Date: Fri, 9 May 2003 13:57:27 -0500 (CDT) From: Steve Ludtke <stevel@blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke@bcm.tmc.edu To: Thomas Goddard <goddard@cgl.ucsf.edu> Hi again. I just ran across a bug I thought I'd report. The session file is rather large, so I won't attach it initially. Let me know if you have problems reproducing it. Anyway, I have loaded several volume data sets which represent different versions of the same structure. Then: 1) set 'independent' rotation mode 2) set one model so it is active, but not shown (in the model panel) 3) rotate the models 4) set the model in 2 to be shown again Even though it was active, the model in 2 was not rotated. I have a complex scenario of models where I need to do this operation frequently, so right now all my rotations keep getting messed up unless I make sure all the models are active AND shown before rotating anything. Cheers... PS - This happens with both the current 1700 version and the previous one. -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke@bcm.tmc.edu | Co-Director stevel@alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds Date: Fri, 9 May 2003 15:04:20 -0500 (CDT) From: Steve Ludtke <stevel@blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke@bcm.tmc.edu To: Thomas Goddard <goddard@cgl.ucsf.edu> Not THAT big a rush. Whenever you have a chance :^) Anyway, I was trying to avoid having to explain the whole situation, but here goes. I have a PDB model, a density map based on the PDB model and 3 different EM maps of the same molecule (each a little different). All are aligned and centered. What I want to do is have the EM map(s) with overlaid PDB structure on the left side of the screen and the x-ray map with overlaid structure on the right half of the screen. Then I use 'independent mode' to rotate everything about its own center so I can see how the EM map and x-ray map compare. As long as everything is active and displayed, it works beautifully (except the PDB model center seems very slightly off, so you see a very small amount of the centering artifact you described). Anyway, on the 'EM' side, I have 3 models overlaid. Generally I want to turn their display on and off as I rotate each one around and look at them. However, even though all 3 remain active, when I turn off the display of a model (ONLY in independent mode), it no longer gets rotated properly. Hope that helps clarify... cheers. -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke@bcm.tmc.edu | Co-Director stevel@alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds From: Tom Goddard The problem is that indepedent rotation mode only rotates about the the center of the displayed part of the model. If nothing is displayed there is no center to rotate about. Date: Fri, 9 May 2003 20:02:39 -0500 (CDT) From: Steve Ludtke <stevel@blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke@bcm.tmc.edu To: Thomas Goddard <goddard@cgl.ucsf.edu> I understand. I sort of figured it was something like this. Well, I'll give you my perspective as a 'user' from the EM community. As funny as it seems, I would actually want the opposite of the behavior you stated. That is, the molecules would always rotate about their 'true' center even if part wasn't displayed. The best solution from my perspective would either A) have a different 'independent' mode where things always rotated about their true centers or B) Make it so models that aren't displayed at all use their true center. This doesn't seem quirky to me. If the model is active, you assume some sort of rotation will occur. Presumably if part of the molecule is visible, the whole thing still gets rotated, just about a different center. So, it's odd for it not to get rotated at all.

From a user perspective, a problem I keep running into is that I accidentally do a rotation when not all of the molecules are active. This produces a relative rotation that is virtually impossible to undo through the GUI. Translations aren't a problem. They're pretty easy to 'undo' almost perfectly. But rotations are really tricky. When that happens I end up having to revert to my last saved session. So, having the model not rotate at all just because it isn't visible is doubly annoying...

Anyway, just my perspective... -- ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke@bcm.tmc.edu | Co-Director stevel@alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds Hi Steve, I agree it is odd for the undisplayed model not to be rotated at all. It seems reasonable that when the model is undisplayed it should use the center of the whole model if you are using independent rotation mode. There is the additional problem that the centers of the models don't coincide. When you display an isosurface, it uses the center of the bounding box that just contains the surface. It does not use the actual bounds of the whole density map. I see that Chimera has support for fixing the center of rotation for each model. This could be used to get exactly the rotation behaviour you want. But we need a user interface to let you say which models you want to group together with a common center. I could write something like this in Python. This would address both the undisplayed models not rotating, and the not quite right centers of rotation. I realize that accidentally unaligning two models in Chimera is a disaster -- it usually means starting over. I think we need a rotation and translation undo to address this. Tom