[Jmol-users] Questions
Just a couple of questions about things I have been observing with jmol.1. I have a colleague who uses a HP tablet PC in the classroom --,and everyplace else for that matter. It is running the tablet version of XP. However, jmol pages will not run on that machine with the latest incarnation. Earlier versions did, and I am not sure where the break point is. 2. I am running on a Mac (as most of you know) and have OS 10.4.3 and the latest version of java released yesterday. Jmol seems to run with no hitches. My page reloads a different pdb structure into the same jmol window (replacing the previous one) at a click of the mouse. Works fine in Safari. However, in Firefox, the first image loads fine, but there is a long delay before I can get the second one to appear. Subsequent images load rapidly. This issue cropped up several interations ago (again not sure when). Is this a jmol problem or a java embedding plugin issue? Has anyone else observed it?Phil Bays J. Philip Bays Department of Chemistry and Physics Saint Mary's College Notre Dame IN 46556 [EMAIL PROTECTED]
Re: [Jmol-users] centerAt boundbox coordinates
> > On Nov 16, 2005, at 3:43 PM, Miguel wrote: > >> >>> Is there a way to get Jmol to tell me the current centerAt boundbox >>> coordinates, once I have changed the center by a command such as >>> "center 124:a.ca" ? >> >> Not sure exactly what you are asking with the phrase 'current centerAt >> boundbox' > > what I meant was > "current centerAt boundbox coordinates" > I think that is different. There is no such thing ... or, better said ... I still don't understand what you are asking. > i.e., the current coordinates that jmol is using, so that I could > issue the command > centerAt boundbox x y z > using the coordinates in place of x,y,z. I don't understand. > so, if I say > > center atomno=23 > > then i would like to be able to say, > > centerAt boundbox xcoord ycoord zcoord OK ... I think that you are getting confused by 'boundbox' I think what you want is: center atomno=23; show center; centerAt absolute Note that in this case, since you specified only one atom, then the center that is reported by 'show center' will be the coordinates of that atom. So that when you say 'centerAt absolute x y z' you will be pluggin in the coordinates from X > and get the same result. I am looking for the values of xcoord, etyc. > that will give me the same result as "center atomno=23. > > I don't think that is addressed by what is below, if I understand it > correctly. You want to specify absolute coordinates for the center of rotation. center absolute Note that this is quite different from 'boundbox' or 'average' Miguel --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_idv28&alloc_id845&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] centerAt boundbox coordinates
On Nov 16, 2005, at 3:43 PM, Miguel wrote: Is there a way to get Jmol to tell me the current centerAt boundbox coordinates, once I have changed the center by a command such as "center 124:a.ca" ? Not sure exactly what you are asking with the phrase 'current centerAt boundbox' what I meant was "current centerAt boundbox coordinates" I think that is different. i.e., the current coordinates that jmol is using, so that I could issue the command centerAt boundbox x y z using the coordinates in place of x,y,z. so, if I say center atomno=23 then i would like to be able to say, centerAt boundbox xcoord ycoord zcoord and get the same result. I am looking for the values of xcoord, etyc. that will give me the same result as "center atomno=23. I don't think that is addressed by what is below, if I understand it correctly. ...F Here is some stuff in random order that might help: For a given molecule, the boundbox is always the same. The axes are drawn from the center of the boundbox to the centers of the faces of the boundbox. Since the boundbox is always the same the axes are always the same. set boundbox on; set axes on; With recent versions of Jmol, the default center is the center of the boundbox. You can show the center coordinates with: show center; You can then change the center in a number of ways center ; show center; Or, you can use the centerAt command: centerAt average; show center; centerAt boundBox; show center; centerAt absolute 0 0 0; show center; It is somewhat complicated, but 'average' and 'boundbox' can also take relative offsets. In the sample below, the second command will have the center be 10 anstroms along the X axes to the right of the default boundbox. centerAt boundBox; show center; centerAt boundBox 10 0 0; show center; Miguel --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_idv28&alloc_id845&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_idv28&alloc_id845&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] centerAt boundbox coordinates
Miguel, have I got this wrong? show center Delivers the coordinates of the center of the model. Units are in Angstroms. Output is in the form center: (centerX, centerY, centerZ) This is static, right? Ooh -- no, it's not. It changes when the molecule is recentered. That's interesting -- a way to get the coordinates of a particular atom shown: center [CYS]4.O;show center;center It should probably read "current display center"? Bob Miguel wrote: Is there a way to get Jmol to tell me the current centerAt boundbox coordinates, once I have changed the center by a command such as "center 124:a.ca" ? Not sure exactly what you are asking with the phrase 'current centerAt boundbox' Here is some stuff in random order that might help: For a given molecule, the boundbox is always the same. The axes are drawn from the center of the boundbox to the centers of the faces of the boundbox. Since the boundbox is always the same the axes are always the same. set boundbox on; set axes on; With recent versions of Jmol, the default center is the center of the boundbox. You can show the center coordinates with: show center; You can then change the center in a number of ways center ; show center; Or, you can use the centerAt command: centerAt average; show center; centerAt boundBox; show center; centerAt absolute 0 0 0; show center; It is somewhat complicated, but 'average' and 'boundbox' can also take relative offsets. In the sample below, the second command will have the center be 10 anstroms along the X axes to the right of the default boundbox. centerAt boundBox; show center; centerAt boundBox 10 0 0; show center; Miguel --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_idv28&alloc_id845&opÌk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_idv28&alloc_id845&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] centerAt boundbox coordinates
> Is there a way to get Jmol to tell me the current centerAt boundbox > coordinates, once I have changed the center by a command such as > "center 124:a.ca" ? Not sure exactly what you are asking with the phrase 'current centerAt boundbox' Here is some stuff in random order that might help: For a given molecule, the boundbox is always the same. The axes are drawn from the center of the boundbox to the centers of the faces of the boundbox. Since the boundbox is always the same the axes are always the same. set boundbox on; set axes on; With recent versions of Jmol, the default center is the center of the boundbox. You can show the center coordinates with: show center; You can then change the center in a number of ways center ; show center; Or, you can use the centerAt command: centerAt average; show center; centerAt boundBox; show center; centerAt absolute 0 0 0; show center; It is somewhat complicated, but 'average' and 'boundbox' can also take relative offsets. In the sample below, the second command will have the center be 10 anstroms along the X axes to the right of the default boundbox. centerAt boundBox; show center; centerAt boundBox 10 0 0; show center; Miguel --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_idv28&alloc_id845&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] centerAt boundbox coordinates
Is there a way to get Jmol to tell me the current centerAt boundbox coordinates, once I have changed the center by a command such as "center 124:a.ca" ? Frieda /// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] zoom in 10.00.43
> Hi, > > The zoom setting in jmol.jar seems to have changed between 10.00 and > 10.00.43 - so my scripts written in 10.00 are wrongly zoomed in 10.00.43. > Is there a reason? I believe that the only difference in zoom level occurs when the applet is not square. In 10.00 the applet was scaled so that the molecule would fit within the *smaller* of the two dimensions (when displayed with spacefill 100%). With more recent releases, the molecule is scaled so that it fits within the *larger* of the two dimensions. This is an intentional change. I do not anticipate future changes in this default behavior. Note that there was also a change in the default center position of a molecule. For most molecules this was very minor. Detail == An applet is a rectangular area with width and height specified in pixels. In general, applets should be square. Molecules have a center of rotation and a radius. The default center of rotation was changed after the 10.00 release. With the 10.00 release the default center of rotation was the average position of the centers of the atoms (which some people call the 'unweighted center of gravity'). The BoundBox is defined by the largest and smallest coordinate value for atom center positions along the x, y, and z cartesian axes. (try 'set boundbox on; set axes on;') In more recent prereleases of Jmol the center position defaults to the center of the BoundBox. With most molecules, the difference between the average position and the center of the BoundBox is very small. The primary motivation for this change in default center of rotation was for backwards-compatibility with Chime. The radius of a molecule is defined as the distance from the center to the outside of the furthest atom when the atoms are displayed 'spacefill 100%;'. The idea is that if you load a molecule and say 'spacefill 100%;' then the entire molecule will stay visible in all orientations. In previous releases the smaller window dimension was used. This was intentionally changed to be the larger window dimension. This is because the primary reason for using a rectangular applet is to show an elongated molecule ... in which case it is more useful to have the molecule scaled to fit within the larger dimension. Miguel --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_idv28&alloc_id845&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] zoom in 10.00.43
Hello, John This may be the cause (former post by me and Miguel's reply): > I am using a rectangular applet (I know Miguel does not recommend this, > but it works nicely, I have long narrow molecules and need space for > text). > I am finding a difference in the default zoom according to which version > of > Jmol I use. > I would like to know if this is known, intentional, or casual. > 10.00 opens the molecule with a zoom level so that it fits within the > shorter > dimension (vertical, in my case). This is what the docs say it should do. > 10.00.11 , 10.00.24 and 10.00.42 fit the zoom to the longer dimension > (horizontal). This is an intentional change. The default scaling is now to the larger window dimension, not the smaller. Miguel --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] zoom in 10.00.43
Hi, The zoom setting in jmol.jar seems to have changed between 10.00 and 10.00.43 - so my scripts written in 10.00 are wrongly zoomed in 10.00.43. Is there a reason? Thanks John
Re: [Jmol-users] CHIME to JMol data interchange?
Hi, Shravan I am not sure what you mean by "generate graphs" in Chime. It would help if you provide us a link to what you have now, using Chime. > I believe > JMol does not posess the capability to generate graphs and is just > used to create animated 3-D images for the data present in the PDB --- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
