Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo
Op 23-2-2011 10:12, Rzepa Henry schreef: I appreciate a debate on this topic may or may not be suited for the Jmol list, but if anyone wants to add their opinion, I would welcome this, if only because my synthetic organic chemistry colleagues need to know what the most realistic description of this iconic potential surface is! I think the synthetic organic chemist should realize that what is shown is not a potential surface, but one degree of freedom singled out. To put it crudely: the molecule is wobbling all the time, hopping from one possible path to the other, distorting any symmetry all the time. More realistic, although not so appealing maybe as the animations shown. My original was based on a series MOPAC IRC calculations starting from selected transition state maxima. Hens -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] message command
Dear Rick, Eric,
What the simpler solution is I don't know, but I can tell what I do
(since a long time, before jmol.js emerged, so it could be a bit
outdated...):
Write your comments in javascript in a data array data[1], data[2] where
the index corresponds to the frame number it is related to, and use
function JSAnimcontrol (appname,frameno) {
document.some.textarea.value = data(frameno);
}
In the applet include AnimFrameCallback='JSAnimcontrol'
For an example look at the source of
http://cheminf.cmbi.ru.nl/wetche/organic/cyclohexane/jm/mecyc.html
which looks cumbersome, but it is entirely generated by script from a
computational output file.
Hens
Dear Rick,
In FirstGlance in Jmol, I use the message command and
messageCallback(). (I do not use jmol.js.) I use message to mark
the beginning and end of blocks in the message stream. Then I use
those marks to parse out what I need.
You could do the same, something like this:
message begin comment
message Here is a two-line comment
message that I would like to display in a textarea.
message end comment
Then you need to write javascript to watch each line coming through
messageCallback(), and trap lines following begin comment, then
display in the textarea what was trapped when end comment comes along.
Perhaps someone else knows a simpler way?
-Eric
At 1/8/07, you wrote:
I have several anaimations where I would like to print comments to a
textarea controlled by the animation sequence. I have experimented with the
SetCallback(meassageCallback, javascript_function) which works well,
except that I get messages from everything (status, error, echos etc). Is
there a way to limit this to just the message commmands? (set loglevel does
not have the desired effect.)
Thanks, Rick Spinney
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[Jmol-users] lines in frames
A short question, concerning lines and planes in an animation (multiple XYZ file). When I call a script like frame 1 draw line1 120 (atomno=1) (atomno=2) draw plane1 200 PERP PLANE $line1 the line is shown in all frames of the animation, while the plane turns out to be attached to frame1 only. Is there a way to confine a line to a particular frame too? And vice versa, to show the plane in all frames? (Context: I'd like to show in an animation that eclipsed 2,3-dichlorobutane has a plane of symmetry, while the most stable all trans conformation has an inversion center, visualized by drawing lines between related atoms). Hens - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] surfaces and JVXL files
Hi Frieda Solvent-accessible surfaces of macromolecules are what I am accustomed to using vis Chime, hence what I am seeking to create. However I have to admit that I am not aware of what the distinction is between isosurface and solvent-accessible surface... Isosurface became the name of the command in Jmol to generate surfaces, probably because the first surfaces were molecular orbitals. Orbitals do not have a particular size; the values of the function get smaller and smaller with distance from the molecule, and surfaces are created by connecting points with the same value. Hence isosurface. Same for electron density, for which an isosurface can be drawn that coincides more or less with the van der Waals surface. Or much smaller, or larger, depends on what feature you would like to show. To solvent accessible surfaces this doesn't apply. There is only one, given the radius of the solvent. However, all these surfaces, spheres and so on are currently created with the command isosurface. Hens (At this time Bob is really crossing the ocean, but I wouldn't be surprised if he is reading his e-mail and working on Jmol. Or is it still out of the question to take a pencil, let alone your laptop with you?) - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] surfaces and JVXL files
Hi Frieda, While Bob is crossing the ocean: As I understood it, JVXL files can be generated from any surface displayed by Jmol. The JVXL lines are written to the Java console (if your browser has one..Mine at home hasn't, so I can't test what I'm writing here). The source of the surface could be a CUBE file, but not necessarily. Cube files (often very large) are produced by quantum chemistry programs (Gaussian in particular) to describe orbitals or electron density, and the surface (at a particular contour level) can be written out in the much smaller JVXL format. This doesn't apply to macromolecules. For proteins something like surface resolution 6 solvent 3.0 should create a solvent-excluded surface, after a while. Or surface sasurface radius for the solvent accessible one. Also this surface could be written out by the applet in JVXL format, and it might be more efficient to offer the JVXL file on your web page rather then recalculating it by the surface command. Hens Hi All, I am interested in fast rendering of surfaces for large molecules. It seems that Bob Hanson has invented a file format for this purpose, called JVXL. I have seem Angel Herraez's and Bob's test pages for surfaces, but I am still puzzled as to how to get started in doing this. To create a JVXL surface file in Jmol, do you first have to load a CUBE file into Jmol? I have started to read a little about CUBE files but am unfamiliar with them. How do you generate a CUBE file? Frieda /// - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Interpolation in animation?
Egon Willighagen wrote: On Tuesday 01 August 2006 21:20, Eric Martz wrote: 1. I would be pleased to see a simple linear interpolation option built into Jmol. The need for such morph animations is becoming more common as more structures are solved in different conformations. Having it built into Jmol would save a lot of time and make this kind of visualization more accessible to a much wider authorship. Thanx for this elaborate discussion, though I haven't read it in detail yet. But I do already want to mention an concept triggered by your email, and might also be mentioned in your email... Some long time ago I was discussion interpolation with someone (might have been Hens...?), and this someone suggested that a linear interpolation is fine, *especially* if done on the internal coordinates instead of the Eucledian ones. Using the internal coordinates ensures that bond length and angles are reasonable for the interpolated steps. Quite possible Egon. Our examples were about small molecules, and the animations often involved rotations of groups in the molecule. In these cases a linear interpolation of cartesian coordinates is not what you want. Maybe the four-point spline interpolation suggested by Michael would work better, but we found it simpler to do the interpolation outside Jmol (or Chime then). Starting from a MOPAC multi-structure file in internal coordinates, we use(d) a script to produce any number of intermediate structures. This method doesn't seem practical in the case of moving proteins though. Or do you think the sequence PDB -- internal -- interpolate -- PDB feasible? Hens - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] orbitals as cartoons
Jonathan Gutow wrote: Bob, I think I see where you are going, but am a little worried. If it is a cartoon, it needs to be clear that it is. .. I think a tool like Jmol should be used to provide as accurate a representation of things as we can. Thus in relation to orbitals the use of .cube and .jvxl files seems like a good idea. I do see how someone might want to think about the orbitals on a molecule in terms of the cartoon orbitals, but I still think that learning to use the more complete MOs is better. Yes, I agree with the last statement. However, I can also imagine applications where a cartoon better explains what you're trying to tell. As is done in pictures in text books, showing a cartoon of a pi system instead of a more complicated MO. In particular I'm thinking of showing free electron pairs (a subject which returns regularly in this forum), for instance as a cartoon of an sp3 (or sp2, or ...) orbital on a nitrogen atom. Is that an option, Bob? Often the calculated MO describing this f.e.p. shows many more contributions that you don't want to show at this point. [Now we can prepare ourselves for the discussion on how to show the 2 fep's on a carbonyl oxygen] Hens ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] orbitals as cartoons
Bob Hanson wrote: What we can now do is depict isosurfaces for: (a) CUBE files, (b) essentially equivalent but 1/500 the size JVXL files, (c) atomic orbitals centered at (0,0,0) and aligned with the molecular xyz axis. The fact that we can do (c) suggests that any reasonable built-in function could be mapped. The isosurface method is just calling: value = getPsi2(x,y,z) so I don't se why we couldn't substitute in a few other functions as well -- perhaps a small set of hybrids. The real question is simply: How does one orient these so that they are actually useful in relation to molecules? You mean: like a p orbital at any heavy atom, perpendicular to the plane of the atom and its neighbours? And an sp3 type, pointing along the axis defined by the other three substituents at an atom? Or a hybrid of the two, defined by the deviation from planarity of the central atom? I think that would be great, and cover many text book examples. Hens ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] proposed addition to Jmol web site
Angel, They are very clear, should be a great help. Hens Hi all. Looking at several recent posts, it seems that new Jmol users tend to visit the demo- example pages on the Jmol web site, copy the source code of the page, then make their changes and find that they don't work, usually because of testing on hard disk, without using a web server. So, I have thought it could be a good idea to provide advice right there on the example pages. I have rewritten the pages for simple example and UI controls example so that the code is shown and commented alongside the Jmol applet and controls. I have put this new versions at http://biomodel.uah.es/pruebas/jmol/examples/index.html so that, if the community finds them adequate, I will send the files to some of the administrators and they put them on Jmol web, substituting the current example pages. Please, give your opinion. --- All the advantages of Linux Managed Hosting--Without the Cost and Risk! Fully trained technicians. The highest number of Red Hat certifications in the hosting industry. Fanatical Support. Click to learn more http://sel.as-us.falkag.net/sel?cmd=lnkkid=107521bid=248729dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- All the advantages of Linux Managed Hosting--Without the Cost and Risk! Fully trained technicians. The highest number of Red Hat certifications in the hosting industry. Fanatical Support. Click to learn more http://sel.as-us.falkag.net/sel?cmd=lnkkid=107521bid=248729dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] displaying orbitals/isosurfaces...
Jonathan, Very nice page indeed. I once made a page with gaussian calculated AO's, and found that a 3p orbital had some of the 2p mixed in, resulting in too many nodal planes. A problem which you managed to avoid. http://cheminf.cmbi.ru.nl/wetche/organic/srm1j/index.html On top of Miguels suggestion to add a 'translucent' option I'd like to point at the 'slab on;slab 50' command to remove the front half of the displayed surface. Hens Is anyone interested in a perl script that generates a web page using jmol to view multiple selectable isosurfaces/orbitals? An example of the kind of page it generates may be seen at: http://www.uwosh.edu/faculty_staff/gutow/Orbitals/Cl/Cl_AOs.html The perl script is a bit of a rough and ready job. I am hoping to eventually make something (maybe Java) that my students can use to post rotatable orbitals as part of web posters I have them make of their in-class calculations. I also wonder if something like the page linked above should be added to the examples pages on the main Jmol site? There is no examples of surfaces there yet. Jonathan --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] altLoc and disorder
Bob Hanson wrote: I just meant that's how I implemented it -- for crystals -- where runs are not the issue. (or are they?) Well, somebody already mentioned the relation with partial occupancy, a phenomenon found in crystals. A quick check showed that of the 1400 CSD structures with a trifluoromethylphenyl-group, 700 show disorder in the CF3 group. Read this comment in the experimental section of ACACIQ.cif (and shiver): F24-F26, F31-F33, F44-F46 and F51-F53, from four trifluoromethyl groups, are disordered over two sites with occupancies 0.60:0.40. F34-F36, F41-F43 and F54-F56, from three trifluoromethyl groups, are disordered equally over two sites. The dichloromethane solvent molecule is also disordered. CSD software shows the disordered locations as crosses, not connected to other atoms. The current xtalx site treats all atoms as part of the same molecule and draws bonds between all those fluor atoms. [Try url http://www.cmbi.ru.nl/wetche/organic/ACACIQ.cif in the loader.] So also here we have to decide how to separate the coordinates (prevent bond generation) and to display the disorder. Like showing the altloc positions transparent, to a degree determined from the occupancy factor? Hens --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] connected() -- and functional groups
Hi Bob, Nice initiative. I don't have the definite file yet (think about ring detection techniques during your sabbatical ;) ), just a few additions: define ~nitroN nitrogen and connected(3) and connected(2,~sp2O) define ~nitroO ~sp2O and connected(~nitroN) define ~nitro ~nitroN or ~nitroO define ~carboxylateC ~sp2C and connected(2,~sp2O) define ~carboxylateO ~sp2O and connected(~carboxylateC) define ~carboxylate ~carboxylateO or ~carboxylateC define ~nitrilN nitrogen and connected(1) and connected(carbon) define ~nitrilC carbon and connected(2) and connected(1,~nitrilN) define ~nitril ~nitrilN or ~nitrilC define ~amideN nitrogen and connected(3) and connected(1,~carbonylC) With amines/imines things get complicated rather quickly. Combined with the connect command one could set a number of bond types: connect 1.42 (~sp2C or nitrogen) (~sp2C or nitrogen) aromatic connect 1.345 (~sp2C or nitrogen) (~sp2C or nitrogen) double connect 1.21 (carbon or nitrogen) (carbon or nitrogen) triple connect (~carbonylC) (~carbonylO) double modify connect (~nitroN) (~nitroO) aromatic modify connect (~carboxylateC) (~carboxylateO) aromatic modify This is a translation of some of my perl script lines defining bond types. Applying these rules is a matter of taste, to some extent. Some prefer three double bonds in benzene rather than 6 aromatic ones, etc. In heterocyles, caffeine being a good example, bond typing becomes rather arbitrary anyhow. To be continued. Hens Something interesting, I think, for the organic chemists: Check out: http://fusion.stolaf.edu/bh/confchem/demo.htm?demo=3 This page highlights the new connected() capability and uses the script file http://fusion.stolaf.edu/bh/confchem/~groups.txt which is called by an embedded #jmolscript: command (not available in Jmol 10.2) in taxol.pdb. Lots of possibilities here, I think. Maybe someone will write the definitive organic functional group definition file? I don't have time to do much more than what is there. (Maybe some mistakes.) Bob --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] partial bond
Bob, I think the point is that there is a role for a bond type that looks like a single, thick, dotted line, not solid+dotted as in aromatic; not thin and dotted like typical hbonds. The fact that there is a file type that registers this suggests that it is warranted. Hens, for the life of me I can't find support for partial01 in the history of CML file readers. That was in there? Miguel will have to look into this when he gets back. In the mean time, you can certainly use connect. Are these animations? Connect can do a nice job of displaying such bonds. Example: http://cheminf.cmbi.ru.nl/wetche/organic/carbonyl/chime2/nucleoj.html [Excuse for the chime2, still there for historical reasons ;)] An animation indeed, with bonds being formed and broken. This uses Jmol 10.00.11. The mCML file contains several partial01 bonds, displayed as dotted. (Angel: note that we use type A for not really aromatic, but partial12 bonds. ) Currently I use a Perl script that calculates the bond order -based on distances- and writes the multipleCML file. It is for this particular reason that I use the CML format. Using the same distance information I could rewrite this to a series of Jmol commands, as in your example below, and stick to multipleXYZ files. I'll experiment with that anyway. However, as the partial01 support used to be there, and these type of bonds can still be drawn by Jmol, is it really so difficult to re-implement it? Haven't I seen you doing things much more complicated the past couple of weeks? For example, here would be a trick to assign all long bonds between specific atoms as normal-width dashed bonds, assuming there were several frames with animation: connect 1.6 3.0 (atomno=1) (atomno=2) create single connect 1.6 3.0 (atomno=1) (atomno=2) modify hbond The first creates a standard-diameter single bond. The second turns into a dashed line. This, I think, might be even better than the partial01 bond idea, because you would have full flexibility over what is going to be indicated and what isn't, and you could decide exactly what distances would be displayed as dashed lines. What isn't possible at this time (but we have discussed it as a possibility) would be something like: connect 1.6 3.0 (atomno=1) (atomno=2) create hbond RADIUS 0.05 (SOMETHING like that, anyway), where the bond radius would be created at the time of connection. Would you have use for that? Not if we are talking about real hbonds here. I brought up the hbond only because it is dotted. On the other hand, I can imagine that some people find the hbond a bit too thin. Hens --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] partial bond
To follow up on this: I realized that the suggestion to interpret partail01 as an hbond wasn't such a good idea, as hbonds are drawn as thin lines. However, when I checked Bob's 10.1 demo page I noticed something odd (to me). The last caffeine command CONNECT MODIFY HBOND turns all the existing single bonds (between atoms selected in the previous command) into thick partial single bonds. So these still exist. The comment says #modified hbonds take previous bond's diameter, but it seems the other way around, #previous bonds take hbond appearance. Do I interpret this correctly? And, can the CML bondtype partial01 be drawn again as a partial single bond with default wireframe value? Hens Sorry for bringing this up rather late, but I noticed that with all the recent changes in the bond features one of my favourites got lost: in reaction mechanisms I use the partial01 bond type as defined in a cml structure file. It was drawn as a dashed bond, now it is displayed as a single bond. Maybe it is solved if the partial01 bond in a CML file is interpreted as a hbond? Hens --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: Polyhedra connections
Bob, Incredible what a nice, estetically pleasing pictures one can make this way with a few commands. The facet type of depiction I really like, as it doesn't hide the central atom. Not knowing what (or who? New sponsor?) maxFactor was I changed the number to e.g, 1.9, and that froze the applet, so some checking needs to be done probably. For the rest: great! Hens folks interested in polyhedra and/or connections, please take a look at this page. Several new ideas there: -- facet depiction for polyhedra -- selectable number of bond connections in polyhedra -- select connected(min_bonds, max_bonds, atom selection set) -- variable number of bonds in polyhedra, not just 4 or 6. --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] internal coordinate spinning and rotating -- request for comment
Bob, At the end of a difficult but ultimately satisfying day, I offer the following page for comment: http://www.stolaf.edu/people/hansonr/jmol/test/json/spin.htm Worked great for me, except one thing: Clicking an axis to rotate it didn't work with my MS IE6/WindowsXP; it was in Mozilla Firefox/Linux that I found out that the far end of the axis is clickable. For the rest: flawless! Hens --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] internal coordinate spinning and rotating -- request for comment
Bob Hanson wrote: I'm guessing that your IE cached something; it makes no sense that IE/Windows works differently from Firefox/Windows in this case. My IE/Windows works fine. You're right; working fine now. Sorry for the inconvenience. Hens --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] to Miguel
Bob Hanson wrote: Twenty-three left shift plus one, He makes our beautious Jmol run. With many thanks and loads of praise, to Him today this glass I raise. To find a coder so enlightened, it almost makes me slightly frightened, But, no, in truth I cannot write a single tiny bit or byte That would disparage one so swell as Who in silico we call Miguel. So join me now to fete Miguel, His virtual self we know so well, I challenge you to write more lines, of any sort or any kinds. Happy Birthday, Miguel!! In Spanish, Dutch or German tongue, we sing this Happy Birthday song, wij kennen hem slechts virtueel, maar onze feestdronk is zijn deel, De kurk waarop Jmol drijft, en meester van de code blijft, die niet moe wordt ons te leren, vragen exact te formuleren, Jmol naar top-positie bracht, slimme oplossingen bedacht, die niet genoeg kan worden gelauwerd, driewerf hoera voor Michael Howard! Hens Borkent --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] applet -- callback brainstorming
Hi Bob, AS A USER, WHAT DO YOU WANT? a) Do you implement callbacks? If so, which ones? AnimFrame to synchronize other Javascript functions with an animation Pick to identify atoms, in particular in our molecule editor Message to return measurements, now largely replaced by monitors though b) What WOULD you use if you had it available? This pretty much serves our needs. Although we do a lot of other things in scripts that are not directly related to callbacks. You suggested reading the second line of an XYZ file, but this can be done by a script outside Jmol as well, where the results are being processed. c) What sort of information (exactly) are you looking for? d) Is there a particular format that you would like to see, other than just the current text-stream of messages? e) Is it important to you that this mechanism be backward compatible? Well yes. We could always maintain a current version of Jmol of course, in case we don't find the time to rewrite our pages. (I wish I had your efficient way of working.) Greetings, Hens --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Define a bond
Hi Eran, Hi, Is there an option to artificially create and show a bond between two atoms, even if the distance between them is smaller or larger than the range which is considered by default for a covalent bond? Eran There is no script command to create a bond, but there is a workaround to create the same effect. In CML files you can define bonds between any two atoms, and in that case the default Jmol definitions are overruled. You can even make a CML file consisting of two identical structures, only differing in the definition of one (or more) extra bonds. Now make a button that animates the structure, and the effect is that the bond is switched on and off. Send me a structure file if you want me to try it. Regards, Hens Borkent CMBI, Nijmegen --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] CHIME to JMol data interchange?
Hello Shravan, Hi All, We are trying to migrate an application from CHIME to JMol. We have a setup which requires CHIME to read a *.pdb file and build an IR spectra graph with the information provided. There is another frame where CHIME creates an animated visual of the loaded PDB data. It sounds like you are inquiring about JCamp compatibility in Jmol. The message below is from the Jmol list archives; I hope it will get you further. Hens Folks- I know that some of you may be interested in displaying spectral data (which is possible with chime) to go along with chemical structures in jmol. We've got a java applet which will display jcamp spectral data! The project's home base is at sourceforge: http://sourceforge.net/projects/jchemapplet/ . It's a work in progress and we'd love to have your feedback and suggestions about how to improve it. You can see a demonstration of the applet from the project home page ( http://jchemapplet.sourceforge.net/ ). It's possible that one or both of the students involved will continue working in the fall term, and your comments will help shape the work that will be done. Huge thanks to Bob Hanson for helping us work through the data compression algorithms. The best way to submit your feedback is probably via the sourceforge site, so that we can keep track of the suggestions and our progress. -Jennifer Jennifer Muzyka Associate Professor of Chemistry Centre College 600 W. Walnut Street Danville, KY 40422 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://web.centre.edu/muzyka 859-238-5413 fax 859-236-7925 --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_id=7628alloc_id=16845op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] decimal places in measurements
Phillip Barak wrote: I must weigh in here. I'll be surprised if the hundredths place has reasonable significance in any protein crystal structure. But Jmol is so adept at rendering non-proteins, too! :-) And crystallography isn't the only source of coordinates. But for the rest the point is taken. Hens --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: decimal places in measurements
Miguel wrote: I like this but prefer one digit to the right for Angstroms. If noone makes a strong argument to the contrary then we will change it to one digit. I support Rich in that one digit (in Angstroms) is too few for comparing bond lengths in organic structures, two is the minimum, three is mostly used in cartesian coordinates. (Ever seen cartesian coordinates in pm or nm?) Hens --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] axes and planes
Miguel wrote: Currently, the pmesh code only supports triangles and quadrilaterals. I did not see any reason to support polygons any bigger than that ... I even hesitated before putting in quadrilateral support. You are defining a plane ... Three non-colinear points are sufficient. Q: Why do you want to have 5 points? Most of the time my script generates 4 corners, so it seemed logical to write a pmesh rectangle. Or a pentagon when I get 5. But the more general solution for a script would be to write triangles only, even if that implies that one has to create a number of partly overlapping ones to cover the whole area, because the directionality is not known. I'll experiment with that. Hens --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] color bonds not atoms
Hi Brandon, Hello, I was wondering if there is a way to color the bonds of the structure instead of the atoms. The answer is rather intuitive: set bondmode and;select atomno1,atomno=2;color bonds blue Hens --- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_id=7412alloc_id=16344op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: release the signed applet?
Miguel wrote: hi Miguel, a suggestion: can you release the signed Jmol applet as a compiled update? seems like it would address a lot of the recent (and ongoing) issues about local use of the Jmol applet. I know we can get the signed applet from CVS-HEAD, but I imagine the extra steps involved are an obstacle for many people. The signed applet has been released as part of the prerelease version that is available from: http://sourceforge.net/project/showfiles.php?group_id=23629 Note that in one particular case, Hens decided that the Signed Jmol Applet did not adequately meet their needs. To be complete: that case was importing (multistructure) CML files. Moreover, there didn't appear to be a need for a signed applet. As discussed at length here the normal applet works if you maintain the proper path structure. A signed applet invokes some extra security checks, which we'd rather like to avoid in the use of our cd-rom. Hens --- This SF.Net email is sponsored by: New Crystal Reports XI. Version 11 adds new functionality designed to reduce time involved in creating, integrating, and deploying reporting solutions. Free runtime info, new features, or free trial, at: http://www.businessobjects.com/devxi/728 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: 'set measurements ...' to update *all* labels
Hi, To add to the confusion: we are talking about different things here. As I understood it, Chris was talking about changing the units during measurements, say from the default nm to angstroms, and then updating the values already being displayed. In one particular structure. [a problem I never encountered and I have no opinion on] Then Miguel threw in an older question, about dynamically transfering a measurement from one model to the next, in an animation. This is very useful in an (XYZ or CML) animation, characterized by models/frames with all the same atoms in the same order (and to be distinguished from multi-model PDB files which can be completely different molecules). In the animations the select command is not involved: you do not select a new model, you simply go to the next frame (well, maybe Jmol does internally?). So Jmol could do a check which multimodel system we have, and translate the measurements to all frames if appropriate. As I see it now it could be done on the basis of the file type (XYZ/CML vs PDB), but that is only a first order approach that will run into ambiguities soon. Or we separate the two completely and reserve different commands for say 'frames' and 'models' . Hens Would it be possible to have the set measurements ... command update the units on *all* distance labels? Perhaps both behaviours could be supported, say, something like set measurements ...affects subsequent measurement labels set measurements ALL ...affects all measurement labels Several other people have asked for this, so you are not the only one. I think that having a 'setting' to control the behavior would be OK. We need to specify the behavior a bit more ... Let's talk a little bit about what the criteria would be for deciding whether or not the measurements get replicated. Different frames/models are can be completely different. Sometimes they all contain exactly the same atoms in exactly the same order ... only the position changes. This is what happens in many animations. why not linking the set measurements command to the current selected set, this was consistent and flexible. select all select /3 regards, Jan From one frame to the next, we need to decide whether or not the measurements could be replicated. I suppose that we use one or more of the following: - the two frames have the same number and types of atoms in exactly the same order - the atom numbers of the elements being measured are the same - the atom numbers and types of the elements being measured are the same Don't know ... does anyone have any other thoughts. Miguel --- SF email is sponsored by - The IT Product Guide Read honest candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595alloc_id=14396op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: two targets on the same page
Hervé,
Let your button call a javascript function, and in this function you
send any script to any applet you like
document.jmol1.script('script1...');
document.jmol2.script('script2...');
In this way one can construct toggle buttons as well, which I don't find
in the current jmol.js
Is this what you meant?
Hens
Hi
Is there any way to send a command (script) to two different
jmolapplets on the same page by the way of one single button, radio
group, checkbox or menu ?
Or even better send to different commands to two applets on the same
page?
I have tried several synthaxes but I couldn't get it.
Hervé
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[Jmol-users] Re: Questions regarding surfaces
Miguel, The vanderWaals surface is useful to colour-code other information on it. In Chime one can display the electrostatic potential (ESP) or the lipophilicity on the vdw-surface. Especially the ESP is useful, but in Chime it turned out to be rather difficult to override the default charges that it assumed present in a molecule, and the colour range. (I'm using past tense I notice!) Does Jmol read the optional (4th) charge column in a XYZ file? Moreover Chime read Gaussian cube files to plot orbitals, or the electron density. Problem is that these are huge files, and Chime plotted only one phase of the orbital anyway so it was a rarely used option. Orbital plotting would be very useful if a more compressed format was adopted for the 3D surface information. Hens I have a question regarding surfaces ... Certainly there is a need for a Connolly surface ... Q: Is there really any need to have a vanderWaals surface? Q: What type of surface(s) does Chime support? --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag--drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: charge in XYZ format
Miguel, Q: Please confirm that if I put in support for partial charges in the range (-1 partialCharge 1) inside the XyzReader then you will test and use this capability. Yes, I will. Hens --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag--drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] vibrations
Colleagues, To return to a familiar subject: visualization of vibrations. In Chime I used multipleXYZ files, written out by MOLDEN for a particular vibration and as calculated by Gaussian, MOPAC, etc. In Jmol I can still animate these mXYZ file, however the animation doesn't run smoothly. After one cycle it waits for a second before it restarts. So the animation doesn't look like a vibration. So my first question is: can this delay be avoided? I know that people are working on reading and displaying vibrations directly from Gaussian output. Can I select -scriptwise- a particular one of the 3N-6 vibrations? Will this feature be extended to MOPAC output? Hens --- This SF.Net email is sponsored by: Sybase ASE Linux Express Edition - download now for FREE LinuxWorld Reader's Choice Award Winner for best database on Linux. http://ads.osdn.com/?ad_id=5588alloc_id=12065op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] writing text with animations
Brian Keay wrote: To Whom It May Concern: I'm in the process of creating animations for the Web site http://www.keayb.uklinux.net using Jmol10pre12 and I was wondering if there is a way to print text to the screen while the animation is playing, for example, in order to explain to the viewer what is being displayed. Thank you and best regards. Brian Keay It can also be done by javascript; Define data lines containing the frame number: data[1]=text1 data[2]=text2 etc In the applet add: AnimFrameCallback='JSAnimcontrol' and in function JSAnimcontrol (name, framenr) document.formname.textareaname.value = data[framenr] ; Something like that, try it. Regards, Hens Borkent --- SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 Save 50% off Retail on Ink Toner - Free Shipping and Free Gift. http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] dummy atoms
Miguel, You should also be able to select them as 'select elemno=0' Note that I have not tried either of these things. If they do not work then let me know. It works, thanks. The script command: restrict elemno=1 excludes the dummy atoms from the display. Hens --- SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 Save 50% off Retail on Ink Toner - Free Shipping and Free Gift. http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] dummy atoms included/excluded
Rene Kanters wrote: I am using JMol to look at Gaussian 03 output and wanted to know whether in a future version JMol will also show dummy atoms. Since I am using z-matrix optimizations, several of the angles that are important to me are defined using a dummy atom. It looks like JMol uses the standard orientation to parse for the multiple structures in a log file, which has the dummy atoms stripped. If it were to look for the Z-Matrix orientation: it would find the cartesian coordinates of all the atoms. The added advantage of using the Z-Matrix orientation is that it will also not flip my molecule around (which the standard orientation sometimes does). Thanks, Rene On this subject: There are two sides to this: Jmol *is* showing dummy atoms when they appear in XYZ files, and I didn't find a simple command to *exclude* them from the display. Did I overlook something? It would be convenient if they could be addressed by the element name 'dummy' or by the atom type X / Xx / XX. Miguel: a dummy atom is a point in space on a position where there is no atom, but which is convenient to include in the definition of the positions of real atoms, or a group of real atoms. Example: one can write the structure of cyclopropane very efficiently in internal coordinates ( z-matrix) using the center of the ring as the origin, i.e. by placing a dummy atom there. Or: to measure the distance to a benzene ring, one could take the center of the ring as a reference point. Hens Borkent --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] models and frames
Miguel, However if that can be controlled in JMol by a script command set models nmr|anim ( set frames nmr|anim ?) it would be a good solution to distinguish between the two applications. Why is there a need to distinguish between the two? You're right. What I meant is that there should be an option to display the frames sequentially or (all or some selected) on top of each other. That's clear now. Chime requires that all framed structures in a file have the same atoms in the same order. Not so for pdb-models I guess, I'm not sure though. Is this a restriction we would like to question? Is it present in JMol? My plan is to try to do something reasonable ... not crash. If it looks bad then don't play it as an animation. Please let me know if you see any fundamental problems with this. I don't, I agree completely. Hens --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] xyz vs pdb
:tim wrote AFAIK (again), xyz files are generally useful for small molecules but not for larger macromolecules. but maybe that's not quite accurate? Well, it is not so much the size that matters, as does the extra information a pdb file carries for proteins: e.g. secondary structure, amino acid labels, chains, models, and connect records. For non-proteins only the latter apply: bonding information in HETATM lines. Could be very usefull in small molecules too, for instance to show double bonds. Which opens new vistas! Currently in Chime XYZ animations we can't show multiple bonds, but if we equate PDB NMR Models to XYZ frames it could be possible to define the bonding scheme for each separate structure! How to create such PDB models (from computational packages) is another question; I'm willing to edit the files by hand if need arises. I don't recall: was it ever discussed to finetune the distance criteria in JMol in order to decide upon the bond type? Hens --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Chime2JMol
Hi, There is one more small issue concerning Chime to JMol migration: while Chime starts numbering atoms (and everything else) at zero (a programmers choice), JMol starts numbering with atom 1 ( a chemists, or any other 'normal' person's choice). So there is a decision to be made: stick to Atom-one, and increase all your numbers in current scripts by one (not a big deal), or adopt the Chime numbering. My vote would be for the former. Furthermore I support Pat Carroll's compliments for JMol, and his request for a measuring panel (dist, angle. dihedral) and adjustable atom radii. Rasmol scripts have a provision for both: set picking distance etc. (would require a mechanism to place the result somewhere) , and 'spacefill number'. Greetings, Hens Borkent --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
