Hi all,
for those who use PDB files:
http://cszamudio.spaces.live.com/Blog/cns!9BCF6F9D6772B8F5!1566.entry
Egon
--
[EMAIL PROTECTED]
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6
-
This SF.net email is spon
Thanks, Craig. That's just what I needed.
Craig T Martin wrote:
> Bob,
>
>As someone else pointed out, i think, when you access the signed
> applet, it will ask you for permission to run. A dialog will pop up
> before Jmol fully loads. If you get that dialog, and then everything
> after th
On May 3, 2007, at 11:17 PM, Bob Hanson wrote:
>
> with
>
> dataFormat = 0
>
> I think we would support the current default -- just whitespace, no
> columns or anything:
>
> 3.434 1.234 5.3434
> 3.4 this is ignored 3.456 6.543
>
nice.
>>
>> x = load("charges.dat")
>> set dataFormat -2
>> data "
well, that's your clue. Use
message @x
to see the whole message (115 bytes). It will say, "HTTP Error 500 -
Internal server error"
That's an indicator that you have the wrong URL or something is amiss
with your server.
See http://www.checkupdown.com/status/E500.html
I think it's nothing to
Timothy Driscoll wrote:
>
>>set dataFormat n # take data from nth column
>>
>>set dataFormat -n # take data from nth column, reading atom values in
>>column 1.
>>
>>That might be pretty powerful. Very simple to implement.
>>
>>
>>
>that syntax sounds good to me (though maybe something like da
Hi Bob,
I can do all of this on my local install (except, yes, the color
syntax was wrong -- least of my worries ;).) The problem is that
none of it works on the applet on my web server.
My first problem is just loading foldx.dat. If I do this through the
console of my web applet, I get:
Sam, you should be doing all this testing from a Jmol console -- pull
that up from the popup menu and work from it.
It's far easier than trying to get it going this way.
you can't say
color atoms cartoons property_foldx
one or the other:
select *
color atoms property_foldx
color cartoons prope
On May 3, 2007, at 7:14 PM, Bob Hanson wrote:
> Good work and good summary, Tim. Sorry about "property_" not being
> clear.
no worries; I figured it out.
> The dual-column file format sounds excellent to me. What we will
> need is a
> function name. But load() isn't it. load() just puts the
Cool, this helps.
I am still having trouble with getting the DATA command to work,
though. Is there something obviously wrong with the following? I
verified that execution stops due to the DATA statement.
jmolScript('x=load("foldx.dat"); select *; DATA "property_foldx
@x" ; color atoms c
Bob Hanson wrote:
> Jmol 11.1.30 is ready for release, Nico.
> load =
Impressive!
> OK, features. Not too many:
Not too many? You MUST be kidding!
> full support for switching languages, including a new "language" menu item
> ---
frame number is _modelNumber. So for that you say:
set echo top left
echo This is model %{_modelNumber}.
That will automatically update on its own.
Displaying the current file name will require a macro.
But here's an interesting trick: You can now set the callbacks to be
to Jmol scripts instead
Hi, Sam
> Also, is there some way to access the error log? Debugging applets
> without error messages is painful.
On my WindowsXP:
Firefox and IE: right-click on the Java icon in the taskbar (bottom right of
the screen),
choose "Open console" (one separate for each browser)
Opera: menu "To
Good work and good summary, Tim. Sorry about "property_" not being clear.
The dual-column file format sounds excellent to me. What we will need is a
function name. But load() isn't it. load() just puts the file data into
x. So the filter isn't there.
So it has to be a property of the data command.
On 3 May 2007 at 14:05, Bob Hanson wrote:
> I think this was a wonderful idea that will really enhance Jmol.
> Thank you for suggesting it, Martin.
>
> I have checked in for 11.1.30 full support for language switching.
Wow!
I would never have dreamt of this.
Can't wat to put my hands on this re
Hi Tim
> I would like to display pdb file name and frame number using an echo
> command. is there a way to access this info, akin to displaying
> residue names, etc.?
I think at least filename can be retrieved using getProperty, but would have
to look it up. (no time now)
> alternatively
On 03/05/2007, at 11:45 PM, Timothy Driscoll wrote:
> On May 3, 2007, at 6:10 AM, Bob Hanson wrote:
>
>> Can you just summarize what is involved in setting one up? Is it as
>> simple as using
>>
>> jmolInitialize(".",true)
>>
> oh, sorry. I have not used Jmol.js for this. regardless, it was as
Yes, certainly. Macs and PCs are different, though. Can you find the
Java Console (PC) or
System logs (I think) directory on your Mac. Macs dump this to a file;
PCs just display in on a
console.
Use
loglevel = 5
to get voluminous reports of what is going on, and use
message @x
or
show x
to
Bob Hanson wrote:
> Jmol 11.1.30 is ready for release, Nico.
>
See my other mail, there's a bug somewhere when running monster_script.spt.
Can you fix it before I release 11.1.30 ?
Nico
-
This SF.net email is sponsored by
Ok, that helped. Now I'm stuck on step 2, if you can believe that!
the data command seems to be failing. I put the following in my
javascript code:
jmolScript('x=load("foldx.dat"); select *; data "property_foldx @x";
color red;');
I verified that the "load" command worked, but the "data"
Jmol 11.1.30 is ready for release, Nico.
Signed applet tests successful and, for example, loads files directly
from RCSB's depository simply with
load =
where = is an equal sign followed by a four-digit ID. I recommend
that if you want to use the signed applet you use the single-file
I think this was a wonderful idea that will really enhance Jmol.
Thank you for suggesting it, Martin.
I have checked in for 11.1.30 full support for language switching.
#
# Jmol.js (prior to jmolApplet):
#
#jmolSetCallback("language", "de")
#
# Jmol scripting:
#
#language
I would like to display pdb file name and frame number using an echo
command. is there a way to access this info, akin to displaying
residue names, etc.?
alternatively, I know this info before writing my script - is there a
way to link an echo command to a particular frame? in other words,
hi,
thought I would followup this thread with some feedback, having tried
to implement various flavors of this recently.
1. coloring based on a built-in property works well and is very cool:
y = {*}.occupancy.all
data "property_charge @y"
propertyColorScheme = "bwr"
color ato
all files loaded by an applet must be from the current directory of
subdirectory. Can't have "../"
Samuel Flores wrote:
>Hi Bob,
>
>I am trying to follow this advice you gave Tim. I have an applet and
>want to color my molecule by a parameter which I store in a file
>called 'foldx.dat.' I
Also, is there some way to access the error log? Debugging applets
without error messages is painful.
Sam
On May 3, 2007, at 1:09 PM, Samuel Flores wrote:
> Hi Bob,
>
> I am trying to follow this advice you gave Tim. I have an applet
> and want to color my molecule by a parameter which I
Bob,
As someone else pointed out, i think, when you access the signed
applet, it will ask you for permission to run. A dialog will pop up
before Jmol fully loads. If you get that dialog, and then everything
after that goes smoothly, then the signed applet is working.
It will only ask
Hi Bob,
I am trying to follow this advice you gave Tim. I have an applet and
want to color my molecule by a parameter which I store in a file
called 'foldx.dat.' I am stuck on the first step, though -- loading
the data file. I have the following line in my javascript:
jmolScript('x=load(
Bob Hanson napsal(a):
>Angel, that's just some particular applet's implementation. We could do
>it that way.
>Or we could do it as a script so you can change language anytime after
>the applet is loaded.
>Let me see what I can do.
>
>Bob
>
>
>
>
Bob and Angel,
thank for suggestions. Sorry to
Angel, that's just some particular applet's implementation. We could do
it that way.
Or we could do it as a script so you can change language anytime after
the applet is loaded.
Let me see what I can do.
Bob
Angel Herraez wrote:
>Hi Martin:
>
>I am also interested in this.
>
>The information
On May 3, 2007, at 6:10 AM, Bob Hanson wrote:
> Can you just summarize what is involved in setting one up? Is it as
> simple as using
>
> jmolInitialize(".",true)
>
oh, sorry. I have not used Jmol.js for this. regardless, it was as
easy as calling the signed applet files in the applet tag.
as
Bob wrote:
> no, there is not. But I think we can set that up.
Wonderful news! I've being reading several pages of applets that
accept a
I've done so in a test, using jmolAppletAddParam(), and it puts the
correct param, but of course does nothing.
> how about a Jmol.js command that designat
El 3 May 2007 a las 13:56, David Leader escribió:
> I was hoping you wouldn't ask. I'm still using version 10, in that it
> does what I want and if it's not bust...
Well, David, it does NOT do what you want. Enhanced zoom was added
later. :-)
Hi Martin:
I am also interested in this.
The information on my Wiki page is all I could gather regarding this
topic. I guess this is more of a Java technical question, maybe you
should direct your question to some Java discussion forum.
> I am interested in it, because if using Jmol in compute
Bob wrote:
>David, what version are you using?
I was hoping you wouldn't ask. I'm still using version 10, in that it
does what I want and if it's not bust...
...but if upgrading to the latest version fixes it, then I'll upgrade.
David
--
__
Message: 3
Date: Wed, 02 May 2007 19:14:11 -0500
From: Bob Hanson <[EMAIL PROTECTED]>
Subject: [Jmol-users] signed applets
To: jmol-users@lists.sourceforge.net
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
I looking for someone who is using the signed
no, there is not. But I think we can set that up.
how about a Jmol.js command that designates the language before the
applet is loaded?
jmolSetLanguage("fr")
Is it necessary to be able to switch languages at will after the applet
is loaded? If so, that's a bit
trickier, but I think it can be
David Leader wrote:
> I'm working with Jmol again (after several months) in relation to my
> database-driven web app and have one question and what I fear may be
> a feature request.
>
> 1. There is a limit to the extent that I can zoom a motif of a few
> amino acids in a large protein, which is
Dear Jmol users/developpers,
Is there a possibility to change language of Jmol applet directly (via
some variable or parameter), not by way described by Angel
(http://wiki.jmol.org/index.php/User:AngelHerraez) = via Java Control Panel?
I am interested in it, because if using Jmol in computer lab
David, what version are you using?
David Leader wrote:
>I'm working with Jmol again (after several months) in relation to my
>database-driven web app and have one question and what I fear may be
>a feature request.
>
>1. There is a limit to the extent that I can zoom a motif of a few
>amino ac
I'm working with Jmol again (after several months) in relation to my
database-driven web app and have one question and what I fear may be
a feature request.
1. There is a limit to the extent that I can zoom a motif of a few
amino acids in a large protein, which is marginally insufficient for
m
Bob wrote:
> Can you just summarize what is involved in setting one up? Is it as
> simple as using
>
> jmolInitialize(".",true)
As far as I know, that's how it works, yes.
I've used it rarely.
I don't know anything about how to *prepare* the signed applet.
And answering to Anthony, yes, apart
The reason I ask is that I created what I thought were signed applets,
but they don't work as I expected them to.
Bob Hanson wrote:
>Can you just summarize what is involved in setting one up? Is it as
>simple as using
>
>jmolInitialize(".",true)
>
>?
>
>Timothy Driscoll wrote:
>
>
>
>>On May
Can you just summarize what is involved in setting one up? Is it as
simple as using
jmolInitialize(".",true)
?
Timothy Driscoll wrote:
>On May 2, 2007, at 8:14 PM, Bob Hanson wrote:
>
>
>
>>I looking for someone who is using the signed applet.
>>
>>
>>
>hi Bob,
>
>I have used it, though
No, its the thing that lets an applet read any file from any server on
the web.
You know if you are using it, because you get a big message from the
browser asking if you want to accept the
certificate. (I think; I haven't used this myself.)
C Anthony Lewis wrote:
>Bob,
>
>Is that the "thing" o
Ewen, reading this I see I didn't quite answer your question. You really
have two options:
1) (Easiest) Let Jmol calculate the MEP data (not really a surface) from
charge information.
2) (Also possible) Use a program to create the MEP cube data (many Mb),
and have Jmol read that.
If you are in
Ewen, I think Angel covers it pretty well. Thank you, Angel.
The file formats from which Jmol currently reads partial charge
information include:
Chem3D XML (http://www.cambridgesoft.com/)
CML (http://www.xml-cml.org/)
CSF (Sygress, formerly CAChe, by Fujitsu,
http://www.cachesoftware.com/cache/
Hello Ewen
> I use Chime MEP surfaces for teaching basic ideas about molecular
> polarity, but it's not a lightly-taken decision.
>
> I've converted my old Chime resources into Jmol ones now, except the
> ones using MEP surfaces (and the dreaded Sculpt mode). Wanting to
> push on with my Chime -
Bob and Martin,
I've asked Bob before about Jmol and Chime and the apparent ability of Chime to
calculate MEP surfaces. He's consistently and fairly argued that this is not
something Jmol should encompass. This disappointed me because I use Chime MEP
surfaces for teaching basic ideas about mole
Bob,
Is that the "thing" one can use locally, rather it coming from a server?
If so, I may be able to help.
Alternatively, I've just exposed my complete ignorance!
Anthony
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bob
Hanson
Sent: 03 May 2007 01:
49 matches
Mail list logo
