On Tue, 24 Nov 2009, Pancera, Marie (NIH/VRC) [C] wrote:

Hi,

I have been using Chimera for quite some time (I had version Win1.3). This morning, I tried to open it a usual and although it opened, I could not see the black background (it was just gray). When I try to open a file (coordinates) I could not see anything. I uninstalled the program and reinstalled the newest version but the same thing happened. I was wondering if someone else had mentioned that to you (it could be a local issue but I thought I'll check with you as well). Thanks, Marie

Do any other 3D graphics programs work? If not, then you need to reinstall or update your graphics driver. If that's not the problem, please use chimera's Help / Report a Bug dialog to report the bug. That will give me additional information about your system that will help me help you.

- Greg

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

Dear Marie, I believe the units are kcal/mol and higher is less favorable.

However, for several reasons, these values CANNOT be used to compare the stabilities of a wild-type and mutant protein:

- each is only for a local minimum conformation, not the global minimum - they are not free energies, which would include entropic effects - they are only comparisons of the folded state and do not include the relative stabilities in the unfolded state - presumably the structures are not solvated

To make statements about the relative stabilities of the proteins, you would need to do much more sophisticated calculations (not available in Chimera) such as free energy perturbation or thermodynamic integration to calculate values along the relevant legs of the free energy cycle. It is beyond the scope of this mailing list to explain further! There should be many descriptions of such approaches in the literature, textbooks, and software manuals (AMBER, GROMOS, ...).

The "minimize structure" tool is intended only to clean up local strains and conflicts in the structures, not to provide relative stabilities. Best, 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 Feb 2, 2009, at 10:08 AM, Pancera, Marie (NIH/VRC) [E] wrote:

Hello, I am using the minimize structure tool under structure editing. I am using this tool because I would like to compare energies for a WT and a mutant structure (point mutant). I am getting potential energy value in the reply log. I wanted to check with you is there is a unit that I can use for that potential energy. I also would like to know if this means that the higher potential energy value means that the protein is less stable. Foe example, the potential energy for the WT is: 3132.577437 The potential energy for the mutant is: 2858.355152 So that means that the mutant protein has a lower energy and is more stable, right? Thanks you, Marie