Re: [Jmol-users] frame [array of models]?
El 24 Sep 2008 a las 21:17, rob yang escribió: Hmm, that does the trick. What if I want to animate only selected models too? I'm quite sure that there are options for choosing the frame range involved in animation. Check the doc. But maybe not possible for non- contiguous frames. including ones that are not displayed which results in blackout period. Yes, that sounds likely the way it is. How many frames do you have? You could fake the animation by scripting them one at a time and using a loop. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] frame [array of models]?
(following my previous post) Rob, You could also try to **delete** the unwanted frames (I think it's done with a variant of ZAP) then play the animation - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Browser Crahes While Loading Jmol
Hi Vinu El 25 Sep 2008 a las 12:31, vinu manikandan escribió: I had mailed the Jmol users blog couple of times, may be i was not clear in my question that's why ididn'tget any answers. Maybe. Anyway, the list is so active that sometimes messages just drop down too quickly. Don't hesitate to insist. Sir this is the code i used in my CGI script. Html Headscript type=text/JavaScript src=Jmol.js/script/head Bodyscript type=text/JavaScriptjmolInitialize(jmol)/script script type=text/JavaScript jmolApplet(150, 1UW5.pdb; select all; color green; select 1- 55;color red; select all; spacefill off; wireframe off;cartoon); First, I think you need load 1UW5.pdb; you probably have it already, or the molecule would not load at all. Sir the values 1 and 55 is not static it will change. But the PDB structure will be the same.The values are coming from another program. But, will the page be reloaded with the new values? Then, there is no way to avoid loading the model again. But the browser should load it from the cache, so there is no delay. My problem is that with such a script the Jmol loads the PDB structure every time andbecauseof that mybrowsercrashes frequently. This is the problem, but it should not happen irrespective of your page code. Please, specify which browser version and Java version you are using. Try another browser to see if the problem is still there. Is there any way such that Jmol loads the PDB structure one Time but mapping can be done without loading the structure again and again. If you can have a setup where the other program provides the new values without reloading the page, then you could achieve what you want separating the script for the load line, for example with a button or better a javascript event. If you tell me how your other program can provide the new mapping to the page (e.g. in a form or a javascript variable), I can tellyou how to put that part separate from the model loading. If, contrarly, the program provides a full page reload, then there is no possibility to avoid reloading the pdb model. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Browser Crahes While Loading Jmol
Vinu manikandan wrote: Sir I restructured the program in such away that the different values are provided in the same page for example 1)1-55, 2)100- 120, 3)130-140 and I want to select these regions in the Jmol with out loading the protein structure again and again on the PDB Structure 1UW5.pdb one by one by providing a hyperlink to each of these values. When I had given the simple hyperlink a href=PDB.pl?s=1e=10pdb=1UW5.pdb1-10/a Yes, if you use the hyperlink in that way you reload the page. You just need to send Jmol a script from within the page. Using a link it would be something like: (I assume that you are using Jmol.js) script type=text/javascript jmolLink(select 1-10; color cyan; , 1-10) jmolLink(select 1-55; color cyan; , 1-55) jmolLink(select 10-120; color cyan; , 100-120) /script The first argument is the script, teh second is the text displayed as hyperlink (may be anything you want). The color cyan is just an example of a way to act on the selected residues. Dots or halos are other good choices for highlighting. You can also use buttons or a drop-down menu instead of the hyperlink --just cosmetic, it depends on which look you prefer; it will work the same. Sir, can you provide me an alternative way such that the Loading of the Protein happens a single time and mapping can be done multiple times. See above Sir,I am using the new Mozilla Fire fox 3.0.2 and the Java jre6. I had checked this with other Browsers such as IE6, Safari and New Google Browser Chrome. Good, the purpose of my question was whether you are also experiencing crahses with the other browsers (in which case the problem may be in the page code) or only in Firefox (then it's a browser-specific problem). - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] final testing appreciated
also, you can add parameters like that as though they were callbacks: jmolInitialize(./, JmolApplet.jar) jmolSetCallback(draggable, true) jmolApplet(400) On Thu, Sep 25, 2008 at 3:31 AM, Angel Herraez [EMAIL PROTECTED] wrote: Re: draggable applet Here is a partial copy of my previous post (4 Sep.) --- Forwarded message follows --- [...] I've tested it and it works. The applet detaches (Firefox 3 and Chrome) and stays as a borderless window with a tiny close button (that returns it to the browser), no way to resize. Maybe useless, but cool! This is the code I've used: jmolInitialize(./, JmolApplet.jar) jmolSetDocument(0) var s= jmolApplet(400) s = jmolAppletAddParam(s,draggable, true) document.write(s) jmolSetDocument(document) --- End of forwarded message --- - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] final testing appreciated
That sounds like a good explanation, but unfortunately I had the same problem on both WinXP and linux I also cleared the FF cache on both platforms (in addition to re-starting FF and also re-starting the computer (WinXP). I may go back and try it again, but like I said, I'm happily using the signed Applet now -Tom PS - No, I did NOT clear the java cache -- I have no idea how to do that under linux!! On Thu, Sep 25, 2008 at 1:35 AM, Angel Herraez [EMAIL PROTECTED] wrote: El 24 Sep 2008 a las 17:35, Thomas Stout escribió: Oh, I restarted everything - including the computer and re-downloaded My experience with Firefox (Win) is that on some occasions it caches the applet and insists on using the cached copy even after restart and even if a new applet version is being tried. Apart from trying hard reload of page, closing and reopening Firefox, you may need to clear Firefox and/or Java caches. That would explain Tom's problem, since only the unsigned RC14 applet would have been cached and the signed one would eb recognized as a different one. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] frame [array of models]?
ooh, yes, that's a neat option. zap 1.2,1.4,1.6,1.8 etc. Note that the original frame designations don't change. After this frame 1.3 is still frame 1.3. But if you try to go to frame 1.4, then you just get all frames because frame 1.4 no longer exists. Bob On Thu, Sep 25, 2008 at 3:24 AM, Angel Herraez [EMAIL PROTECTED] wrote: (following my previous post) Rob, You could also try to **delete** the unwanted frames (I think it's done with a variant of ZAP) then play the animation - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] final testing appreciated
It's the Java cache. On Thu, Sep 25, 2008 at 9:55 AM, Thomas Stout [EMAIL PROTECTED]wrote: That sounds like a good explanation, but unfortunately I had the same problem on both WinXP and linux I also cleared the FF cache on both platforms (in addition to re-starting FF and also re-starting the computer (WinXP). I may go back and try it again, but like I said, I'm happily using the signed Applet now -Tom PS - No, I did NOT clear the java cache -- I have no idea how to do that under linux!! On Thu, Sep 25, 2008 at 1:35 AM, Angel Herraez [EMAIL PROTECTED]wrote: El 24 Sep 2008 a las 17:35, Thomas Stout escribió: Oh, I restarted everything - including the computer and re-downloaded My experience with Firefox (Win) is that on some occasions it caches the applet and insists on using the cached copy even after restart and even if a new applet version is being tried. Apart from trying hard reload of page, closing and reopening Firefox, you may need to clear Firefox and/or Java caches. That would explain Tom's problem, since only the unsigned RC14 applet would have been cached and the signed one would eb recognized as a different one. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] final testing appreciated
Just found this (well, not me, Google of course): Clearing Java cache on Linux, Mac, Windows: http://www.uwplatt.edu/oit/howto/java-cache.html - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Issues with FireFox on MacOS...that's odd...
signed applet! :) On Wed, Sep 24, 2008 at 10:05 PM, Jonathan Gutow [EMAIL PROTECTED] wrote: Rob, Even with this plugin there is a problem if you access files locally on your computer. FF appears to pass absolute paths to files rather than relative. This causes security errors when the applet tries to load files like scripts from the hard disk. -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] ff3 vs safari.. again.. load
Hi all,
So here's something new that's confusing me. I am loading a multi-structure
mol2 file. That's as simple as it gets, right? That's what I thought too till
safari spoke. In Firefox3, the molecule loads no problem. In safari, it
doesn't.. *unless* I put in an alert message right before the load command.
Below is the barebone of my code. It seems like something is out of sync in
safari that I need to slow it down (alert message) for the script to catch up.
Help. Thanks.
-Rob
html
head
script src=/submit/jmol-11.6.RC15/Jmol.js/script
script type=text/javascript
function loadLigands(structure) {
var load_script = load + structure + ;select all; spacefill 20%;
wireframe 0.35;;
//alert(load_script); // --UNCOMMENT THIS ALERT MESSAGE TO GET IT
TO WORK IN SAFARI-
jmolScript(load_script);
}
function messageCallback(app, msg) {
msg = + msg+;/* convert callback message into string (recommended
by other Jmol users) */
if (msg.match(/ScriptException/)) {alert(=== Jmol SCRIPT ERROR ===\n +
msg);}
else if (msg.match(/java\.security\.AccessControlException/)) {alert(===
Java Error ===\nA Java error prevented loading of the structure);}
else if (msg.indexOf(ERROR)=0 msg.indexOf(load ) = 0)
{alert(msg);}
}
/script
/head
bod
body
onload=loadLigands('file:///Library/WebServer/Documents/toy/vs_analysis/result0.mol2');
script type=text/javascript
jmolInitialize(/submit/jmol-11.6.RC15/, JmolAppletSigned.jar);
jmolSetCallback(messageCallback,messageCallback);
jmolApplet([600, 450]);
/script
!-- end jmol --
/body/html
_
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Re: [Jmol-users] ff3 vs safari.. again.. load
no kidding! What's firing the loadLigands() function? A button? A callback
(that could be the problem -- not good to run jmolScript from a callback on
some platforms, I think).
Try using
setTimeout(loadLigands(''),100)
in whatever call is doing that. I know the quotes are pain there. You might
implement it this way:
function loadLigands(structure, trigger) {
if (!trigger) {
setTimeout(loadLigands('+structure+',1),100)
return
}
var load_script = load + structure + ;select all; spacefill 20%;
wireframe 0.35;;
jmolScript(load_script);
}
This starts a new thread so that the thread involved in the user clicking
can complete, and the load can go by a different thread.
But really, that's very odd.
Bob
On Thu, Sep 25, 2008 at 10:32 AM, rob yang [EMAIL PROTECTED] wrote:
Hi all,
So here's something new that's confusing me. I am loading a multi-structure
mol2 file. That's as simple as it gets, right? That's what I thought too
till safari spoke. In Firefox3, the molecule loads no problem. In safari, it
doesn't.. *unless* I put in an alert message right before the load command.
Below is the barebone of my code. It seems like something is out of sync in
safari that I need to slow it down (alert message) for the script to catch
up. Help. Thanks.
-Rob
html
head
script src=/submit/jmol-11.6.RC15/Jmol.js/script
script type=text/javascript
function loadLigands(structure) {
var load_script = load + structure + ;select all; spacefill
20%; wireframe 0.35;;
//alert(load_script); // --UNCOMMENT THIS ALERT MESSAGE TO GET
IT TO WORK IN SAFARI-
jmolScript(load_script);
}
function messageCallback(app, msg) {
msg = + msg+;/* convert callback message into string
(recommended by other Jmol users) */
if (msg.match(/ScriptException/)) {alert(=== Jmol SCRIPT ERROR
===\n + msg);}
else if (msg.match(/java\.security\.AccessControlException/))
{alert(=== Java Error ===\nA Java error prevented loading of the
structure);}
else if (msg.indexOf(ERROR)=0 msg.indexOf(load ) = 0)
{alert(msg);}
}
/script
/head
bod
body
onload=loadLigands('file:///Library/WebServer/Documents/toy/vs_analysis/result0.mol2');
script type=text/javascript
jmolInitialize(/submit/jmol-11.6.RC15/,
JmolAppletSigned.jar);
jmolSetCallback(messageCallback,messageCallback);
jmolApplet([600, 450]);
/script
!-- end jmol --
/body/html
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Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
-
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[Jmol-users] State script bug re: cavity
Dear Bob,
The following appears to me to be a bug in Jmol 11.6.RC12 that
prevents a cavity from being displayed from a state script. I have
not spent the time to test it in 11.6.RC16 because I doubt it has
been fixed there (but I stand ready to be corrected).
Go to
http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo/ch_view2/chapter.htm
(This is Jmol 11.6.RC12.)
Open the console and enter these commands to show a cavity near the ligand:
select :a
isosurface cavsurf minset 250 POCKET cavity 1.2 5
Display the state and copy the state script.
Reload the page. Open the Console. Execute the state script.
The following error occurs:
script compiler ERROR: unrecognized expression token: )
calculate surfaceDistance WITHIN ({0:2961 11848:11867}) ;
This problem is preventing me from showing this cavity at
http://proteopedia.org/wiki/index.php/Avian_Influenza_Neuraminidase%2C_Tamiflu_and_Relenza#Cavity_in_N1:_An_Opportunity_for_Drug_Design
Thanks, -Eric
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Re: [Jmol-users] State script bug re: cavity
Oy. Thanks, Eric. Turns out there are a couple of issues here -- calculate
surfacedistance as well as set antialiasdisplay. ARGH. OK, I will get that
fixed. I don't think it has anything to do with the cavity business,
actually.
On Thu, Sep 25, 2008 at 12:43 PM, Eric Martz [EMAIL PROTECTED]wrote:
Dear Bob,
The following appears to me to be a bug in Jmol 11.6.RC12 that
prevents a cavity from being displayed from a state script. I have
not spent the time to test it in 11.6.RC16 because I doubt it has
been fixed there (but I stand ready to be corrected).
Go to
http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo/ch_view2/chapter.htm
(This is Jmol 11.6.RC12.)
Open the console and enter these commands to show a cavity near the ligand:
select :a
isosurface cavsurf minset 250 POCKET cavity 1.2 5
Display the state and copy the state script.
Reload the page. Open the Console. Execute the state script.
The following error occurs:
script compiler ERROR: unrecognized expression token: )
calculate surfaceDistance WITHIN ({0:2961 11848:11867}) ;
This problem is preventing me from showing this cavity at
http://proteopedia.org/wiki/index.php/Avian_Influenza_Neuraminidase%2C_Tamiflu_and_Relenza#Cavity_in_N1:_An_Opportunity_for_Drug_Design
Thanks, -Eric
-
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
-
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[Jmol-users] set backgroundModel filemodel
Hi all, I am loading 2 separate files. The 1st file contains 1 structure, and the 2nd file contains multi-models. In an animation, I'd like to keep the structure in the 1st file constant in the background, while playing through the models in the 2nd file. I am loading the 1st file first, then using loading append to load in the 2nd file. I know the function set backgroundModel is my friend here, but I couldn't get the right format here. From the doc, For a multifile context, the model must be give in file.model format. So if the 1st file has the name f1.pdb, I've tried 'set backgroundModel f1.pdb.1;' without any luck. Any suggestions? Thank you as always. -Rob _ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] set backgroundModel filemodel
Rob, the file.model is numeric. So, if you do load f1.pdb load append f2.pdb (or the same, load files f1.pdb f2.pdb ) then you need set backgroundModel 1.1 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] State script bug re: cavity
OK. That's fixed. Eric, if you want to try the fix right away, grab the
files from
* http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip*
the version is 11.6.RC17_dev
Bob
On Thu, Sep 25, 2008 at 2:30 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Oy. Thanks, Eric. Turns out there are a couple of issues here -- calculate
surfacedistance as well as set antialiasdisplay. ARGH. OK, I will get that
fixed. I don't think it has anything to do with the cavity business,
actually.
On Thu, Sep 25, 2008 at 12:43 PM, Eric Martz [EMAIL PROTECTED]wrote:
Dear Bob,
The following appears to me to be a bug in Jmol 11.6.RC12 that
prevents a cavity from being displayed from a state script. I have
not spent the time to test it in 11.6.RC16 because I doubt it has
been fixed there (but I stand ready to be corrected).
Go to
http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo/ch_view2/chapter.htm
(This is Jmol 11.6.RC12.)
Open the console and enter these commands to show a cavity near the
ligand:
select :a
isosurface cavsurf minset 250 POCKET cavity 1.2 5
Display the state and copy the state script.
Reload the page. Open the Console. Execute the state script.
The following error occurs:
script compiler ERROR: unrecognized expression token: )
calculate surfaceDistance WITHIN ({0:2961 11848:11867}) ;
This problem is preventing me from showing this cavity at
http://proteopedia.org/wiki/index.php/Avian_Influenza_Neuraminidase%2C_Tamiflu_and_Relenza#Cavity_in_N1:_An_Opportunity_for_Drug_Design
Thanks, -Eric
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
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This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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Re: [Jmol-users] projection bug
please provide a Jmol state file and structure file that clearly demonstrates this. On Thu, Sep 25, 2008 at 3:24 PM, Victor Chest [EMAIL PROTECTED]wrote: Hi all, There is some problem with projection of bounded atoms of same type on screen in version 11.6 RC16 (there is no this bug in version 11.4.6): atom on the back plan is slightly bigger then another one on the front. It is hardly to see with short bonds... Thanks, Victor --- On *Thu, 9/25/08, Victor Chest [EMAIL PROTECTED]* wrote: From: Victor Chest [EMAIL PROTECTED] Subject: jmol-11.6 bug To: [EMAIL PROTECTED] [EMAIL PROTECTED] Date: Thursday, September 25, 2008, 1:54 PM Hi, I found some error in visualization of bounded atoms in version 11.6 RC16 (there is no this bug in version 11.4.6): atom on the back plan is bigger then another one on the front. In case of short bond it is not recognizable enough so I created some artificial example (see attachment test.gif file). Left panel is Jmol 11.4.6, the right one is 11.6 RC16 Thanks, Victor -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
