Re: [Jmol-users] [Fwd: [Bug 269973] Java applet causes all typing in browser to

[<nvervell@cl...>]

De: Bob Hanson <hansonr=40stolaf.edu>
>
>PLEASE take a moment and VOTE FOR THIS BUG=21
>
>https://bugzilla.mozilla.org/show=5Fbug.cgi?id=3D269973
>
>It's a known bug; we need it FIXED=21

Agreed and done.

I suggest also to vote for this one which depends on a fix to the bug abov=
e to be fixed:
https://bugzilla.mozilla.org/show=5Fbug.cgi?id=3D256763

Nico

Re: [Jmol-users] "select visible"?

[Bob Hanson <hansonr@st...>]

I will investigate this fully and get back to all.


Bob


-- 

Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:hansonr@...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein

Re: [Jmol-users] "select visible"?

[Miguel <miguel@jm...>]

> Miguel wrote:
>
>>
>>Be advised that this 'isVisible' flag was designed for internal use onl=
y.
>>More importantly, the concept of 'visible' is not as well-defined as on=
e
>>might think.
>>
>>If this makes it into 'production' code then we will need to make sure
>> that
>>the concept is well-documented and well-understood.
>>
>>
> Sure. I agree. It would go under the category of =22atom expressions=22=
.
> Please say more, Miguel.

The internal 'isVisible' flag was designed for the 'hover' and to detect
which atoms are selected based upon 'clicking' behavior.

It could very easily be the case that when atoms are not currently
displayed on the screen (because they are zoomed or translated) then the
atoms are not 'visible'. I don't remember.

> Perhaps what =22visible=22 means. Currently, I
> think, it means:
>
> (1) the atom is in a displayed frame

Yes, that is the way that the 'isVisible' flag works ... but I am not sur=
e
that is the desired behavior for the 'visible' set.

> and
>
> (2) the atom has at least one of the following:
>
>         a. spacefill > 0
>         b. wireframe > 0
>         c. a halo highlight
>
> Note that cartoons and such do NOT constitute visible, because they are=

> not atoms.

I am not sure that is completely true. There may be other schematic
representations where the atoms are considered visible. I don't remember.=


> When you have:
>
> select *
> wireframe off;spacefill off; cartoon on
> select visible
>
> you get:
>
> 0 atoms selected
>
> The only secondary structural visualization that constitutes visible is=

> =22backbone=22, which is really
> a wireframe connection between alpha carbons in a protein or (what?)

Phosphorus or chain-terminating Oxygen.

> in a nucleic acid. So
>
> select *
> wireframe off;spacefill off; backbone on
> select visible
>
> gives you (for 1crn.pdb):
>
> 46 atoms selected
>
>
> More to know?

I think that we would be better off reimplementing the 'visible' set to
explicitly be the things that you want it to be.

That way, it will be well-defined and will not get messed up if/when
someone works on some other part of the code.

In addition, this will also avoid the confusion associated with whether o=
r
not the frame was repainted.

Finally, I don't think that the 'visible' set should have an implicit
restriction based upon the currently displayed frame. No other sets behav=
e
that way. I think I would be more in favor of a 'visible' set that
includes all atoms in all models. If necessary, then we could add another=

set which represented all atoms in the currently displayed models. One
could AND the two sets together to get the currently visible atoms.


Miguel

Re: [Jmol-users] "select visible"?

[Angel Herraez <angel.herraez@ua...>]

El 27 Feb 2006 a las 7:47, Bob Hanson escribi=F3:
> The only secondary structural visualization that constitutes visible is 
> "backbone", which is really
> a wireframe connection between alpha carbons in a protein or (what?) in 

Phosphorus atoms in a nucleic acid.

> a nucleic acid. So
> 
> select *
> wireframe off;spacefill off; backbone on
> select visible
> 
> gives you (for 1crn.pdb):
> 
> 46 atoms selected

I guess those 46 atoms are the alpha carbons. Right?

Re: [Jmol-users] "select visible"?

[Bob Hanson <hansonr@st...>]

Miguel wrote:

>
>Be advised that this 'isVisible' flag was designed for internal use only.
>More importantly, the concept of 'visible' is not as well-defined as one
>might think.
>
>If this makes it into 'production' code then we will need to make sure that
>the concept is well-documented and well-understood.
>
>
>  
>
Sure. I agree. It would go under the category of "atom expressions".
Please say more, Miguel. Perhaps what "visible" means. Currently, I 
think, it means:

(1) the atom is in a displayed frame

and

(2) the atom has at least one of the following:

        a. spacefill > 0
        b. wireframe > 0
        c. a halo highlight

Note that cartoons and such do NOT constitute visible, because they are 
not atoms.
When you have:

select *
wireframe off;spacefill off; cartoon on
select visible

you get:

0 atoms selected

The only secondary structural visualization that constitutes visible is 
"backbone", which is really
a wireframe connection between alpha carbons in a protein or (what?) in 
a nucleic acid. So

select *
wireframe off;spacefill off; backbone on
select visible

gives you (for 1crn.pdb):

46 atoms selected


More to know?

Bob

Re: [Jmol-users] "select visible"?

[Miguel <miguel@jm...>]

> I still think that =22select visible=22, as a command built into Jmol, =
might
> be
> a very worthwhile addition to the command set.

Please define 'visible' ... as you see it :-)


Miguel

Re: [Jmol-users] "select visible"?

[Miguel <miguel@jm...>]

> as a matter of fact, there is.... in the prototype:
>
> http://www.stolaf.edu/people/hansonr/jmol/test/json
>
> I added this because it seemed so useful in terms of getting just
> the atomInfo for the visible:
>
> myArray=3DjmolGetPropertyAsArray(=22atomInfo=22,=22visible=22)
>
> for example.

Be advised that this 'isVisible' flag was designed for internal use only.=

More importantly, the concept of 'visible' is not as well-defined as one
might think.

If this makes it into 'productin' code then we will need to make sure tha=
t
the concept is well-documented and well-understood.


Miguel

Re: [Jmol-users] Re: Moodle Jmol Filter

[Bob Hanson <hansonr@st...>]

Geoff,

yes, works great.

As for changing Jmol.js, now that I think of this it isn't probably=20
necessary. I'm not sure exactly how your moodle business works. Is it=20
just that there is this filter directory that contains the applet?

If so, and you have full page-content freedom, then really the solution=20
is just to make sure you do not ever have TWO <script ... src=3DJmol.js>=20
tags on any one page. The way those links worked, I wasn't sure you had=20
control over this. The problem was that the caffeine applet was NOT=20
independent of the applet in the upper right side panel.(The second=20
load, with its own <script...src=3Djmol.js> tag erased the button script=20
info of the first applet.) Somewhere along the way (actually, WHILE I=20
was investigating this) you removed that second <script> tag, so that=20
solved the problem in a simpler way.

But if moodle is putting together fragments that you don't necessarily=20
know will be on the page together, then this fix to Jmol.js is necessary.

Q: Are there times that one CANNOT assume that only one <script ...=20
src=3Djmol.js> tag is present on a page? (Because, perhaps, a larger=20
system is putting together pages, and it may be pulling from different=20
resources in an altogether not fully predictable way?

If so, we need to change Jmol.js so that it CAN be loaded twice and also=20
so that jmolInitialize() can be run twice.

Bob
Geoff Rowland wrote:

>Thanks for the feedback
>
>Bob, I am a little bemused by your first comment, as the controls do
>seem to work for me for multiple applets (at least for Internet Explorer
>and Firefox).
>
>Anyway, I have implemented both your suggestions at:=20
>
>http://moodle.yeovil.ac.uk/course/view.php?id=3D63=20
>(though not yet updated the download zip files)
>
>i.e. I have updated the Jmol applet from 10.00 to 10.00.48
>
>and edited the Jmol.js file as follows:
>
>
>if(_jmol) exit();
>////////////////////////////////////////////////////////////////
>// Basic Scripting infrastruture
>////////////////////////////////////////////////////////////////
>function jmolInitialize(codebaseDirectory, useSignedApplet) {
>//  if (_jmol.initialized) {
>//    alert("jmolInitialize() should only be called *ONCE* within a
>page");
>//    return;
>//  }
>
>
>Is this what you meant?
>
>The controls (still) work for me for Internet Explorer, Firefox and
>Opera (on Windows XP & Fedora 4), although the Opera/Linux combination
>is rather slow.=20
>
>Does this fix things for you?
>
>Regards
>
>Geoff
>
>
> =20
>
>>  1. Re: Moodle Jmol Filter (Egon Willighagen)
>>  2. Re: Moodle Jmol Filter (Bob Hanson)
>>  3. Re: Moodle Jmol Filter (Bob Hanson)
>>   =20
>>
>
> =20
>
>>Message: 1
>>   =20
>>
>
> =20
>
>>Excellent! It's much like the code people wrote for including Jmol
>>   =20
>>
>applets >in Wikis.
> =20
>
>>Added a page to Jmol's wiki:
>>http://wiki.jmol.org/MoodlesUsingJmol
>>   =20
>>
>
> =20
>
>>Message 2
>>I think there needs to be a bit more development before this is ready=20
>>for public use.
>>   =20
>>
>
> =20
>
>>refering to
>>   =20
>>
>
> =20
>
>>http://moodle.yeovil.ac.uk/course/view.php?id=3D63&topic=3D3
>>   =20
>>
>
> =20
>
>>The radio buttons do not work if there are multiple applets on the
>>   =20
>>
>page.
> =20
>
>>The problem is that your filter is pulling in Jmol.js twice and=20
>>initializing twice.
>>   =20
>>
>
> =20
>
>>A simple fix to your version of jmol.js should fix this:
>>   =20
>>
>
> =20
>
>>1)   add at the top of jmol.js: =20
>>   =20
>>
>
>
> =20
>
>>if(_jmol) exit()
>>   =20
>>
>
> =20
>
>>2) remove the alert() message at the beginning of jmolInitialize()
>>I see this is being changed as I write....
>>   =20
>>
>
> =20
>
>>Message 3
>>I would recommend updating your version of Jmol.js. You are using one=20
>>   =20
>>
>>from 2004. Opera is not supported, and there will be other OS problems.
>
>
>Yeovil College
>Mudford Road
>Yeovil
>Somerset
>BA21 4DR
>UK
>
>Tel: +44 (01935) 423921
>Fax: +44 (01935) 429962
>
>Website: http://www.yeovil.ac.uk
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>
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=FE=C7=A5=FD=C9=9D=FEH=9D=F7=8E=FFn'=DB=8D{=DBO=DDj=DB^=B8=DB=FF=FF=FF=FF=
=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=FF=
=FF=FF=FF=FF=FF=FF&j%=FE=EB=1E=AE=C9=9A=8AX=A7=82X=AC=B4=99=A8=97=FB=ACz=BB=
=FF=96+-=B3=FB(=BA=B7=1E~=8A=E0{=F9=DE=B6=1Bm=A6=CF=FF=FEX=AC=B6=CF=EC=A2=
=EA=DCy=FA+=81=EF=E7z=DF=E5=8A=CBl=FEX=AC=B6)=DF=A3=F8=E6=A2_=EE=B1=EA=EC
> =20
>

[Jmol-users] [Fwd: [Bug 269973] Java applet causes all typing in browser to be backwards]

[Bob Hanson <hansonr@st...>]

PLEASE take a moment and VOTE FOR THIS BUG!

https://bugzilla.mozilla.org/show_bug.cgi?id=269973

It's a known bug; we need it FIXED!

Bob Hanson

-------- Original Message --------
Subject: 	[Bug 269973] Java applet causes all typing in browser to be 
backwards
Date: 	Mon, 27 Feb 2006 01:15:11 -0800
From: 	bugzilla-daemon@...
To: 	hansonr@...



Do not reply to this email.  You can add comments to this bug at
https://bugzilla.mozilla.org/show_bug.cgi?id=269973


ria.klaassen@... changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |hansonr@...




------- Comment #29 from ria.klaassen@...  2006-02-27 01:15 PST -------
*** Bug 328688 has been marked as a duplicate of this bug. ***



-- 
Configure bugmail: https://bugzilla.mozilla.org/userprefs.cgi?tab=email

Re: [Jmol-users] "select visible"?

[Bob Hanson <hansonr@st...>]

Eric, I just added one fix to "visible" that you are going to tell me I 
need to do today. :)

In general Jmol waits until the end of a script to "refresh" the
model. It is at this refreshing point when what is visible and what is 
not is determined.
Thus, the command:

restrict carbon; select visible;

would not necessarily work as expected. (The other atoms might still be 
"visible" until after the script completes.)

I've checked in changes that fix this; jar files are available in

http://www.stolaf.edu/people/hansonr/jmol/test/json

Bob

Eric Martz wrote:

> At 2/26/06, Bob Hanson wrote:
>
>> it is, in fact,
>>
>> select visible
>>
>> [snip]
>
>
>> Should do the trick, right?
>
>
>
> You bet, Bob. Outstanding! -Eric
>
>
>
>
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[Jmol-users] Re: Moodle Jmol Filter

[Geoff Rowland <Geoff.Rowland@ye...>]

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IGJlZW4gbWFkZSB0byB2aXJ1cyBjaGVjayB0aGlzIGRvY3VtZW50IGhvd2V2ZXIgd2UgdGFr
ZQ0Kbm8gcmVzcG9uc2liaWxpdHkgZm9yIHZpcnVzZXMgcmVjZWl2ZWQuDQoNCi0tLS0tLS0t
LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t
LS0tLS0tLQ==

Re: [Jmol-users] "select visible"?

[Bob Hanson <hansonr@st...>]

a pleasure. ooooh, I see

  center visible

is especially nice!


Eric Martz wrote:

> At 2/26/06, Bob Hanson wrote:
>
>> it is, in fact,
>>
>> select visible
>>
>> [snip]
>
>
>> Should do the trick, right?
>
>
>
> You bet, Bob. Outstanding! -Eric
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting 
> language
> that extends applications into web and mobile media. Attend the live 
> webcast
> and join the prime developer group breaking into this new coding 
> territory!
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> _______________________________________________
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> Jmol-users@...
> https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] "select visible"?

[Eric Martz <emartz@mi...>]

At 2/26/06, Bob Hanson wrote:
>it is, in fact,
>
>select visible
>
>[snip]

>Should do the trick, right?


You bet, Bob. Outstanding! -Eric

Re: [Jmol-users] "select visible"?

[Bob Hanson <hansonr@st...>]

Eric Martz wrote:

> At 2/25/06, you wrote:
>
>> as a matter of fact, there is.... in the prototype:
>>
>> http://www.stolaf.edu/people/hansonr/jmol/test/json
>>
>
it is, in fact,

select visible

"visible" is now a selectable token, like "helix" or "carbon"

Try it out at 
http://www.stolaf.edu/people/hansonr/jmol/test/json/property.htm

You can say:

select visible and not carbon

select within(2.0, oxygen) and not visible

select within(2.0, visible)

etc. That way it can also be used in

jmolGetPropertyAsArray("atomInfo","visible")

because that second parameter is just anything
that can be selected.

Should do the trick, right?

Bob

Re: [Jmol-users] "select visible"?

[Eric Martz <emartz@mi...>]

At 2/25/06, you wrote:
>as a matter of fact, there is.... in the prototype:
>
>http://www.stolaf.edu/people/hansonr/jmol/test/json
>
>I added this because it seemed so useful in terms of getting just
>the atomInfo for the visible:
>
>myArray=jmolGetPropertyAsArray("atomInfo","visible")
>
>for example.

Thanks, Bob. I agree that this is very useful. However, if I understand 
what you are telling me, it is not "select visible". I would have to write 
a javascript loop to construct select commands from the myArray, as I 
understand it.

I still think that "select visible", as a command built into Jmol, might be 
a very worthwhile addition to the command set.

-Eric 

Re: [Jmol-users] "select visible"?

[Bob Hanson <hansonr@st...>]

as a matter of fact, there is.... in the prototype:

http://www.stolaf.edu/people/hansonr/jmol/test/json

I added this because it seemed so useful in terms of getting just
the atomInfo for the visible:

myArray=jmolGetPropertyAsArray("atomInfo","visible")

for example.


Eric Martz wrote:

> I have scripted a view by displaying all atoms, then using "restrict 
> not" to subtract atoms, chains, or groups listed in javascript arrays 
> -- "chipping away" at the molecule step by step. The result is a view 
> of a specified subset of the atoms.
>
> Now I want to center the remaining visible atoms. But I don't have a 
> convenient way to select them.
>
> Is there a command along the lines of "select visible" or "select 
> displayed"?
>
> If not, should there be, for convenience? Perhaps it would not be 
> difficult to add?
>
>
> ----
> Eric Martz, Professor Emeritus, Dept Microbiology
> University of Massachusetts, Amherst MA US
> http://www.umass.edu/molvis/martz
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting 
> language
> that extends applications into web and mobile media. Attend the live 
> webcast
> and join the prime developer group breaking into this new coding 
> territory!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] "select visible"?

[Eric Martz <emartz@mi...>]

I have scripted a view by displaying all atoms, then using "restrict not" 
to subtract atoms, chains, or groups listed in javascript arrays -- 
"chipping away" at the molecule step by step. The result is a view of a 
specified subset of the atoms.

Now I want to center the remaining visible atoms. But I don't have a 
convenient way to select them.

Is there a command along the lines of "select visible" or "select displayed"?

If not, should there be, for convenience? Perhaps it would not be difficult 
to add?


----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz

Re: [Jmol-users] DOCUMENTATION Re: Bugs for "restrict not" vs. (wireframe or backbone) and bondmode

[Bob Hanson <hansonr@st...>]

Eric Martz wrote:

> Dear Bob,
>

> Please add these to the manual (or corrected/improved versions if 
> these are not quite right/clear).
>
> RESTRICT
>
> For wireframe and backbone, "restrict" unconditionally follows "set 
> bondmode or", thereby ignoring the actual "set bondmode" setting. That 
> is, it unconditionally hides bonds (or backbone rods) connecting to 
> all atoms not included in the restricted set.
>
> [Presently under RESTRICT it says: "NOTE: This command cannot be 
> reversed without reloading the model!". As far as I understand, this 
> is incorrect and should be removed. That is, "restrict not x" followed 
> by "select x; {display}" re-displays x.]
>
right, thanks. Will do.


> SET BONDMODE
>
> The bondmode setting applies only to the wireframe and backbone displays.
>
I've added something a bit more specific:

AND: When script commands affect a set of atoms, BOTH atoms must be in 
the set for the bonds also to be affected. Similarly affects the display 
of backbone units in the selection of protein residues and nucleic acid 
bases.
OR: When script commands affect a set of atoms, EITHER atom may be in 
the set for the bonds also to be affected. Similarly affects the display 
of backbone units in the selection of protein residues and nucleic acid 
bases.


> BACKBONE
>
> The "backbone" command obeys the bondmode setting (see "set bondmode").
>
>
I revised:

Shows the backbone of a protein or nucleic acid macromolecule by 
connecting the alpha carbons. The selection of backbone units to display 
depends upon the currently selected atoms and the {#.set (bond 
styles)~bondmode} setting.


Bob Hanson

[Jmol-users] DOCUMENTATION Re: Bugs for "restrict not" vs. (wireframe or backbone) and bondmode

[Eric Martz <emartz@mi...>]

Dear Bob,

Thanks so much for your quick and authoritative response, and for the bug fix.

Please add these to the manual (or corrected/improved versions if these are 
not quite right/clear).

RESTRICT

For wireframe and backbone, "restrict" unconditionally follows "set 
bondmode or", thereby ignoring the actual "set bondmode" setting. That is, 
it unconditionally hides bonds (or backbone rods) connecting to all atoms 
not included in the restricted set.

[Presently under RESTRICT it says: "NOTE: This command cannot be reversed 
without reloading the model!". As far as I understand, this is incorrect 
and should be removed. That is, "restrict not x" followed by "select x; 
{display}" re-displays x.]

SET BONDMODE

The bondmode setting applies only to the wireframe and backbone displays.

BACKBONE

The "backbone" command obeys the bondmode setting (see "set bondmode").


----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz

Re: [Jmol-users] Bugs for "restrict not" vs. (wireframe or backbone) and bondmode

[Bob Hanson <hansonr@st...>]

Thanks, Eric.

The exact operation of restrict in 10.00.48 consists of:

a) invert the selection
b) set the bondmode to OR temporarily
c) set all selected bonds to wireframe 0
d) return the bondmode setting to its original value
e) turn off all labels of selected atoms
f) turn off all selectable shapes (balls, cartoons, etc.)
g) invert the selection back to its original setting


Eric Martz wrote:

> It seems to me that "restrict not x" should have the same effect as 
> "select x; [display] off". That is, both should hide the display 
> (wireframe, backbone, trace, cartoon) of the atomset x. This is true 
> for some, but not for other displays; the latter cases seem to me to 
> be bugs.
>
>
well, it's different. Restrict is "stronger" in the sense that any bonds 
to the removed atoms are also hidden.

> -----------------------------
> Problem 1, restrict not vs. wireframe & bondmode: Suppose you display 
> some DNA with wireframe. The command "restrict not phosphorus" makes 
> all the phosphorus-oxygen bonds disappear. This happens regardless of 
> "set bondmode and/or". This seems to me to be a bug: the 
> phosphorus-oxygen bonds should disappear after "restrict not 
> phosphorus" only after "set bondmode or".

the above sequence explains this behavior.

> ---------------------------------
> Problem 2, restrict not vs. backbone and bondmode: I want to hide a 
> single residue in a protein or nucleic acid backbone with "restrict 
> not [residue]". This works for trace and cartoon (which do not obey 
> bondmode), but not for backbone. For backbone, you have to "restrict 
> not" two consecutive residues before a gap appears in the backbone.
>
Ah, Good catch. This is a bug. It is fixed by switching steps (d) and 
(f) above.

I've uploaded these changes; the jar files in my prototype site can be 
tested; I find

select *;backbone 1.0
restrict not SER

works correctly -- two single-residue gaps.

these corrections are in:

http://www.stolaf.edu/people/hansonr/jmol/test/json/

for now.

[Jmol-users] Bugs for "restrict not" vs. (wireframe or backbone) and bondmode

[Eric Martz <emartz@mi...>]

It seems to me that "restrict not x" should have the same effect as "select 
x; [display] off". That is, both should hide the display (wireframe, 
backbone, trace, cartoon) of the atomset x. This is true for some, but not 
for other displays; the latter cases seem to me to be bugs.

The following behaviors were observed with Jmol Applet 10.00.48.

-----------------------------
Problem 1, restrict not vs. wireframe & bondmode: Suppose you display some 
DNA with wireframe. The command "restrict not phosphorus" makes all the 
phosphorus-oxygen bonds disappear. This happens regardless of "set bondmode 
and/or". This seems to me to be a bug: the phosphorus-oxygen bonds should 
disappear after "restrict not phosphorus" only after "set bondmode or".

In contrast, the "wireframe" command appears to work correctly. Using 1d66, 
where chain D is DNA,

select :d and not phosphorus
wireframe

shows the phosphorus-oxygen bonds when "set bondmode or" but not when "set 
bondmode and" (correct). Furthermore,

select :d
wireframe
select phosphorus
wireframe off

hides the phosphorus-oxygen bonds when "set bondmode or" but leaves them 
visible when "set bondmode and" (correct).

---------------------------------
Problem 2, restrict not vs. backbone and bondmode: I want to hide a single 
residue in a protein or nucleic acid backbone with "restrict not 
[residue]". This works for trace and cartoon (which do not obey bondmode), 
but not for backbone. For backbone, you have to "restrict not" two 
consecutive residues before a gap appears in the backbone.

Indeed, "set bondmode and/or" affects this behavior, but "restrict not" 
initially behaves as though "set bondmode and" (even though the initial 
behavior for wireframe is "set bondmode or"!). Thus, if you "set bondmode 
or" and then "restrict not [residue]", a gap is produced in the backbone.

The apparent default behavior of "set bondmode and" for "restrict not" 
commands vs. backbone contrasts with the "backbone" command itself. The 
"backbone" command initially behaves in accord with "set bondmode or" 
(correct). Before issuing any "set bondmode" commands,

select :d and not 10:d
backbone

produces a backbone with a gap around residue 10 (correct for default "set 
bondmode or"). Furthermore,

select :d
backbone
select 10:d
backbone off

makes a gap in the backbone at residue 10 (correct for default "set 
bondmode or").

---------------------
Using the "select x; [display] off" method provides a workaround for the 
failure of the "restrict not x" method to work properly. However, the bugs 
in "restrict not" vs. wireframe and backbone are confusing, and should be 
fixed.

The above "bugs" are true for protein as well as for DNA.

-Eric


/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz

Biochem 3D Education Resources http://MolviZ.org
See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://workshops.proteinexplorer.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.proteinexplorer.org
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
       http://bioinformatics.org/mailman/listinfo/molvis-list
- - - - - - - - - - - - - - - - - - - - - - - - - - - */

Re: [Jmol-users] Moodle Jmol Filter

[Bob Hanson <hansonr@st...>]

Geoff,

I would recommend updating your version of Jmol.js. You are using one 
from 2004. Opera is not supported, and there will be other OS problems.



Egon Willighagen wrote:

>On Thursday 23 February 2006 23:57, Geoff Rowland wrote:
>  
>
>>I just wanted to draw your attention to the recently developed 'Jmol
>>Filter' for the open source virtual learning environment Moodle. The filter
>>is a PHP/Javascript 'wrapper' which enables teachers to easily add Jmol
>>applets to their online Moodle courses - with not much more than a link to
>>an uploaded chemical structure file.
>>    
>>
>
>Excellent! It's much like the code people wrote for including Jmol applets in 
>Wikis.
>
>Added a page to Jmol's wiki:
>
>http://wiki.jmol.org/MoodlesUsingJmol
>
>Egon
>
>  
>

Re: [Jmol-users] Moodle Jmol Filter

[Bob Hanson <hansonr@st...>]

I think there needs to be a bit more development before this is ready 
for public use.

refering to

http://moodle.yeovil.ac.uk/course/view.php?id=63&topic=3

The radio buttons do not work if there are multiple applets on the page.
The problem is that your filter is pulling in Jmol.js twice and 
initializing twice.

A simple fix to your version of jmol.js should fix this:

1)   add at the top of jmol.js:  

 if(_jmol) exit()

2) remove the alert() message at the beginning of jmolInitialize()

I see this is being changed as I write....


Egon Willighagen wrote:

>On Thursday 23 February 2006 23:57, Geoff Rowland wrote:
>  
>
>>I just wanted to draw your attention to the recently developed 'Jmol
>>Filter' for the open source virtual learning environment Moodle. The filter
>>is a PHP/Javascript 'wrapper' which enables teachers to easily add Jmol
>>applets to their online Moodle courses - with not much more than a link to
>>an uploaded chemical structure file.
>>    
>>
>
>Excellent! It's much like the code people wrote for including Jmol applets in 
>Wikis.
>
>Added a page to Jmol's wiki:
>
>http://wiki.jmol.org/MoodlesUsingJmol
>
>Egon
>
>  
>

Re: [Jmol-users] Moodle Jmol Filter

[Egon Willighagen <e.willighagen@sc...>]

On Thursday 23 February 2006 23:57, Geoff Rowland wrote:
> I just wanted to draw your attention to the recently developed 'Jmol
> Filter' for the open source virtual learning environment Moodle. The filter
> is a PHP/Javascript 'wrapper' which enables teachers to easily add Jmol
> applets to their online Moodle courses - with not much more than a link to
> an uploaded chemical structure file.

Excellent! It's much like the code people wrote for including Jmol applets in 
Wikis.

Added a page to Jmol's wiki:

http://wiki.jmol.org/MoodlesUsingJmol

Egon

-- 
e.willighagen@...
PhD student on Molecular Representation in Chemometrics
Radboud University Nijmegen
Blog: http://chem-bla-ics.blogspot.com/
http://www.cac.science.ru.nl/people/egonw/
GPG: 1024D/D6336BA6

[Jmol-users] Moodle Jmol Filter

[Geoff Rowland <Geoff.Rowland@ye...>]

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