On 23-1-2010 11:31, Angel Herráez wrote:
> You have a point, Rich, but what kind of options could we have for nonprotein
> molecules?
> There is select by element and by symmetry already. The list of selectable
> elements could
> be certainly expanded (ideally, to cover all elem
be more useful
for whatever molecule is being displayed rather than being directed
towards proteins.
Rich
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Out of intrest why is that setting called "Frank"?
>
Yeah. Look up franking.
Rich
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Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to
x27;m assuming are the result of some strangeness
in the MD calculations rather than coming from Jmol.
Rich
On 1-10-2008 13:25, Robert Hanson wrote:
> Question: Can you watch this movie on your machine? If so, how's the
> resolution?
>
> http://www.stolaf.edu/people/hansonr/tem
order you want) and let you export it as a movie
in the format you choose.
Rich
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enus and program defaults would be able to
customized by an external file. If the file is there modify the
interface accordingly, if not, fall back on the internal defaults.
Rich
On 4-5-2008 12:20, Angel Herráez wrote:
> Hi Rich
>
> I see your point --more or less--. I gather that you w
n for the
structure of the pop-up menu of the applet. But the functionality of the app
needs to be accessible from where new users expect to find it.
Rich
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openbabel and the Bondi values in as available sets. Allow the
user to specify a set either as a complete replacement for the defaults
or just a partial overwrite of one of them. Still permit element by
element definition.
Rich
>>
>
>
>
---
't be a problem.
> 6) If not just carbons, suggestions for resolving dihedral selection.
>
see 5
> 7) full model or selected subsets?
>
no opinion
Rich
-
Using Tomcat but need to do more? Need to sup
he rest of us. I know there is a lot that
goes into the background of the algorithms that we hardly ever see
because "it just works". But without that effort the program wouldn't be
any where near as functional. Your work is deeply appreciated.
Thanks,
Rich
--
erators are given
>> these should be preferred.
>>
Alan,
What does vcif say about these files?
Rich
-
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre
u clip it and, say, put it into a Word document?
>
Don't use Word; but will clip from FF and safari and paste into photoshop
> 3) Can you save it to a file that is about 32K and loads independently
> as a JPEG?
>
Yes.
Rich
-
, such
as protons, you can't even "see" (crystallographically) it gets even
trickier.
Rich
-
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-inte
ons. This last is the only
way to come up with a guess for -OH positions (and, rarely, NH
positions) because you need to look at all potential acceptor and donor
heavy atoms and rank their importance.
Rich
-
Using Tomc
1:08 PM
5/7/2006")
yep
then reload
http://fusion.stolaf.edu/chemistry/jmol/xtalx/xtalx.htm
no such file
Rich
---
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrate
ds k04041.res and
the crystal lattice appears and I can rotate it and click on the radio
buttons and have them work. If I try and load another molecule from the
drop-down menu of available models I get the freeze when clicking on the
load button.
Rich
--
come in as a
connected molecule for now and say "primitive atoms".
Rich
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Down
On 4-5-2006 17:35, Bob Hanson wrote:
Rich, and others interested,
This is in relation to http://www.stolaf.edu/people/hansonr/jmol/xtalx
[EMAIL PROTECTED] wrote:
> If I wanted to high-light (or restrict the visibilty) two molecules
> based on a particular pair of symmetry operatio
t the app. Safari2.0.3 seems to work OK.
Rich
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Download IBM WebSphere Application Ser
form them back to the
crystallographic system. Then apply the symmetry operators once you have
the "real" coordinates.
Rich
---
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with
nit cells then some program has to
apply the needed symmetry operators for the space group. Jmol is not yet
capable of generating the symmetry-related atoms; the necessary
ingredient of a programmer with java knowledge and crystallographic
symmetry underst
for a particular molecule should not be changed by *any* display
function. The functions that *do* alter the chemical nature (bonding,
bond order, atom type) must be entirely separate from the display choices.
Rich
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And there is certainly no need to
bend-over backwards to write special-case code to support its
deficiencies. The mmCIF/CIF formats have all sorts of functionality
built in to the atom/group naming to support atom disorder / alternate
conformations / multiple models.
Rich
--
On 4/30/05 9:10, Sebastian Lisken wrote:
Thanks a lot for the positive replies. I really should have put less
"fewer" ;-)
typos in my request, by the way. Talk about carelessness. :-)
It was a good reminder Sebastian. We all get carried away somet
factor curve coefficients]
for this form the zeroth element of the equation would need to be
calculated so the Z value of the element could be determined (and hence
the element identity derived).
Rich
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x27;
observation is that this is true but I don't have any technical
specifics to back that up.
Rich
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It&
On 1/8/05 16:03, Miguel wrote:
[snip]
Not that I just implemented
star on|off|{size}|percentage
To support bonded atoms. One can say
select *; spacefill off; wireframe; select !bonded; star 20%
Thanks! I'll adjust my script to fit.
d when a page is written back to the user from the perl CGI
module. Is that possible?
If you are unable to confirm this behaviour I could spend some time to
convert the existing script into a generic one to illustrate the problem
(who knows, doing so might even solve it ).
Rich
-
;loadInLine" problem 100% under
control I have reverted to the method of putting the files in a
directory under the server-root; I'd rather have a different location
but I don't know where the applet is allowed to get them from (other
than server-root) when the page has be
If the html of a jmol-including page is created by a cgi-script where
can the molecule files be located? Must they be in a directory off the
server-root? I tried a few other locations and didn't hit on one that
worked (other than the server-root choice).
On 1/6/05 20:18, Miguel wrote:
Safari works correctly when I use jmolApplet(480,"load /testmol.pdb"); but
if I read the pdb contents into a string (properly constructed, it works
in FireFox) and use:
jmolApplet(480);
jmolLoadInline("$pdb");
the I get a crash in Safari:
Ric
On 12/31/04 10:41, Philip Bays wrote:
Rich:
Can you send a web page URL to try this on, so i can try as well and we
are all looking at the same thing? I am also running 10.3.7 but have
a Logitech wireless scroll mouse.
Sure Phil. The real website is behind the corporate firewall but I put a
elite), driver version 2.5.1
(latest download), wheel-scrolling setting is listed as "fast" and
scrolls about 12 lines of text per "click".
Rich
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It happens when the scroll-zoom hits the upper limit.
Rich
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On 12/30/04 17:35, Miguel wrote:
Rich wrote:
I have a 3-button mouse with scroll-wheel but when I use it to zoom (in
the applet) the zoom-steps are too large. Is there a way for an applet
script to define a much smaller increment for the zoom-wheel so it is
more like the shift-left button
it is
more like the shift-left button zooming?
Rich
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don't want to
change the view position or any other display parameters).
Rich
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h out
and then send them along for consideration.
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of Materials Studio so I can't check the
CIF it creates to see if there are any oddities that might throw a
parser off-track (the quoting of R-3 is unnecessary though); could you
create a CIF of a non-proprietary compound and post it?
Rich
---
0; font label 14 sansserif
bold"
and the label appears just touching the default atom sphere directly
"east" of the atom. But no matter what value I try for the y-offset (1 -
4) the label goes to the default "north-east" position (using 0 4 for the
offsets does put the label
)
> must be in either the directory containing JmolApplet.jar or a
> subdirectory of that directory.
>
> Rich, I would try that again just be absolutely sure when you put all
> the files in the same directory and use "./" for your codebase that it
> really doesn't
et the same effect.
>
> They must have changed something.
>
> I tested the 'Listen' approach on my 10.3.3 system before I sent it to
> you.
I think the difference may be related to our network environment.
Rich
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SF email
The labeloffset portion of this command doesn't appear to do anything:
"select elemno>1; set labeloffset 1 0; label %a; font label 14 sansserif
bold"
The labels show up in the same place as when no command is given.
Rich
-
x27;#'
>> Add:
>> Listen 127.0.0.1:80
>
> I'll poke around a bit and see what I can come up with. I just love
> getting down and dirty with httpd.conf :-)
The above doesn't appear to work for OSX but what you can do is set
Bindaddress to the machine name / IP a
> Someone wrote:
who be dat? :-)
>
> Q: Are all the things in the same directory?
>
> 1. html file 2. JmolApplet.jar 3. Jmol.js 4. .pdb ?
yes, that was one of the configurations tried.
>
> Different browsers behave in different ways with applets running through
> file:// instead of http:/
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> On Tuesday 21 December 2004 15:13, Rich wrote:
>> Do the plugins need to be written in Java or is the ABI able to use
>> "other-language" modules?
>
> In principle Java... but Java can wrap libraries
Do the plugins need to be written in Java or is the ABI able to use
"other-language" modules?
Rich
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