Re: [Jmol-users] [PhyloSoC] Google Summer of Code proposal for 3D protein-structure evolution visualization
Hi Hilmar, Bob is the current code wizard... my Jmol code is long past history, but we are using it in Jmol, and that needs an overhaul anyway... I have been GSoC mentor in the past already, but could be available for co-mentoring... Bob, do you fancy a Google SoC T-shirt? Egon On Fri, Mar 26, 2010 at 8:51 PM, Hilmar Lapp wrote: > Hi Egon, > > we're trying to recruit a co-mentor for Chris. Could you fancy yourself > co-mentoring? It'd be great to have you on board with this project and with > the NESCent community in the larger sense. -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google Summer of Code proposal for 3D protein-structure evolution visualization
Hi, Egon: Thank you for your reply. > That means you will have a first full time mentor from the NESCent? If we find a sufficiently qualified student and if this particular project gets accepted (Nescent currently has 17 proposed projects, and, if past experience is any guide, we might get around 6 slots from Google, see https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2010) then, indeed, I would be the primary mentor (although I don't work for Nescent). Christian Egon Willighagen wrote: > Hi Christian, > > On Fri, Mar 26, 2010 at 1:32 AM, Christian M Zmasek > wrote: >> I am the main developer of the Archaeopteryx phylogenetic tree viewer >> (http://www.phylosoft.org/archaeopteryx/). >> >> For this year's Google Summer of Code (http://code.google.com/soc/) we >> developed a proposal to essentially extend Archaeopteryx with Jmol so >> that it can be used for 3D protein-structure evolution visualization, see: > > That's great to hear! > >> https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2010#Visualization_of_Protein_3D_Structure_Evolution > > Members of the Blue Obelisk community have tried in the past to get in > as mentoring organization, but that always failed... > >> I was wondering if a Jmol developer or experienced user would be willing >> to help with this project, as "co-mentor". >> In this case, "co-mentoring" would mean helping out with questions >> specific to Jmol (time commitment is expected to be minimal, maybe >> 1h/week or less for the duration of the program -- 3 months). > > That means you will have a first full time mentor from the NESCent? > > Egon > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem filling an html list
Bob,
I can't find where is referring to the function we were speaking some day
ago.
function myfunc(appId,b,c,d) {
alert([appId, b, c, d])
}
thanks
--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---
From: Robert Hanson [hans...@stolaf.edu]
Sent: Friday, March 26, 2010 4:01 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] problem filling an html list
Oops!
http://chemapps.stolaf.edu/jmol/docs?ver=11.10&search=callback#setcallback
--
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
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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Re: [Jmol-users] problem filling an html list
Oops! http://chemapps.stolaf.edu/jmol/docs?ver=11.10&search=callback#setcallback -- 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 -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Molecular Editor Problem
{a}.xyz == {b}.xyz
With {a} == {b} by itself it is just checking whether the NUMBER of atoms in
set a is the same as the NUMBER of atoms in set b.
Bob
On Fri, Mar 26, 2010 at 5:43 AM, Rolf Huehne wrote:
> On 03/26/2010 06:30 AM, Otis Rothenberger wrote:
> > Bob,
> >
> > I'm making some progress on your suggestion to check and branch during
> the
> > addition of atoms (below). One problem that I'm having is comparing
> points,
> > so I thought that better check with you. If I have two points defined, a
> and
> > b, shouldn't the following syntax produce a true or false based on xyz
> > identity of the points?
> >
> > If ({a} == {b}){do stuff;};continue on to other stuff;
> >
> > I can send you the specific code, but I thought I'd ask about my basic
> > understanding of point math and logic first. My problem is that the above
> > seems to be true for points that are not the same.
> >
> The scripting documentation on Jmol math says:
>
> point == point
> true if the distance between the points is less than 1E-6.
>
> So the coordinates must not be identical.
> Maybe it helps if you compare the individual xyz values instead:
>
> if ({a}.x == {b}.x AND {a}.y == {b}.y AND {a}.z == {b}.z)
>
> Regards,
> Rolf
>
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> 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
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
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Re: [Jmol-users] Molecular Editor Problem
Thanks Rolf,
Since it looks like I'm using correct syntax, I'll send the problematic
code:
var pa = -.2;var a = {atomIndex=_atomPicked};select a;flash;var t=a.xyz;
var p = a.xyz*2 - {connected(a)}.xyz;if({atomIndex = _atomPicked and
connected(1)} == 1){p = a.xyz;pa = .1;}
var x = p.x;var y = p.y + pa;var z = p.z + pa;set appendNew false;
var w = '1\ntest\nC ' + x + ' ' + y + ' ' + z + '\n';data 'append @w';var i
= {*}[0].atomIndex;
connect (atomIndex=_atomPicked) (atomIndex=i) single;
The above has an extraneous var t=a.xyz, which I'll explain below. In the
above, I'm using a -.2 adjustment to the z coordinate prior to the use of
Bob's chirality retention code. I cannot use Bob's code on terminal C atoms
because this often creates unrecoverable linear additions of the new atom,
so the above takes all terminal atoms via my chirality destroying route. The
- .2 adjustment is a work around in Bob's chirality retention route to take
care of superimposition of the new atom and the clicked atom. What I really
want to do is use the following "if" statement:
if({atomIndex = _atomPicked and connected(1)} == 1 || {t} == {p})
This statement should catch a trouble maker in Bob's chirality retention
code. The case where the new atom exactly coincides with the clicked atom.
The problem is that the above seems to result in every atom click meeting
the condition. Since the work-around works, I should move on. However, point
comparison will help me clean up other problem aspects of this process, so
I'd like to understand the problem.
Otis
On Fri, Mar 26, 2010 at 6:43 AM, Rolf Huehne wrote:
> On 03/26/2010 06:30 AM, Otis Rothenberger wrote:
> > Bob,
> >
> > I'm making some progress on your suggestion to check and branch during
> the
> > addition of atoms (below). One problem that I'm having is comparing
> points,
> > so I thought that better check with you. If I have two points defined, a
> and
> > b, shouldn't the following syntax produce a true or false based on xyz
> > identity of the points?
> >
> > If ({a} == {b}){do stuff;};continue on to other stuff;
> >
> > I can send you the specific code, but I thought I'd ask about my basic
> > understanding of point math and logic first. My problem is that the above
> > seems to be true for points that are not the same.
> >
> The scripting documentation on Jmol math says:
>
> point == point
> true if the distance between the points is less than 1E-6.
>
> So the coordinates must not be identical.
> Maybe it helps if you compare the individual xyz values instead:
>
> if ({a}.x == {b}.x AND {a}.y == {b}.y AND {a}.z == {b}.z)
>
> Regards,
> Rolf
>
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
--
Otis Rothenberger
http://chemagic.org
--
Download Intel® Parallel Studio Eval
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Re: [Jmol-users] problem filling an html list
On 03/26/2010 03:47 PM, P.Canepa wrote:
> Bob, Angel
> which function is going to be
>
>
> function myfunc(appId,b,c,d) {
> alert([appId, b, c, d])
>
> }
> I cannot find any explanation on
> http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=11.10&search=callback#setcallback
> .
>
"myfunc" is just an example Javascript function that will show you the
content of the (first) four parameters returned by the callback in an
alert box.
You can replace "myfunc" by your own function name and can replace the
"alert" command by any commands needed fo your purpose.
Regards,
Rolf
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
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Re: [Jmol-users] problem filling an html list
Bob, Angel
which function is going to be
function myfunc(appId,b,c,d) {
alert([appId, b, c, d])
}
I cannot find any explanation on
http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=11.10&search=callback#setcallback
.
Thanks ,piero
--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---
From: P.Canepa [pc...@kent.ac.uk]
Sent: Friday, March 26, 2010 2:36 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] problem filling an html list
Bob,
can you give me the INTERNET url not your local?
file:///C:/jmol-dev/workspace/Jmol-documentation/script_documentation/index.htm?ver=11.10&search=callback#setcallback
Thanks, Piero
--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---
From: Robert Hanson [hans...@stolaf.edu]
Sent: Wednesday, March 24, 2010 11:26 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] problem filling an html list
in Jmol:
set loadStructCallback "myfunc"
on the page:
function myfunc(appId,b,c,d) {
alert([appId, b, c, d])
}
I don't recall the exact parameters now. See
file:///C:/jmol-dev/workspace/Jmol-documentation/script_documentation/index.htm?ver=11.10&search=callback#setcallback
On Wed, Mar 24, 2010 at 6:12 AM, P.Canepa
mailto:pc...@kent.ac.uk>> wrote:
Exactly that's what I am doing, i am using the div as you said !
how does set loadStructCallback work ?
Thanks
--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---
From: Robert Hanson [hans...@stolaf.edu]
Sent: Wednesday, March 24, 2010 11:04 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] problem filling an html list
The way you do this is create a there but do not populate it until after
the page is loaded and the file has been read. Then, in the jmolApplet load
script give the javaScript command to tell your web page that it is time to
populate the div. That uses document.getElementById("somedivid").innerHTML =
"". Or you could set loadStructCallback to a function on your page that
will do the updating after files are loaded. That might be better.
Bob
On Tue, Mar 23, 2010 at 12:05 PM, P.Canepa
mailto:pc...@kent.ac.uk>>>
wrote:
Dear All
I have a javascript function LoadModels() which should load the models in an
external HTML list ! How can I let the list be populated when I load the page?
This would have to happen just after the jmolApplet(["520","520"] has been
called!
I can make it to work if I do as below
jmolInitialize(".","jmol/JmolAppletSigned0.jar");
jmolApplet(["520","520"], " script
scripts/reset.spt; background white" );
LoadModels();
Thanks Piero
--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail:
pc...@kent.ac.uk>
mobile: +44 (0) 7772-9756456
---
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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
Re: [Jmol-users] problem filling an html list
Piero, always starting from http://chemapps.stolaf.edu/jmol/docs/ (which is linked from Jmol's website) so http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=11.10&search=callback#setcallback -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem filling an html list
Bob,
can you give me the INTERNET url not your local?
file:///C:/jmol-dev/workspace/Jmol-documentation/script_documentation/index.htm?ver=11.10&search=callback#setcallback
Thanks, Piero
--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---
From: Robert Hanson [hans...@stolaf.edu]
Sent: Wednesday, March 24, 2010 11:26 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] problem filling an html list
in Jmol:
set loadStructCallback "myfunc"
on the page:
function myfunc(appId,b,c,d) {
alert([appId, b, c, d])
}
I don't recall the exact parameters now. See
file:///C:/jmol-dev/workspace/Jmol-documentation/script_documentation/index.htm?ver=11.10&search=callback#setcallback
On Wed, Mar 24, 2010 at 6:12 AM, P.Canepa
mailto:pc...@kent.ac.uk>> wrote:
Exactly that's what I am doing, i am using the div as you said !
how does set loadStructCallback work ?
Thanks
--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---
From: Robert Hanson [hans...@stolaf.edu]
Sent: Wednesday, March 24, 2010 11:04 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] problem filling an html list
The way you do this is create a there but do not populate it until after
the page is loaded and the file has been read. Then, in the jmolApplet load
script give the javaScript command to tell your web page that it is time to
populate the div. That uses document.getElementById("somedivid").innerHTML =
"". Or you could set loadStructCallback to a function on your page that
will do the updating after files are loaded. That might be better.
Bob
On Tue, Mar 23, 2010 at 12:05 PM, P.Canepa
mailto:pc...@kent.ac.uk>>>
wrote:
Dear All
I have a javascript function LoadModels() which should load the models in an
external HTML list ! How can I let the list be populated when I load the page?
This would have to happen just after the jmolApplet(["520","520"] has been
called!
I can make it to work if I do as below
jmolInitialize(".","jmol/JmolAppletSigned0.jar");
jmolApplet(["520","520"], " script
scripts/reset.spt; background white" );
LoadModels();
Thanks Piero
--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail:
pc...@kent.ac.uk>
mobile: +44 (0) 7772-9756456
---
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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.
-- Josia
Re: [Jmol-users] Molecular Editor Problem
On 03/26/2010 06:30 AM, Otis Rothenberger wrote:
> Bob,
>
> I'm making some progress on your suggestion to check and branch during the
> addition of atoms (below). One problem that I'm having is comparing points,
> so I thought that better check with you. If I have two points defined, a and
> b, shouldn't the following syntax produce a true or false based on xyz
> identity of the points?
>
> If ({a} == {b}){do stuff;};continue on to other stuff;
>
> I can send you the specific code, but I thought I'd ask about my basic
> understanding of point math and logic first. My problem is that the above
> seems to be true for points that are not the same.
>
The scripting documentation on Jmol math says:
point == point
true if the distance between the points is less than 1E-6.
So the coordinates must not be identical.
Maybe it helps if you compare the individual xyz values instead:
if ({a}.x == {b}.x AND {a}.y == {b}.y AND {a}.z == {b}.z)
Regards,
Rolf
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
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