Re: [Jmol-users] How to show hbonds as dotted, not dashed?
Hi John
I'm afraid that is the design and cannot be changed.
You can play a trick, though, using partial bonds which can be rendered as
dots:
hbonds calculate;
select connected("hbond",all);
connect (selected)(selected) partial modify;
set partialDots on;
wireframe 0.07;
color bonds lime;
select all;
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Re: [Jmol-users] Console Again
> Also, $("#JmolApplet0_console").length equals zero, which suggests that the
> div of that name
> does not exist.
... that gives a length of one in one of my pages
Do you have a url I can look at?
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Re: [Jmol-users] Console Question
Hi Otis
Not sure if I get your exact intention.
JSmol creates the automatically, at least on
first invocation,
so rather than ading that div myself, I'd try forcing its css properties.
Hav you tried a rule with !important ?
> But evidently a movable absolute object inside a position fixed object does
> not work.
This phrase is not clear to me. If it's absolute positioning, it is relative to
either the page or any parent which is positioned.
JSmol's console div is outside the body tags, so it has no parent ... I guess
the html tag will be the reference.
So let's say you add this in your page
#JmolApplet0_console {
left:800px !important;
top:8px !important;
}
What happens?
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Re: [Jmol-users] Fwd: installing JSmol extension
I've just visited (first time) http://dipc.ehu.es/bondslam/index.php/Hypervalence and I can see both molecule and surface So either you just fixed it or there is some caching problem --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] Fwd: installing JSmol extension
Hi Henry! To me it sounds like some js library incompatibility (edit mode vs. view mode). The UNKNOWNReader part sound very suspicious. What happens if, from the non-working page, you open JSmol console and paste the command to load the isosurface? -- 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
Re: [Jmol-users] png files created in jsmol
Hi João Even though the PNG files are not validated by pngcheck, they are rendered correctly by many programs. It should be easy to implement the setting of 'set imageState off' in the page source for the Sage project, and then the product of the Export menu would be compliant. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] JSModel demo control problem
David, this is great fun! Please check out http://biomodel.uah.es/JSmol/responsive-size-1.htm Height of JSmol will always match height (I didn't think this was easy or even possible, but it's amazingly simple code) The key for versatility is to always set width and height to 100% in Info. Then use an outer container + css and js to control the size. And then these css units that I discovered recently and once again do the magic: "vw" "vh", meaning percent fraction of the window width or height. The big difference against classic % is you can use vw for the height! So the result here is a set size of 400px for JSmol, as long as it fits within the screen width. If not, 90% of it. And always square. I believe this will be great for the phones. David Leader wrote: > The problem with the width/height thing is that one can´t do a shrinkwrap like one can with an image and do a width:100%, height: auto. > My problem is that 280 px is actually just too large for the iPhone, so I > have to hack that a bit, and in truth it's too small for modern large displays --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] JSModel demo control problem
Hi David
Yes, cache problems are rather hard when they appear. Not only the htm
(easy) and js (not so much) files, but also script files that JSmol "remembers"
and the browser does not care about.
And there is often an issue when you update JSmol version in pages.
> However, I have reverted to an old version of JSmol because the following
> command no longer
> works:
>
> ["select nucleic; colour cpk; colour green; select *a; colour white;",
> "Distinguish chains" ],
>
> The select *a; colour white; bit doesn´t work to colour the second chain
> white on the recent Jmol
> version. Has the syntax has been changed? I could look myself but this is
> really killing me.
I think this has been discussed before in this list. That syntax for selecting
chains was supported, but it is not very precise and some versions stopped
supporting it.
You should be safe adding a colon before the chain,
select *:A
also uppercase vs. lowercase chain ID is not seen different by default, but
there is an increasing need to differentiate between both (large PDB models)
and Jmol supports it
https://chemapps.stolaf.edu/jmol/docs/#set_chaincasesensitive
> Oh, there´s one more thing that would be nice. That is if you could scale the
> frame as you
> switched to mobile, keeping the same proportions. For example, I have width:
> 280, height: 280. As
> far as I can see from the instructions I can set width: 100% but the height
> doesn´t change. Even
> serving different hard-coded sizes for different sized viewports would help.
Yes, you can set width and height to 100% in Info but then your page must
include a div with explicit css width and height that envelopes the JSmol
object.
i.e.
var Info = {
width: "100%",
height: "100%",
use: "HTML5",
j2sPath: "mol/j2s",
disableInitialConsole: true
}
myJmol = Jmol.getApplet("myJmol", Info);
Jmol.script(myJmol,"load mol/B11mer.txt; set background [51,51,51];
restrict nucleic; colour cpk; rotate x 90; zoom 125; spin on;");
It may be not so easy to change the size of the container depending on the
platform, but that's css + js external to JSmol. Also you might not get it
square shaped (not really a problem if it's rectangular, only you may need to
set zoomLarge false in Jmol script)
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Re: [Jmol-users] JSModel demo control problem
I agree that reset should stop spinning, but not that rotate also does it Anyway, there are workarounds by checking the special _spinning variable -- 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
Re: [Jmol-users] JSModel demo control problem
It seems that "rotate" cancels the spin
I have no clue if this has ever been by design.
You could apply a fix by reading the spinning state before doing the rotate
and reapplying it later:
Jmol.jmolCheckbox(myJmol,
"reset;",
"ss = _spinning; reset; rotate x 90; if (ss) { spin on; }",
"Base-stacking");
And why do you have in your spin checkbox those complex commands?
Jmol.jmolCheckbox(myJmol, "spin off; spin on;", "spin on; spin off;",
"Spin", true);
I would just do
Jmol.jmolCheckbox(myJmol, "spin on;", "spin off;", "Spin", true);
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Re: [Jmol-users] JSModel demo control problem
Hi David it does look strange. Have you tried with a former Jmol version? i.e is this specific to 14.20.2? -- 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
Re: [Jmol-users] loading gzipped files
Hi Jeff Regarding the font, it should cycle through about 4 steps, coming back to small size. I don't know about Mac, but in Windows Jmol creates a ".jmol" folder in the user's home folder, wher you can see a "history" and a "properties" file. Try editing them or just delete them and Jmol will create then anew, maybe fixing the issue. I have seen that work for window size and position at least As for loading zipped files, I agree: I just tested 14.20.2 with a .jmol file (that uses zip format), nothing is loaded and this is the error: ERROR en guión: java.lang.NoClassDefFoundError: org/apache/tools/bzip2/CBZip2InputStream Some of the recent additions broke this, I guess --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] PubChem Load
Dear Otis I have seen several files from PubChem that come with more than one structure, using load :whatever So that is the norm rather than the exception. It's easy to browse them if you load into the Jmol application and use the arrow buttons in the toollbar. Sometimes, the 2nd or 3rd is more interesting than the 1st one! -- 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
Re: [Jmol-users] Java in macOS High Sierra ... is still available.
Thank you, Henry I've added your obser vations in http://wiki.jmol.org/index.php/Troubleshooting/Java_Problems -- 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
Re: [Jmol-users] getting the applet ID
Thank you, Bob, Paul and Otis The issue is not easy. Proteopedia has both JS and PHP code that allows pages to be created by users. So no, I don't always know what is the name of the particular JSmol object since it is not created manually; they have sequential ids, but the key is that a scene script will be applied to any one of those jmolapplet1, 2, etc. Local storage in the browser might be useful but I am not confident with that technique. We have now a solution that works, although a little convoluted it is fast. I just wondered if there could be a read-only variable in Jmol script that provides what the callbacks know how to provide, i.e. the object ID /applet name. Thanks -- 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
Re: [Jmol-users] getting the applet ID
Thanks, Bob
> Well, if you wrote the page, you should know, right? ;)
Not necessarily ;-) I mean, applets are generated quasi-automated by some
back-end code.
> All applets are registered in Jmol._applets.
Could be. The problem is to know which of those is involved at a certain
instance.
All this is for automatic, generalized code being run behind the curtains in
Proteopedia. We are after ways for a "scene" (that links to a state script) to
do something in the page area related to that JSmol object.
So I thought that the safest way would be to call this from within JSmol,
instead of from the page, since the same "scene" link may be applied to
different JSmols.
I have managed a solution using an echoCallback. Not too clean, but seems
to do the trick.
Page JavaSscript has this:
function readTheApplet() {
window['calledAppletID'] = arguments[0].replace(/jmolapplet/i,'');
}
and the Jmol script has this:
set EchoCallback "readTheApplet";
set echo dum 0 0; echo ".";
set EchoCallback none; echo;
The global Javascript variable "calledAppletID" in the page then will hold the
ID.
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[Jmol-users] getting the applet ID
Callbacks return as their first parameter the ID of the JSmol object (e.g. "jmolApplet1") I wonder if this ID could be retrieved directly from a script. I could not find anything e.g. among the readonly variables Any hints are welcome -- 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
Re: [Jmol-users] display of contacts in two frames/models
Oh, thanks Bob I should have known, since contacts are a kind of isosurface! I knew ID is essential to have several at a time, but I missed that bit now. This is going to look great! Thanks --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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] display of contacts in two frames/models
It seems that the result of "contact" cannot be present separately in the two
frames when 2 models have been loaded. Only the latest generated set of
contacts is displayed, and only in the current frame (even if calculated from
atoms in the other frame).
Is there a way around? We would like to have two frames, each with its
contacts, and switch the display between the 2 frames
And yes, I am specifying the atoms of only one frame when I generate the
contacts, like:
frame 1; contact {Leu/1}{*/1 and not Leu}
frame 2; contact {Leu/2}{*/2 and not Leu}
Thanks,
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Re: [Jmol-users] Important Account Information - Reconfirm Mailing List Subscriptions
Yes, the email looks ugly indeed. Rather than following the link, I signed in into sf.net, went to user area and there was a button to renew subscriptions. So it looks perfectly authentic. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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] cloning part of a model into another frame
Dear Bob,
Is there a way to extract some residue fron the loaded model and clone or
duplicate it in a new frame/model?
I am trying
ff1 = load('=pdbe/1foz')
load "@ff1"
But I don't know how / if I can extract a subset of atoms from that ff1
variable
(and e.g. create a new model using load data).
Is this possible?
Thanks
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Re: [Jmol-users] Jmol Anniversaries?
Henry, there is some recollection on history at http://jmol.sourceforge.net/history/index.en.html which I made time ago from several sources. I cannot guarantee its accuracy or completeness Maybe I will move that to a page in the Wiki -- that's an idea --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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] using mutate on the first model with 2 loaded files
Hi Bob Any chance that I can use "mutate" on a first model when I have loaded two models (2 files into 2 frames)? I am testing the different syntaxes from the documentation but it seems impossible. Some sections do mention "in the last model". Can you please confirm? Thanks --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] How does Jmol know the \alpha-helix and \beta-sheet
Hello, Huan Jmol uses 2 methods: 1st if the pdb file contains HELIX and SHEET records, Jmol uses those. 2nd if that is not the case, Jmol will calculate secondary structures using the DSSP algorithm Even in case #1, you can force calculation with DSSP (and see the difference) using the command calculate structure dssp There is also another option, calculate structure ramachandran which I guess does what you expected, i.e. use the dihedral angles All of those do not depend on hydrogens, I believe. See documentation at https://chemapps.stolaf.edu/jmol/docs/#calculate Also this: http://proteopedia.org/wiki/index.php/Secondary_structure#How_Jmol_Deter mines_Secondary_Structure Cheers! · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- 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
Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol
Of interest on this topic, this article has just been published: Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design Shuguang Yuan, H.C. Stephen Chan, Zhenquan Hu https://doi.org/10.1016/j.tibtech.2017.03.009 --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] labeling residue by position relative to observer
Great solution
I just noted this in the documentation (under "functions"):
point({x,y,z}, true)gives the screen coordinates {sx, sy, sz} corresponding
to
the 3D coordinates {x, y, z}.
point({sx,sy,sz}, false)gives the 3D coordinates {x, y, z}
cooresponding to
the screen coordinates {sx, sy, sz}.
Bob, I think that sx, sy, sz should be listed under "atom properties"
https://chemapps.stolaf.edu/jmol/docs/#atomproperties
That's where I looked for it when Luciano asked.
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Re: [Jmol-users] labeling residue by position relative to observer
Ciao Luciano Although Jmol obviously "knows" the screen-Z position of an atom (used e.g in perspective, fog, slab and depth, rotate best), I can find no command that will retrieve that value. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] ...still problems with the extended display...
Hi Marco I have also observed some failures in Jmol Application saving properly the window positions and size. Deleting the history file resets the issue, as you have noticed. This did not happen in older versions, but I have been unable to find the cause. I am curretly using Win10 I did not think of this before since you started the discussion with JSmol (or so I understood). The saving of window settings to a history file only applies to Jmol standalone application. · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- 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
Re: [Jmol-users] scripting syntax
[I'm moving this to the jmol-users list] Hi Jeff I foresee no problem in your scripts. My advice is that you right-click and open the Console, then paste there your scripted commands one at a time and see which one gives the error or fails to work. On 28 Apr 2017 at 15:15, Jeff Sims wrote: > I´m trying to diagnose scripts written a few years ago that are no longer > working in the latest version of JSmol. > The same scripts work correctly in an older version of JSmol: ver. 14.2.4 > (2014-08-03). > After updating JSmol, there is no error in the JSmol console, just a blank > JSmol canvas (no atoms appear). > > I suspect that it´s syntax related to `select´? because nothing is being > selected for color or style, but not sure. > > Here are a few excerpts: (I´ll just include an example of each type of call). > Does any of this look problematic or need fixes? > I can post the full scripts if helpful. > > model 1 > rotate z -108 > rotate y 130 > rotate z 32 > zoom 100 > restrict not :a and not solvent > > select 147-157 and :a > define switch1a selected > > select switch1a or switch2a or switch3a > define allswitcha selected > > select :i and (177,179,181,192,198,199,200,202,205,211) > #numbers are less by 1 than those in the Nature 379 article > define ihb selected > #alpha subunit residues hbonding with beta > > elect (switch1b and backbone) and not (173-176) #these > sw1b residues interact w/beta > select selected or (177,179,181) and :i > define subset1b selected > > select :a and (172,173,174,176,179,185)or (switch2a and backbone) > define subset2a selected > > select :a > color [xFFAD00] #orange > > select gtp > color [x00C000] #guanine green > > select gdp > color [xFF] > > select :i or :b or :g or :d > spacefill on > select atomno=644 and :i > label "\u03b1" > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Jmol-developers mailing list > jmol-develop...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-developers --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] Add atom from command line
Hi Donna You could probably use set appendNew false load append data .. See https://chemapps.stolaf.edu/jmol/docs/#set_appendnew https://chemapps.stolaf.edu/jmol/docs/#loadappend https://chemapps.stolaf.edu/jmol/docs/#loaddata https://chemapps.stolaf.edu/jmol/docs/#data --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] JSmol labels on zoom
Hi Jaime It's always been like that by default, but I think there is an option: set fontscaling on although it is a little tricky to get it working when there is zoom between two applications of labels. See https://chemapps.stolaf.edu/jmol/docs/?ver=14.6#font -- 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
Re: [Jmol-users] Secondary structure does not match DSSP
Hi Nicholas > However, if I issue the command $calculate structure and then redisplay, the > structure > is then shown with a ribbon consistent with DSSP, running from 365 to 373. > Can anyone > tell me why Jmol doesn't display this stretch according to DSSP in the first > place? I am not certain, but it is likely that when you load a file Jmol will use the secondary structure declared in the PDB file, and not the DSSP result unless you invoke this later (using calculate). As far as I can interpret, the pdb file says beta strands for Tyr350---Trp356 Cys370---Pro373 so 365-368 are not a beta strand --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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] Java support in browsers
(I'm following another thread started by David Hibbitts but this is a different topic, so I changed the subject) David, May I ask what is the information you have regarding future support of Java by Waterfox? On 29 Mar 2017 at 15:14, David Hibbitts wrote: > It's hard to know how much any of us should invest in these java-specific > issues given the aggressive nature of browsers toward javascript -- > but my website really serves my research group, not the general public, and > there I can certainly get the users to install Waterfox+JAVA. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] Jmol Keyboard Interaction
Have you checked Jmol's "navigation mode" ? As far as I remember, it used the keyboard. But maybe it is only applicable to the Jmol application. http://chemapps.stolaf.edu/jmol/docs/#navigate http://chemapps.stolaf.edu/jmol/docs/#setnavigation -- 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
Re: [Jmol-users] file caching in JSmol working better than expected
Dear Bob, if we can confirm that, if would be wonderful. Many of my pages no longer work in local, i.e. when run from local files (some undecipherable JS errors prevent it; it seems to depend on paths used and the complecity of the file setup, but I have been unable to pin it down). I am forced to use a local web server for my testing. This at least would give an extra solution Thanks. Good luck in Bolivia again! --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] JSmol applet creation of mo surfaces or contour plot is slow
Hello Bruce I will gladly take a look at your page when I have time, but here are a few comments in advance: 1. Using JSmol-html5 with IE is very slow, indeed. Other browsers are recommendable. 2. Given the current state of Java support, you'd better forget chances of using Jmol-Java. I agree that it is an advantage for large models or, as in your case, isosurface computations. But we are loosing that battle. Firefox just dropped support for plugins, as Chrome did before. I am switching to PaleMoon as my main browser (they will support plugins indefinitely), but Oracle will eventually abandon the offering of the Java plugin. 3. What you might try to do is to save the isosufaces to a file. Loading them later is very fast. I have not a clear idea to what extent your calculation is unique or can be done in advance and the result used repeatedly. 4. If you have the control and expertise, you culd run the calculation in the server (using Jmol.jar or the JmolData.jar that does not use graphics), save the file and then serve it to the client browser. That would be faster, running in Java and not in JSmol-html5. 5. Although you are fine with JSmol.min.js + Jmol2.js, if it safer to move to direct implementation without Jmol2.js. Probably this has no effect on performance, though, but it safer for the future. I would not think you are doing anything wrong, you are just hitting the inherent speed limitations of JSmol. More later, I hope. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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] the announced death of Java - one more push
Dear Jmol users, You should be aware that Firefox has joined the trend to abandon Java applets and the latest release can no longer run Jmol in pages. Of course, JSmol-html5 is perfectly functional. Google Chrome and Microsoft Edge are another 2 major browser that cannot run Jmol-Java. Firefox 52 (released this week) does not support the NPAPI format of plug-íns and hence cannot run Java applets, Shockwave Player animations (DCR files, Macromedia Director), external PDF viewers inside the browser, etc. Running Flash Player animations/videos has been kept as an exception. Please be aware of this for older Jmol pages. If you are the page author / developer , it is most urgent that you convert your pages to use the JSmol.min.js library and enable HTML5 modality by default. http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Converting_pages_from_Jmol_to_JSmol If you are a user / visitor , be sure which browser you pick. MS Internet Explorer (versions 9 to 11) still supports Jmol-Java (and is rather slow with JSmol-html5); Safari in the MacOSX is also running Java. Other browsers that retain Java compatibility are Mozilla SeaMonkey (not clear for how long) and Pale Moon (indefinitely by decision of the developers, at least while Oracle continues to deliver the Java Plugin) More specific details and alternatives at http://www.proteopedia.org/wiki/index.php/Installing_and_enabling_Java -- 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
Re: [Jmol-users] Status of Java applets
Hi Richard I have a lot of pages that have been evolving alongside Jmol changes. I see no reason why "the Jmol applet-based stuff will not be convertible". Can you explain? I've converted all my Jmol applet pages to JSmol, and first I set them to use Java by default, or based on identification of mobile browsers (Java detection has never been reliable). When Chrome (and Opera) quit Java, I added a filter. Last thing I did --last month-- was to set default to Html5-JSmol, not becuase Java does not work but because it is a pain to go through all warnings when you are in a computer you do not control --e.g. in classrooms. But I still keep an option (at the home page for each major section) for the user to choose either Java or non-Java --and using a temporal or permanent cookie. Since I have some fairly large molecules and complexes, using Java when your system allows it is still an advantage. > The thing is, Google complains they are not mobile-friendly. That may be related to other features of page design rather than just to use of Java. If you already have JSmol it's easy to have it working with HTML5 or Java at choice. Hope this helps -- Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Error: Failed to execute 'Send' on 'XHMTLRequest' [Chrome only]
And regarding these worries... > The tmp.aI5qUbCWPc folder changes (it's randomly generated) and I'll be careful that it doesn't > coincidentally collide with the above list. You can redefine and hence override the variable used by Jmol, to always avoid binary handling add for example Jmol._binaryTypes = [".spartan"]; make sure it is called in your page after the Jmol object initialisation has finished and before the load command I am not sure what will happen if you declare it as empty array; spartan will never appear at random, I guess ;-) -- Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Error: Failed to execute 'Send' on 'XHMTLRequest' [Chrome only]
Hi David When I go to http://hibbitts.rc.ufl.edu/tour The (methanol) model loads correctly both in Firefox (Jmol-Java), Chrome (JSmol-html5) and Edge (Jmol-Java) (all in Win10) I also notice that it is running Jmol 14.4.0 from 2015, both Java (Firefox) and JSmol-HTML5 (Chrome) So the page is OK. Maybe a browser cache problem? The error you reported is quite specific of cross-server access limitiations (security) in the file loading, for which Chrome is more strict than Firefox or Edge. I don't see the clue to your problem. -- Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Error: Failed to execute 'Send' on 'XHMTLRequest' [Chrome only]
Ok, those details are useful It is possible that Chrome has recently changed its security policy (and so it would not matter which Jmol version you use) regarding retrieving of files via other browser different to the one the page is in. But this should only affect binary files, as far as I know. The "serverURL" parameter (I quoted this incorrectly in the former message) has a default which in case of trouble needs to be customised. Please see http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Setting_parameters http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Files_and_paths Apart from that, if you could give us a URL with a test page it will be easier to diagnose. David Hibbitts wrote: > 1) They are res files (not binary, shellx format). > > 2) Web-server. > 3) No idea, I doubt I've configured it, where would I find that? -- Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Error: Failed to execute 'Send' on 'XHMTLRequest' [Chrome only]
Hi David This sounds like something related to loading binary files via jsmol.php Please check: 1. What format are your model files? ARe they binary? Does the problem reproduce with plain-text-formatted files (e.g. MOL)? 2. Are you running from web server, or from local disk? 3. How have you configured the Info.server variable? Is that pointing to your own server, or to St Olaf? --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.9.1 released
Dear Bob, I was interested on that new functionality "drag from a url onto the Jmol application" you mentioned recently. Is that included in this release? -- 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
Re: [Jmol-users] set fontscaling true + zoom
Thank you, Bob In fact I was not changing the label, I was setting it for the first time. but I guess the effect is the same. Maybe the docs should say "changing or defining for the first time". Easy solution. El 7 Feb 2017 a las 18:05, Robert Hanson escribió: > > Once a label font size is set with a font scaling factor, if it is necessary > to change the label and not > its size and the zoom is not 100, it is necessary to use set fontscaling OFF > just before changing > the label and then back ON just after. This is because set fontscaling always > uses the current > zoom as part of its calculation. > > On Tue, Feb 7, 2017 at 5:41 PM, Robert Hanson <hans...@stolaf.edu> wrote: > I'll make a note in the documentation that you need to be sure to turn > off > font scaling if you change the label: > > > > set fontscaling off;label xxx;set fontscaling on > > > > On Tue, Feb 7, 2017 at 5:33 PM, Robert Hanson <hans...@stolaf.edu> > wrote: > I might be able to fix it. The problem is that you are changing the > label > after you are setting its sizing factor > > > On Sun, Feb 5, 2017 at 12:06 PM, Angel Herráez > <angel.herr...@uah.es> wrote: > Dear Bob, > > Scaling fonts in labels is very nice. > However I am seeing a funny behaviour: when I manually zoom > between two > label commands, they behave different in size. I checked now and > it also > happens with a scripted zoom. > > Example: > load $caffeine > set fontscaling true > color label yellow > set labeloffset 0 0 > select @14 > font label 24 sans plain 0.02 > label O3 > delay 2.0 > // mouse zoom here! , or "zoom 50" > select @4 > font label 24 sans plain 0.02 > label O5 > > I find this an undesirable behaviour. Is there a way to fix it? > It happens in both 14.8.0_2016-12-17 and a previous 14.6 > > > On 4 Feb 2017 at 7:26, Jmol SVN repository wrote: > > Jmol.___JmolVersion="14.8.2-beta-2017-02-03" > > noting undocumented > > set fontscaling true; font label 10 arial plain 0.020 > > - last number is a fontscaling factor that allows one to set a font > size for > > - labels in angstroms. Roughly, this pointSize * factor is in > Angstroms. > > By hansonr on 02/04/2017 07:26 > > > > > --- > El software de antivirus Avast ha analizado este correo > electrónico en busca de virus. > https://www.avast.com/antivirus > > > -- > 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 > > > > -- > 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 > > > > -- > 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 > > > > -- > 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 > · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- 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] set fontscaling true + zoom
Dear Bob, Scaling fonts in labels is very nice. However I am seeing a funny behaviour: when I manually zoom between two label commands, they behave different in size. I checked now and it also happens with a scripted zoom. Example: load $caffeine set fontscaling true color label yellow set labeloffset 0 0 select @14 font label 24 sans plain 0.02 label O3 delay 2.0 // mouse zoom here! , or "zoom 50" select @4 font label 24 sans plain 0.02 label O5 I find this an undesirable behaviour. Is there a way to fix it? It happens in both 14.8.0_2016-12-17 and a previous 14.6 On 4 Feb 2017 at 7:26, Jmol SVN repository wrote: > Jmol.___JmolVersion="14.8.2-beta-2017-02-03" > noting undocumented > set fontscaling true; font label 10 arial plain 0.020 > - last number is a fontscaling factor that allows one to set a font size for > - labels in angstroms. Roughly, this pointSize * factor is in Angstroms. > By hansonr on 02/04/2017 07:26 --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus WPM$UYFL.PM$ Description: Mail message body -- 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
Re: [Jmol-users] ribbon thickness in jmol
Hi John Sure! You have the width of the standard, flat, ribbons: ribbons 0.4 ribbons 1.5 (meaning angstroms) and if you want thick ribbons you need set cartoonFancy on set ribbonAspectRatio 12 set ribbonAspectRatio 4 (the lower the value, the ticker is the ribbon) plus the above width --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] callback for minimize
Thank you, Rolf
Yes, it seems that although the callbacks can be targeted to a jmolscript, it
does not allow to pick any parameters like it does in Javascript.
After all, even though I was developing in the Jmol aplication console, my
target is a webpage, so I have "outsourced" the processing to a Javascript
function that after checking the arguments returned by the callback, uses a
Jmol script to return the proper action.
In case anyone is interested, this is my example
// webpage, with 2 JSmol panels named jmol1 and jmol2
// script in Jmol (within two otherwise different spt files called by the page):
set MinimizationCallback "jmolMinim";
set echo top center;
echo "initial message"
minimize steps 250;
// Javascript in the page:
function jmolMinim() { //callback, reports starting / running / done
if (arguments[1]=='done') {
if (arguments[0]=='jmol1') {
Jmol.script(jmol1, 'echo "final message 1";')
} else if (arguments[0]=='jmol2') {
Jmol.script(jmol2, 'echo "final message 2";')
}
}
}
The effect is that "initial message" is displayed until the minimization
finishes,
then it is replaced by a different message in each JSmol.
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Re: [Jmol-users] C-P bond not drawn
XYZ files do not include bond information, while MOL and MOL2 do.
So I guess your C--P distances are above what Jmol considers "bonded"
Maybe you can change the default value of
set bondTolerance (decimal)
"When autobonding, the value of bondTolerance is added to the two bond
radii of atoms being tested for a bond. A larger bondTolerance allows atoms
that are further apart than the sum of their listed radii to still be bonded.
This
parameter should be adjusted prior to file loading for proper maintaining of
the Jmol state."
Other possible ways to fix that:
{_P}.bondingRadius =
set bondingVersion
data "element_vdw" 6 1.7; 7 1.8 END "element_vdw"
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[Jmol-users] callback for minimize
Dear Jmolers
I'm trying to set an echo that will display after a minimization has finished.
I prefer not to apply single thread "using set useMinimizationThread false",
so I thought I could us the callback,
but I am unable to make it work
Does anyone have a working example?
This is what I've tried, in the Jmol 14.6.4 application's console:
set echo top;
function mini(a,b,c,d,e,f) { if (b=='done') { echo "finished"; } }
set minimizationCallback "jmolscript:mini";
minimize steps 30;
The minimization runs but there is no reporting.
Or "print" instead of "echo" -- no diference
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Re: [Jmol-users] Color maps for bonds
Hi Max Have you explored the "connect" command? >From your last description, I think that might do what you want. It's easy to select atom pairs by distance, and then you could "reconnect" them and apply color and thickness of bond https://chemapps.stolaf.edu/jmol/docs/#connect · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- 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
Re: [Jmol-users] Color maps for bonds
Hi Max
Two issues here. One is the way to achive this in Jmol scripting. The other is
to specify what you are expecting to achieve, i.e. which is your criteria of
bond ordering + coloring.
Atoms are indexed as the file is read, and so there is no issue: they receive a
sequential number and you can refer to it. They also have many properties
associated to each atom.
Bonds, on the one hand, have no properties attached to them except
thickness and color. On the other hand, it is not so easy to define their
ordering and indexing. Among other things, each bond "belongs" to 2 atoms
and each atom "has" several bonds, so what should their index/order be?
(We recently experienced a case: the same protein, when read from a pdb
file and when read from a cif file, has the same atom indexing in Jmol but
different bond indexing)
I believe that yes, most probably you can iterate or loop over the bonds
collection and assign a color to each bond, read from your data file. But still
the question is in which order those bonds will come, every time you have a
new file.
What are you expecting in this regard when you define your color-data file?
> Good question. Since in the case of coloring atoms by the partial charge I
> don't need to specify
> the atoms, i.e, I think there is a direct correspondence of each line of the
> file for each atom in the
> respective ordering,
YES
> I thought that in the case of bonds we would have the same kind of
> correspondence.
NOT THE SAME (see above)
> I have checked in the manual that specific bonds can be selected by the
> command "select[{i}]" or
> a set of bonds could be attributed to a variable by "x = {atomno < 30}.bonds"
Right, but that x will be a collection of bonds -- in which order, is difficult
to
anticipate.
> and I could change
> the color of the selected bonds to red, for example.
That would mean all bonds attached to that atom get the same red color.
But each bond will also be attached to another atom, then which is the last
color applied to it?
So, in summary, I believe some of these "philosophical" or "logical" questions
need to be answered before trying to find Jmol commands to do what you
want.
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Re: [Jmol-users] use of select bonds
Yes, that seems to be our issue. So we need to redo the state scripts. Thanks On 13 Jan 2017 at 18:07, Robert Hanson wrote: Ah, yes! bonds are indexed COMPLETELY differently -- and are not even the same set of bonds -- in PDB, mmCIF, and MMTF. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] use of select bonds
Thank you, Matt Further testing indicates that he command itself is working as it used to be. Suspicion is now on a possible change in the way bonds are indexed, between old PDB files and recent mmCIF files (this is in Proteopedia which changed the source of files last year) --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] use of select bonds
Hi all
I am not familiar with the use of "select bonds" command, so I am asking
here.
We have somewhat old state scripts (saved in Proteopedia scenes) that
were generated by an older version of Jmol (# Jmol state version 11.8.24
2010-04-26 08:00;).
Right now, Jmol 14.6.0 fails to select the bonds and render their thickness
and color.
The commands in state are of this type:
select BONDS ({5 16 27});
Q: Has this syntax changed, or is it broken?
I've just tried Jmol app 14.6.4 and don't know how to select bonds, my
simple test is failing
load $caffeine
select bonds ({2 3})
Should that work as such?
·
Dr. Angel Herráez
Biochemistry and Molecular Biology,
Dept. of Systems Biology, University of Alcalá
E-28871 Alcalá de Henares (Madrid), Spain
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Re: [Jmol-users] Running Jmol in Linux command line
Sorry, I copied the wrong piece of code in my former reply. This is the correct way: Hello, Huan You are in the right drection. > Actually, I found a very brief introduction in Jmol Wiki website, where listed some commands for loading PDB file and > running script in command line. However, I did not see any command for saving data. Not specifically to save data, but it's the same method for any Jmol command or script. > write ramachandran "OUTPUT_FILE_NAME" That is a Jmol script http://wiki.jmol.org/index.php/Jmol_Application#Command_line_options tells you can use Jmol.jar fileName -J script_commands -s scriptFileName -j script_commands So it's probably a question of quotes; please try this way: Jmol.jar PDB_FILE -J ' write ramachandran "OUTPUT_FILE_NAME"; ' or Jmol.jar PDB_FILE -J " write ramachandran 'OUTPUT_FILE_NAME'; " or, when the filemname is not conflictive (ie it does not use spaces or nonASCII characters) you can omit the quotes: Jmol.jar PDB_FILE -J " write ramachandran OUTPUT_FILE_NAME; " If that fails, or if it is more convenient for you, you can save the script in a text file, e.g. named MYSCRIPT.TXT and then Jmol.jar PDB_FILE -s MYSCRIPT.TXT Jmol.jar PDB_FILE -s "MYSCRIPT.TXT" -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/intel___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Running Jmol in Linux command line
Hello, Huan You are in the right drection. > Actually, I found a very brief introduction in Jmol Wiki website, where > listed some commands for loading PDB file and > running script in command line. However, I did not see any command for saving > data. Not specifically to save data, but it's the same method for any Jmol command or script. > write ramachandran "OUTPUT_FILE_NAME" That is a Jmol script http://wiki.jmol.org/index.php/Jmol_Application#Command_line_options tells you can use Jmol.jar fileName -J script_commands -s scriptFileName -j script_commands So it's probably a question of quotes; please try this way: Jmol.jar PDB_FILE -J 'ramachandran "OUTPUT_FILE_NAME"; ' or Jmol.jar PDB_FILE -J "ramachandran 'OUTPUT_FILE_NAME'; " or, when the filemname is not conflictive (ie it does not use spaces or nonASCII characters) you can omit the quotes: Jmol.jar PDB_FILE -J "ramachandran OUTPUT_FILE_NAME; " If that fails, or if it is more convenient for you, you can save the script in a text file, e.g. named MYSCRIPT.TXT and then Jmol.jar PDB_FILE -s MYSCRIPT.TXT Jmol.jar PDB_FILE -s "MYSCRIPT.TXT" -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/intel ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Interesting find -- Firefox speed doubling
Dear Bob: I am not seeing any difference based on one or several tabs, one or two Firefox windows. It is running at around 40 ms, most of the time actually below it occasionally reaching 50 ms https://chemapps.stolaf.edu/swingjs/phet/site/swingjs/examples/phet/GasPro perties.htm Firefox 50.1.0, Win10 Pro 64 bits, Intel Core i7-4790 @3.6 GHz Chrome reports a similar speed (but the text in the tab is updated more slowly than in Firefox, so I can read all numbers before they go) It's great you are bringing those simulations into HTML5! -- 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
Re: [Jmol-users] error in loading package.js
Pino, I also see the same error. So this is not a cache issue (my first thought). I do not think it has anythng to do with the "load" command, it is previous to building the JSmol object. On the other hand, the error may not be exactly in that js file it mentions; in my experience the error reports from the JSmol library are often not precise. I don't know anything about permalinks With a page this complex, it is hard to track. Can you have some simpler page for testing? Or try a test again with the previous Jmol version --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] Loading zip files with multiple coordinate files
There's always some way with Jmol ;-)
Please try this:
xx = load("3-pdb-files.zip");
zap;
for (i=1;i<=xx.lines.length;i++) { load append "3-pdb-files.zip" manifest
@{xx.lines[i]} }
That may be easily put in a function that takes the file name as argument, if
more convenient.
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Re: [Jmol-users] Loading zip files with multiple coordinate files
Yes, a zipfile made of PDB files fails to load for me too in 14.6.4 It works with files in other formats. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/xeonphi___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Loading zip files with multiple coordinate files
Dear Bob, Well, Jmol does exactly that! When I load a manually created zipfile with 3 files into Jmol 14.6.4_2016.10.02, it loads the 3 molecules in 3 frames. Additionally, the documentation suggests it will do so, since options are there to exclude some files or to ignore the manifest: https://chemapps.stolaf.edu/jmol/docs/#loadzip/jarfilesandjmolmanifest Sample file at http://biomodel.uah.es/angel/Jmol/molecs.zip You can try load http://biomodel.uah.es/angel/Jmol/molecs.zip from the console I'm pretty sure Jmol never went through a ZIP file and looked for files to read. It would have to test each one, and I don't recall that being an option. --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/xeonphi___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Loading zip files with multiple coordinate files
Hi Doug Have you tried to add a manifest to your zip file? According to https://chemapps.stolaf.edu/jmol/docs/#loadzip/jarfilesandjmolmanifest that allows to instruct Jmol to load several files within the zip On the other hand, a quick test I made a zip file with 3 files and without more precautions Jmol 14.6.4_2016.10.02 loads the 3 molecules in 3 frames as you wish. So maybe there is some problem with your zipfile? --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/xeonphi ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] PubChem server is moving to httpS
Will this affect Jmol functionality? e.g. loading files from PubChem "NCBI will begin redirecting all HTTP traffic to HTTPS on Thursday, November 10 at 9 AM EST (2 PM UTC)" https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Can anybody reproduce this issue for me...
For the record: This has been fixed for the next release, per revision [r21288] https://sourceforge.net/p/jmol/code/21288/ -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Can anybody reproduce this issue for me...
Hi Jonathan #2 confirmed, with 14.6.4_2016.10.02: load $caffeine getproperty moleculeinfo // reports moleculeinfo[1].nElements 4 load $caffeine getproperty moleculeinfo // reports moleculeinfo[1].nElements 8 ...and so forth. Every new load increases that by 4 -- cumulative initiliaze does nothing, but zap resets the count #1 I don't see it - - e.g. 13 frames in this: zap; load https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/spartan/C H3FCl_TS_RHF_FREQ.smol?format=raw; getproperty moleculeinfo frame next getproperty moleculeinfo frame next getproperty moleculeinfo frame last getproperty moleculeinfo // no strange reports No issues either with this 7-frame file: load https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/gamess/ H2O_6311%2Bdiff%2BDFTcorr.log?format=raw --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Regarding usage of POV-ray
I can confirm what Kuntal was reporting, and also with a different model
So there is a bug
in PovRay export from Jmol 14.6.4_2016.10.21
Atoms are rendered much bigger. Bonds seem unaffected.
See example:
PNGJ made by Jmol (alanine from NCI):
http://biomodel.uah.es/angel/Jmol/Ala.Jmol.png
PNG produced after PovRay:
http://biomodel.uah.es/angel/Jmol/Ala.pov.png
intermediate files:
http://biomodel.uah.es/angel/Jmol/Ala.pov
http://biomodel.uah.es/angel/Jmol/Ala.pov.ini
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Re: [Jmol-users] Regarding usage of POV-ray
Dear Kuntal That should not happen. Please provide details: - version of Jmol you are using - the Jmol state of you model as you want it rendered -- you can save that usingwrite state "filename.spt"and send us the file, so we can test the PovRay export -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: JSMol change viewer size
Hi Thomas Probably the easiest way: 1.- Define you Info variable with width:"100%", height:"100%" 2.- Wrap your source JSmol, as well as your target JSmol, in a DIV and set their size via CSS. JSmol will always fit the wrapper div, which you can easily resize via css and Javascript --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus -- 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
Re: [Jmol-users] JSmol submenus not working in iOS
> The text field would be a solution but a functional menu would be better. The menu is managed by jQuery-UI so the fix should come from there. I guess there is some mobile-friendly jQuery Jmol users Maybe we should raise funds to buy Bob that iPad ! crowdfunding is the fancy word now ;-) -- 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] export to VRML and X3D
Re: revised VRML output and new STL output Congratulations, Bob I understand this means a change in the VRML output starting with this version. Something worthy to make a note, just in case. Question: what is the status of the X3D export? As far as I remember it was written by matching the VRML export to X3D syntax. Should it be modiified too to avoid spheres etc., or left as is? Anyone has an opinion? -- 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
Re: [Jmol-users] JSMOL load inline function
Glad you solved it As far as I remember, the pipe character serves the same as your \n Inline loading is always tricky! On 26 Sep 2016 at 12:49, Matthew Kennedy wrote: Thank you Angel, in the end, it appears the issue was that it needs to print out the literal \n's in the script line. So the following worked for me: -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSMOL load inline function
You may also need a space between the pipe and the element symbol, so it seems > that lacks newline characters apparently. Jmol needs either those or > vertical > lines (the 'pipe' character, | ) Try inserting a pipe before each new line· -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSMOL load inline function
Mathew, that lacks newline characters apparently. Jmol needs either those or vertical lines (the 'pipe' character, | ) Try inserting a pipe before each new line· Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSMOL load inline function
Hi Mathew Possible sources of trouble (just a guess) - quotes (particularly when they get nested) - line breaks all that related to Javascript handling of your text string If you could provide a sample as plain text of what the php variable outputs., it would help diagnosis. Another idea: write the output first to a , then load that value into JSmol (the browser will parse with less confilcts what is in the textarea in order to pass it along) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Potential bug in reading xyz files
OK, I will ammend the wiki to clarify the issue. But, important: Peter, has this behaviour changed across Jmol versions? It is one thing that Jmol identifies or not the format, as Bob has explained; it is another if there has been a change in behaviour. Thanks -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] deferUncover not working
Thanks, Bob Sorry for the complaint. It seems I was misunderstanding the use of deferUncover > Q: Does https://chemapps.stolaf.edu/jmol/jsmol/cover.htm work for you? > Q: How do these differ from https://chemapps.stolaf.edu/jmol/jsmol/cover.htm ? They work the same, yes. So I was expecting the cover image to stay until I clicked, but instead what happens (by design) is that the image disappears as soon as the model is ready. I guess I was confused probably because of the wording in coverScript and makeLiveImage, see http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info Forget it! Cheers, A. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] failure to use deferApplet with defaultModel
There seems to be a bug when using Info.defaultModel together with
Info.deferApplet
A basic page with the code below
1. displays the image
2. on click, loads JSmol, the loading echo and then the model
3. the model disappears and the loading echo is displayed again
History in the console matches that:
zap;set echo middle center;echo Retrieving data...
load async "=1crn";;zap;set echo middle center;echo Retrieving data...
var Info = {
defaultModel: "=1crn",
deferApplet: true,
coverImage: "some.png",
color: 'white'
}
JSmol 14.6.1_2016.07.11
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[Jmol-users] deferUncover not working
Another problem that looks like a bug:
I am unable to use deferUncover: true,
it has no effect at all, the model loads straight after the image without any
clicks.
This happens both with defaultModel and with a local model loaded via
Info.script
var Info = {
defaultModel: "=1crn",
deferUncover: true,
coverImage: "some.png",
color: 'white'
}
JSmol 14.6.1_2016.07.11
var Info = {
script: "load =1crn",
deferUncover: true,
coverImage: "some.png",
color: 'white'
}
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Re: [Jmol-users] Load JSmol from external host
I am surprised. As far as I know, the jsmol.php is only used for loading models in binary format (and only for some browsers), not for used to load the javascript making the page . Have you tried loading a plain MOL file, for example, or a file from NCI CACTUS using "load $aspirin" ? That would clarify the issue -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Molecule Portrait Maker - Photo-realistic images from JSmol
Hi Chris Nice product idea When you say it's free, do you mean I can get a final quality image? The interface just says "order" -- will one place an order and get the image without paying while this is in beta? I was missing some real samples. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol in Institutional Repositories?
Hi Vin Can you explain more what you are after? I know Dspace only as something related to libraries, either a way to store references or full articles (not sure now) JSmol files are stored in any server that is holding webpages with models. What kind of application or use are you thinking of? -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] can't resize molecule in Jsmol window
Henry,
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Re: [Jmol-users] can't resize molecule in Jsmol window
Hi Henry Apart from sorting out your missing css file, this is my advice: 1.- You probably should get rid of your frames (although I have always been an advocate of frames when they provide functionality) Additionally, your frames definitions have inconsistencies: 69%, 65% 65% -- I do not see the reason. 2.- For heights to work properly in % you must make sure that both your html tag and body tag have their css height:100% 3.- You might try my template at http://biomodel.uah.es/Jmol/resizable/ You would need version 1.1 adapted as in the old "template F" -- I can help if you like it -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] "Augmented Reality": https://github.com/es605/HTMoLar
I have had a little practice using Augmented Reality using a downloadable piece of software --by Colin Berry-- and molecular models exported (VRML) from Jmol: http://www.cf.ac.uk/biosi/staffinfo/berry/AR/ar.html doi:10.1002/bmb.20805 You need to run the software in the computer you want to use (Win / Mac), and do a little text editing on the config files. The models look very crisp; rotation is limited by its visibility of the marker card from the camera. Spacefill, ball and stick, cartoons, molecular surface work fine. Apart from being fashionable, I do not expect that any such viewer will match what can be done with JSmol embedded in a page. https://github.com/es605/HTMoLAR I don't quite see what's the role of AR there. You can see the structure within the web page before accessing the AR page where your webcam is activated and, I guess, for this to work you need to have printed the card with the symbol-marker-QR for the model you choose. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jsmol in GWT
Hi Tom All looks good, but I am not familiar with the GWT environment. There might be some confilct. One question: When are you calling that code? Is the "myContainer" node already created? The error is not helpful, but you could try defining the variable at the beginning (head section) as var myJmol = "myJmol" and later do this var applet = Jmol.getAppletHtml(myJmol, Info); and see it that helps. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Write 2 PDB models?
Dear Bob, that makes sense. I did not realize. Additional problem is that saved pdf file (with 1st model empty) cannot be loaded back into Jmol, it hangs with the spinning cursor forever. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Write 2 PDB models?
Hi Eric I agree it's a bug. I wuld xpect -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Write 2 PDB models?
Hi Eric I agree it's a bug. I would expect both models to be saved, and the doc says "Only the currently selected atoms are saved." If you save to SDF it works as expected. The fact that the file has MODEL ENDMDL means that Jmol is indeed intending to save both. So for proteins, you could instead use write test.jmol which works fine. Of course, that's a binary file (may be an issue if you want to work with local webpages). -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
Sorry, something was preventing models from loading --only in some browsers. I have changed to a newer Jmol version (14.6). Please force reload of the page and it should work now > > a little fun: browse rapamycin structures at PDB: > > > > http://biomodel.uah.es/JSmol/rapamycin.htm > > -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
a little fun: browse rapamycin structures at PDB: http://biomodel.uah.es/JSmol/rapamycin.htm -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rapamycin
Hi Phil Going to PubChem, Compound Summary for CID 5284616 has a "download" menu that offers no 3D structure but says "Protein-bound 3D structures" -- their format are not helpful, but you can search in PDB for rapamycin and will find this ligand as RAP Hence, Jmol console load ==RAP and you have it! Of course, you can browse the different proteins to check the actual "real" 3D structure they bind · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Capture PNGJ file as a variable
El 14 Jul 2016 a las 12:13, Robert Hanson escribió: > Note that by putting a PNGJ file into a variable you can > > -- extract or exchange the image So a question would be, How to apply that extracted image in the page, e.g. as the source of an tag created dynamically in Javascript? -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Install problem on windows 10
The question is Does Windows 10 on a Surface Pro 4 support Java? (I have no idea) El 14 Jul 2016 a las 8:19, Matthew Staab escribió: > > Can Jmol be installed on a surface pro 4 running windows 10? I have been > unable to do so. > > · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Capture PNGJ file as a variable
Chirs, please hav a look at "getProperty image" under http://chemapps.stolaf.edu/jmol/docs/?ver=14.6#getproperty It's only defined as JPEG but does the trick · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Capture PNGJ file as a variable
Chris, the problem is possibly that PNG data is binary, while X3D data is text I am not sure you can put binary data in a javascript variable. So the limitation might be in the js side rather than the Jmol side. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] shortcut for Jmol Scripting Documentation page
Dear Jmol users I have defined a shortcut link to Jmol Scripting Doc, for convenience: http://bit.ly/JmolDoc leads to the Jmol Scripting Documentation page at StOlaf Feel free to use and share it if you wish -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Use of variable in a call to getProperty
Sure! The question is... where to locate it? Goes to the to-do list. Suggestions or actual page edition are welcome On 8 Jul 2016 at 9:59, Robert Hanson wrote: Might be a nice addition to the Wiki. -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] page-developer request - Jmol Unplugged
Dear Bob I will likely get involved on this. For now, just two quick comments that popped up: 1. I have had big trouble running my pages locally since I moved to JSmol. That may be due to them being old and ellaborate, with a combination of folders, pdb or mol files, scripts, common JS files... across folders that I've never been able to figure out which is the key of the problem. I just gave up and resort to either online or local webserver when needed --not that I am happy with that So any contribution from my side will need reserach and possibly relocation 2. Proteopedia has a similar feature in the sense that any Poteopedia page can be packed for download and should run offline - the download includes all components including JSmol and j2s files -- This can be a reference for hosting or methods of delivery. 3. Giving away: Creative Commons licences do a decent job at that - you can pick the conditions you prefer for sharing -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] resolution of JPG images
Hi Rick a few comments: 1. I can recommend that you try PovRay output. It is PNG, transparent background and much better look. You don't need to learn how to use PovRay, producing the images is straightforward. You have to install PovRay, export to PovRay format from Jmol and then save from PovRay to PNG 2. I do not think that JPG may have transparent bacground; it would be white maybe. And as Bob says, the quality is always worse -- the only advantage is smaller files, at the cost of quality loss. 3. Given the way Jmol works for rendering I believe a vector format is not possible. VRML is possibly the closest to that idea, as it is made of "objects", but it is not practical for image production. Do try PovRay with eg 1000 px size, you will be surprised! I have a not particularly brilliant example at http://biomodel.uah.es/Jmol/export-image/exportPNG/ -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Export x3d problem.
> OK, this observation makes perfect sense. It turns out that when you use > cartoonsFancy (or > "cartoonFancy"; they both work, because I got so tired of not remembering > which it was...) a > variable doesn't get reset after the file is created (which is written OK, > right?) and then the screen > rendering dies after that at the point where it is drawing the fancy > cartoons. Jmol still works; it just > doesn't display anything after that point. Well, that's what I was observing when the file was successfully exported. But in some of those cases (in my hands and also in Chris reported problems) the x3d file is not correctly saved (it's very small with no useful data) or there is a network error and the file does not get saved at all. -- Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
