Hi Jon, I just tried Chimera Mac/X11 version 1.3 build 2577 on a Mac laptop, OS 10.4.11 along with X11 1.1.3, and was able to open various PDB files (local and fetched from the RCSB) and manipulate them. Must be something else in the details of your system - perhaps it will be evident from the information that comes with the bug report. 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 Dec 11, 2008, at 11:46 AM, Greg Couch wrote:

On Wed, 10 Dec 2008, Jon Kenniston wrote:

...

Howdy,

Trying to run latest Chimera release version 1.3.2577 on my OSX 10.4.11 with X11 version 1.1.3 and while the chimera program opens, I cannot open a PDB (or at least I can't see the opened PDB - no error message, and bottom left of chimera screen states "Opened XXX.pdb" for about a minute until it goes to blank). Should I try installing an older version of chimera? Any help would be much appreciated.

Thanks,

Jon

Please use the Help / Report a Bug dialog to get this bug into our bug database. It will tell which model Mac you have and what graphics card it has, so we can try to reproduce the bug locally on similar hardware.

The next step would be to try the 1.3.2577 Aqua version of chimera. And if that doesn't work, then try an older version. If one or none of those work is important to know too. All of the versions can coexist on your Mac if you give each version of chimera a different name.

Greg Couch UCSF Computer Graphics Lab _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Luyuan, I'm glad the transparent ribbon raytracing has improved. Now, to your questions: (1) CA atoms not on ribbon. This is because the ribbon is a smooth interpolation, so in some places it does not fall exactly on the backbone atoms. There is no absolute fix currently, but some possible ways to make the figure look better are: - show the CA atoms as larger balls so that it is less obvious that they are not on the ribbon. Maybe you are showing "balls" (default 0.25 of VDW radius) and could instead show "spheres" (equal to VDW radius). If that is too big, you could still use the ball representation but change the model's "ball scale" factor to something larger than 0.25. This can be done by selecting some part of the structure, opening the selection inspector (Actions... Inspect), inspecting "Molecule model" and editing the "ball scale" factor. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ inspection.html#molprop> - instead of showing ribbon, just show the CA atom trace as sticks and any specific CA atoms you want to highlight as balls or spheres. I agree this is not as pretty as the ribbon, however. (2) ribbon too thick? I'm not sure I understand this issue, but it sounds like you could just use the "flat" ribbon, which has no thickness (it does not use the height values). You can switch to this ribbon style with the menu (Actions... Ribbon... flat) or with a command, e.g. ribrep flat You can still change the widths in the Ribbon Style Editor as you prefer. 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 Dec 12, 2008, at 8:16 AM, lvyuan zhang wrote:

Dear Chimera Team, I tried yesterday's build and it worked nice for my purpose. It totally solved the transparent ribbon problem that always bothers me. Thank you so much! Besides that, I still have two concerns. 1. When I show a Ca with both sphere and ribbon, these two do not overlap well. The ribbon supposedly should go through the center of the sphere, but it actually only goes through the edge of the sphere. Can you please solve this? 2. In the ribbon style editor, the heights can not go below 0.05. This becomes a problem when I raytrace a partially transparent helix with low resolution. The image is obviously blurred, and the blurness is caused by the slight shift between the two faces of the helix. It looks better if I save image with high resolution, but you know high resolution takes longer time. Thank you again! Best Luyuan Zhang