Graphical selection not working; other usage problems

[jamestorecaldwell@…]

Hello,
I am a new user.
I can open my PDB in both Chimera and ChimeraX. In Chimera function such as
stick sphere work fine. However, in ChimeraX when I click stick or sphere
the log window records the command and show how many atoms changed but the
image doesn't change. I also cannot select anything in ChimeraX on my PDB
or several others such as 3I5G. I can see the number and name of the
residue when I double click but I cannot select holding Ctrl and click.

Thanks,
James

-- 
*James Caldwell, Ph.D. Chemistry*
Post-Doctoral Research Fellow at the San Diego State University Research
Foundation
Department of Biology
Sanford Bernstein Laboratory, Life Sciences 371
San Diego State University
5500 Campanile Drive
San Diego, CA 92182
Cell phone: (815) 262 9697

[Tom Goddard]

Seems likely that your graphics driver is broken. What computer operating system to you use (Windows, Mac OS, version number)? And could you copy and paste the ChimeraX log panel -- the top part shows the graphics driver version, but copy the whole thing after you do some of these operations that don't work.

The ChimeraX download page notes "Because ChimeraX uses a number of graphics features that only perform well or are available with newer systems, we recommend using ChimeraX on computers three years old or newer." So if you are using an old computer there may not be much hope of getting to work, and you should stick to Chimera.

[jamestorecaldwell@…]

Hello,

Thanks for the feedback.

Newer Macbook Pro (Retina, 13-inch, Early 2015)
OS El Capitan Version 10.11.6 (15G1217)

I have included my PDB file (please do not share it is a revised version of
4QBD.pdb). As I go through the various buttons to change the style, the
only atoms that change are the ones that open as sticks to begin with: the
heteroatoms and the residues the are in contact with them and some others
that I'm not sure why...It does not matter if I select everything first or
not, I see the same result ( I attached the image also)

I really appreciate your help. Thank you

UCSF ChimeraX version: 0.1 (2017-03-27)
OpenGL version: 4.1 INTEL-10.14.73
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.
open /Users/Mako/Desktop/Superpositions/Rigorlike/Emb_AC_refine_46.pdb
Opened PDB data containing 15531 atoms and 15212 bonds
style selAtoms stick
Changed 15531 atom styles
style selAtoms sphere
Changed 15531 atom styles
style selAtoms sphere
Changed 15531 atom styles
style selAtoms ball
Changed 15531 atom styles
color selAtoms byhetero
color selAtoms bychain
color selAtoms random
style selAtoms stick
Changed 15531 atom styles
style selAtoms sphere
Changed 15531 atom styles
color selAtoms byhetero
color selAtoms bychain
color selAtoms byhetero
save ~/Desktop/image1.png supersample 3

On Mon, Apr 10, 2017 at 10:19 AM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu

Emb_AC_refine_46.pdb

image1.png​

[jamestorecaldwell@…]

Added by email2trac

[Tom Goddard]

I guess you mean you want to display the rest of the atoms. You can do that with the icon at the top left (the sphere) or use the command "show". The icons you were clicking change the style or color but do not change which atoms are displayed. If you pause the mouse over each icon it will say what it does.

I've deleted your PDB from the ticket for privacy. In the near future the bug database will be public including attachments, so in the future reply to the bug database with private data (or I will need to delete it so others cannot see it).

[jamestorecaldwell@…]

Hello,

Well, that was simple! I think that was the only icon I did not explore. I
tried every other icon and menu item.

Sorry to bother you.

How does ChimeraX select which residues and hetero atom are going to be
shown as sticks when first opening?


Thanks again,
James


On Mon, Apr 10, 2017 at 2:32 PM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Elaine Meng]

Hi James,
The autostyle rules (what is shown when a structure is first opened) are described here:

<http://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html>

I hope this helps,
Elaine

P.S. If you have further questions, better to use chimerax-users@cgl.ucsf.edu instead of piling things up in this bug ticket - thanks!  :-)