Hi Kenward, Just changing the color or representation should not reset the orientation *achieved by commands* (more explanation below) at the end of the previous panel. There are examples in the demos that come with Chimera (Tools... Demos) - e.g. in the hormone-receptor demo, the position does not reset to the original when switching from panel 2 to panel 3 (FSH undisplayed, leucines in FSH receptor displayed). I also tried playing this demo up to panel 2, opening the demo in the editor (from the Demo dialog, File... Open in Editor), unchecking the roll commands in panel 3, and then clicking Execute to test whether having some movement suppresses a reset bug. However, there was still no reset between panels 2 and 3. I'm using version 1.2304. Note that any rotations/translations performed *manually* will not be incorporated into a panel, only the ones expressed as commands. If you rotated/translated manually, there will be a resetting to the orientation without those manual movements before the next set of commands are applied. Perhaps that is what happened. That is the tricky thing about Demos: everything must be done with commands, and it can take a fair amount of effort to get the orientations you want. Actually, the resetting to the orientation achieved purely by commands is at least partly a feature rather than a bug, because it allows demo viewers to change the view manually within a panel however they desire without disrupting the views the demo creator intended to be visited during the course of the demo. Hope that makes sense... It may be instructive to open the existing demos in the editor as mentioned above, if you haven't tried that already. If the problem persists, let me know what version of Chimera you're using. Also, if you want you could send me your demo file and any associated data files and I could take a more in-depth look next week. About specifying a bunch of atoms over and over, you can name a selection and then use the selection's name. See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#namesel However, a selection can only be named using the menu currently, so for Demos a different approach is required. In similar situations, I bypass selection entirely and instead alias that set of atoms (using the same specifications that you would have used to select the atoms) and then use the resulting alias in subsequent commands. For example: Command: alias key #0:17.a,138.a,190.a #1:38.b,158.b,221.b #2:86.a,247.a,342.a Command: rep sphere key Command: focus key Command: color byatom key The alias statement can include all kinds of specifications - zones, categories such as "ligand," combination operators & | ~ , etc. Man page for "alias": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html Technically we aren't working today. However, I like to check my mail every day and will occasionally answer mail from devoted Chimera users! 8-) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 30, 2006, at 12:30 PM, Kenward Vaughan wrote:
In my demo, I've found that rotating a model about to create a specific view in one panel, followed in the next panel by either changing the atom representation or recoloring the atoms, causes a resetting of the view to the opening orientation. Is this a known issue?
Kenward
ps. BTW, can a selected group of atoms be named at the command line? Another question I can't seem to find an answer to... :( -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$???