Thanks, it definitively helps. Finally I was able to save relative to the map and that was fine. Marie -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, January 05, 2009 5:29 PM To: Pancera, Marie (NIH/VRC) [E] Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Question regarding saving PDB in Chimera Hi Marie, If you just want the transformed coordinates (as shown on the screen), don't check any options. That is, don't use "save relative to" some model. However, that only saves the atomic structure and not the map, so if you had rotated the entire view you would lose their relationship and the fitting. I believe you want to save the atomic model relative to the density map model. To save the original coordinates of a model, you would "save relative to" itself, for example, save model #0 relative to model #0. Normally that would be done if you did something like rotated a bond or added hydrogens but otherwise wanted the same coordinates as input. Another use is if you superimposed or docked #0 and #1 and wanted to save their relative orientations. In that case you could either save #1 relative to #0 (so that the saved #1 would work with the original file for #0) or vice versa, assuming both are atomic structures. In your case, with a density map and an atomic structure, you can only save the atomic structure as PDB, of course. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 5, 2009, at 11:13 AM, Pancera, Marie (NIH/VRC) [E] wrote:
Hello,
I am using Chimera to fit coordinates into EM density.
However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen.
Here is what I do:
File
Save PDB
chose the folder
A file name
A file type
The model that I want to save, i.e the one I see on the screen
And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it.
IS there an easier way to just save what I can see on the screen?
Thanks,
Marie