, February 2, 2006 10:20 am, Bob Hanson said: > I disagree. From a user perspective, "single" and "double" are just > rendering issues of wireframe. Wireframe should be allowed to respect or not respect the underlying connect type. If atoms are connected using a double bond then that *is* th

Re: [Jmol-users] Jmol success

On Wed, February 1, 2006 9:47 am, Miguel said: > >> I was visited by a rep from a book publisher the other day, who gave >> me a booklet with details of the forthcoming 6th edition of Stryer's >> Biochemistry (Berg et al.), the premier textbook for teaching >> undergraduate biochemistry. I quote fr

[Jmol-users] html & xhtml

Further to the discussion of xhtml and html that was on this list a while ago I ran across this website that discusses the disadvantage of using xhtml in any except the most well-constrained environments. http://www.hixie.ch/advocacy/xhtml Rich --

Re: [Jmol-users] selecting atom IDs such as 1h47

On Tue, October 25, 2005 7:49 am, Miguel said: > > Please comment on the following proposal: > * Jmol will support the 'HG11' version > * The Jmol pdbReader code will convert atom names that >match the following format: > H -> H > > Justification: > * No reason to promote the pdb

Re: [Jmol-users] Tripos format

On Thu, October 6, 2005 11:33 am, Miguel said: > This is a good task for a novice who wants to contribute. It is a > self-contained, well-defined task that would provide the opportunity to > gain some experience with Java, CVS, open source development, and Jmol. > > Some possible ideas: > > * Fran

Re: [Jmol-users] decimal places in measurements

On Tue, August 30, 2005 1:29 pm, Egon Willighagen said: > > I remember a discussion on this on the list. But cannot find it with > Google. Last August. > Conclusion indeed was that angstrom where to be phased out. Not quite. Angstrom measurements are deprecated in all aspects other than crystall

Re: [Jmol-users] decimal places in measurements

On Tue, August 30, 2005 12:22 pm, Miguel said: > > I was told that: > > - the Royal Chemical Society mandates that everything be done in > nanometers For molecular structures the standard SI unit would be pm. > - many publications no longer accept angstroms Not that I am aware of. All the jour

Re: [Jmol-users] decimal places in measurements

On Tue, August 30, 2005 12:01 pm, Miguel said: > When displaying distance measurements ... > > Q: Does anyone feel the need to have more than one digit to the right of > the decimal point when measuring in Angstroms? (or 2 digits with > nanometers) [snip] > > I made an executive decision to reduce

Re: [Jmol-users] Publication quality images from applet?

On Mon, August 22, 2005 9:50 am, Miguel said: > * Personally, I have little/no interest in helping to create 'publication > quality images' >- I work on Jmol for free/fun >- my motivation is to help students learn > introductory chemistry/biochemistry > (1)>- publications are

Re: [Jmol-users] Re: side-by-side stereo views

On Mon, July 18, 2005 4:26 pm, Miguel said: > > ... educate me ... :-) OK, you asked :-) More years ago than I want to consider I was doing some research and came across a paper by J.T. Rule titled "Stereoscopic Drawings" (J.O.S.A., 1938) in which he discusses the underlying inadequacies of usin

Re: [Jmol-users] making jmol cgi script?

On Mon, June 20, 2005 6:00 pm, Miguel said: >> I'm trying to make a jmol page using cgi rather than static html. > > Other people have this running successfully. Yep. >> I have the jmol directories where they should be.

Re: [Jmol-users] App version of JMol - images and other things

On Tue, May 24, 2005 10:26 am, Miguel said: >> That works but it is an extra step and does mean a user has to have >> pov-ray installed. It isn't a big deal just a little anoyance that I >> can't >> just say "export that image as a 2400x2400 pixel image" so I can set it >> off to the graphics profe

Re: [Jmol-users] App version of JMol - images and other things

On Tue, May 24, 2005 9:35 am, timothy driscoll said: > > how about exporting as a pov file and using pov-ray? I've had good luck > with that process in the past, though I confess I have not tried it with > Jmol yet. That works but it is an extra step and does mean a user has to have pov-ray inst

Re: [Jmol-users] App version of JMol - images and other things

On Tue, May 24, 2005 9:11 am, Miguel said: > I suggest that you try the Jmol jpeg export. With the image quality set to > 50, the minimum that Jmol supports, then the jpeg images are a little > grainy. At higher graphic quality levels the images look quite good. > They do look good, but... the big

Re: [Jmol-users] Using Jmol in PPT presentations

On Mon, May 23, 2005 1:11 pm, clare sansom said: > Dear all, > > I must apologise if this is a FAQ - until now I have been a lurker on this > list... > > I will be giving a short presentation at the FEBS/IUBMB conference in > Budapest in July about our use of Jmol in teaching an Internet based > co

Re: [Jmol-users] Using Checkboxes in the applet

On Wed, April 13, 2005 1:51 pm, Joost Van Durme said: > Hi, > > I want to use html checkboxes to toggle eg. ribbons on or off. So, when > checked, ribbons are on, when unchecked, ribbons are off. > I'm writing the html page in plain html after loading the applet with > This is the most conveni

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