Re: [Jmol-users] jvxl
Thanks Robert. I will try that and sorry for the missing subject. Cheers, Ed --- On Mon, 11/9/09, Robert Hanson hans...@stolaf.edu wrote: From: Robert Hanson hans...@stolaf.edu Subject: Re: [Jmol-users] (no subject) To: jmol-users@lists.sourceforge.net Date: Monday, November 9, 2009, 1:59 PM Well, sort of. You can store multiple surfaces in a single JVXL file, but right now there's no way to read them all into different frames all at once. However, since the browser will cache the files, you might want to try that. I haven't worked out a way to write a set of surfaces to a file, so you would have to construct this file manually, cutting and pasting. Probably not a solution for you. But it's not terribly difficult. The negative number on the 35 90 Jmol voxel format line tells how many surfaces are in the file. Then the data are just appended: -2 35 90 Jmol voxel format version 0.9 0.03 1318 1114 compressionRatio=416.05264 25704 1 38 ... 34 5 35 5 35 5 36 3 38 1 25695 $x#(]:Fd;VX_3R... -0.03 1317 1102 compressionRatio=418.28854 25695 2 37 3...5 5 35 5 36 3 38 1 25704 #x#%iA=FX8... You would still have to do something like: frame 1;isosurface myfile.jvxl 1 frame 2;isosurface myfile.jvxl 2 etc. I know, not a great solution. Bob On Mon, Nov 9, 2009 at 2:06 PM, Edgar Luttmann elut...@yahoo.com wrote: Hi, I am using JMol to display an animation with surfaces. For performance issues I precalculate those surface and store them as jvxl files. One sample animation consists of 41 frames and currently I need to load 41 jvxl surfaces for this to work. So I am wondering if there is a way to merge all precalculated surfaces into a single file and load that file within JMol. Thanks for any hints and cheers, Edgar -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -Inline Attachment Follows- -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july -Inline Attachment Follows- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Behaviour of set picking label
Wonderful! That's working very nicely now in my application. many thanks, Brian On Tue, Nov 10, 2009 at 08:21:04PM -0600, Robert Hanson wrote: version=11.9.8 # new feature: labels HIDE and labels DISPLAY do exactly that select oxygen labels HIDE select carbon labels DISPLAY On Tue, Nov 10, 2009 at 10:09 AM, Robert Hanson hans...@stolaf.edu wrote: This is fixed for Jmol 11.9.8 and Jmol 11.8.9. select [someAtoms] set toggleLabel hides/shows labels as a toggle. The labels keep their format. The state should be updated appropriately. On Tue, Nov 10, 2009 at 9:45 AM, Brian McMahon b...@iucr.org wrote: On Tue, Nov 10, 2009 at 09:28:08AM -0600, Robert Hanson wrote: On Tue, Nov 10, 2009 at 5:47 AM, Brian McMahon b...@iucr.org wrote: Earlier this year Bob introduced very nice functionality to move a label dynamically by SHIFT-click (application) or CTRL-click (applet) It's the same code -- should be the same key-combination. -- SHIFT, not CTRL Oops, my mistake in reading my own notes. SHIFT-click works for both. ALT-click also seems to work in the applet, though not for me with the application - that might be a feature of my window manager, I guess. My question: is there any way to ensure that after toggling a label on/off using the set picking select label it can be restored with the format it had prior to toggling off? Up until now, whenever a label is turned off it is reset to the standard label. As I mentioned in replying to Angel, the ability to remember an assigned format would be wonderful. Failing that, the ability to specify a different default would be helpful. (2) At this point, I can store the graphics state, using show state, and run it. The result is unchanged. However, if, while I still have set picking select label I SHIFT-click on an atom and move its label, then save the state, and then re-run the saved state, the position of the label has now shifted. Looks like a bug. definitely -- I'll look into that. Excellent. (3) A supplementary question. Having gone through this exercise (i.e. saved the graphics state and re-run it as a standalone script), if I now click on an atom, the application reports that atom's name and position (i.e. it has reverted to the default picking behaviour). Does this imply that the picking mode is not retained within the graphics state? If so, is there any way that it could be? [I am not sure that I would want it to be, but am curious as to the possibility.] That's right, the picking mode is not saved with the state. Not sure why. Probably no reason. OK, noted. The more I play with what I'm doing (silently invoking different picking modes in an attempt to help the user in different contexts), the more I think it wouldn't be such a good idea to save it with the state! Cheers Brian _ Brian McMahon tel: +44 1244 342878 Research and Development Officerfax: +44 1244 314888 International Union of Crystallographye-mail: b...@iucr.org 5 Abbey Square, Chester CH1 2HU, England -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Echo background full width?
Dear Angel, Thank you for your ideas. Idea 2 was brilliant and works perfectly! Yes, when the font size is changed, it adjusts automatically. Idea 1 complicates the need to run these scripts in Molecular Playground and Proteopedia, so was already rejected. At 11/8/09, Angel Herráez wrote: Hi Eric A few (maybe mad) ideas: 1) I guess you don't want this, but, you could put the banner outside Jmol -- and have Jmol call javascript to output the banner text. That way you are sure it is full width (via CSS or javascript, even html). 2) This is not theoretically clean either, but I guess it works: use two echos, one (one or two very long lines of spaces) for the background, another for the text, centered: 3) Maybe use an image (white rectangle, very wide) for the background of Jmol. Oh, that will not fit the text height automatically.. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Moving the center down a little?
Thanks to everyone who helped to release 11.8.9. Its great!
Bob, in http://MolecularPlayground.Org I am trying to let people
rotate the molecule at any time in the animation, including, for
example, during zooming. Therefore I am minimizing the use of moveto
and zoomto because these fight with concurrent
user-induced-rotations, inexorably going to the specified orientation.
So for zooms, I am just running a loop with zoom commands in small
increments. The problem was to make the zoom center stay where I put
the molecule (down a bit). Well, in Jmol 11.8.8 set windowcentered
false did NOT free zoom from recentering in the window center, but I
see that this is fixed in 11.8.9 -- HOORAY! So now set
windowcentered false is the equivalent of Chime's set zoomcenter
off which was very useful.
Jmol continues to rock! -Eric
At 11/9/09, Robert Hanson wrote:
Eric,
Actually, it's just
set windowCentered false
:)
Bob
On Mon, Nov 9, 2009 at 6:38 PM, Robert Hanson
mailto:hans...@stolaf.eduhans...@stolaf.edu wrote:
Eric, there is a way around this, but I have to check to see if
there is a bug there. The issue is that the zoom command also
recenters. The solution is to do the moveto command with the same orientation:
var q = script(show orientation rotation)
moveto quaternion @{!q} 100 0 10
That sets the orientation to the current orientation and zooms to
100% at a translation of 10% in y.
All in one go it looks like:
moveto quaternion @{!script(show orientation rotation)} 100 0 10
Bob
You have the echo background, so that should do it. So I'm not
catching on to the problem, I think.
To test, what I did was this:
load 1crn.pdb
center 1
now I zoomed out so that it was just a spot. With CTRL-ALT, I moved
the spot to wherever I wanted. That's the center of zoom. Now
zooming out, it is rotating about residue 1 at that screen position.
I'm pretty sure that's what you are after.
Is it just that you haven't figured out how to do that with a script?
I see in the state script:
moveto 0.0 { 997 -20 73 172.8} 134.42 -11.6 34.33 {17.231571
12.934429 4.9705715} ...
134.42 is the zoom; -11.6 34.33 are the x and y translations in
screen percent.
Really that should do it. You want something like:
moveto 0.0 { 997 -20 73 172.8} 100.0 0 10 {17.231571 12.934429 4.9705715}
(zoom is 100%, x-translation 0%, y-translation 10%, center model on residue 1)
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonrhttp://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/hansonrhttp://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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Re: [Jmol-users] Moving the center down a little?
whatever, but I didn't fix that. It's the same. Well, in Jmol 11.8.8 set windowcentered false did NOT free zoom from recentering in the window center, but I see that this is fixed in 11.8.9 -- HOORAY! So now set windowcentered false is the equivalent of Chime's set zoomcenter off which was very useful. -- 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
