Regarding use of attribute assignment files and difference between ChimeraX and ChimeraX daily build
Dear Team Chimera,
I am a second-year undergraduate student at IISER, Pune. I have been using ChimeraX for some time. Earlier I have also used some older Chimera versions. They had the kdHydrophobicity under Render by Attribute for residues. However, ChimeraX does not. On reporting a problem, I was told to use attribute assignment files for kdHydrophobicity. I downloaded the file as .txt file with .defattr suffix. Then, following the instructions in the user guide, I tried to use the open command to start using the attribute file. But I was shown an error that no such file existed. I even changed the file location and checked with multiple directories, including where ChimeraX files are stored on my PC to try to open the file, but nothing has worked. Kindly provide clearer instructions on where to save and open the attribute assignment files.
Thank you.
Regards, Suhani Bhattacharyya
Dear Suhani Bhattacharyya, I don't know what filesystems are on your computer. Choose any location where you have permission to save and open files. If the file is named ending in ".defattr" you can use menu: File... Open, list all file types or just the defattr type, and browse to the location interactively to open it.
https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html
Example defattr files including the one for kdHydrophobicity:
https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html#examples
Besides the defattr file, we also provided a second (alternative) way to do this, a command file to make a custom preset for kdHydrophobicity assignment and coloring, see:
https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 23, 2023, at 6:41 AM, SUHANI BHATTACHARYYA via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Team Chimera,
I am a second-year undergraduate student at IISER, Pune. I have been using ChimeraX for some time. Earlier I have also used some older Chimera versions. They had the kdHydrophobicity under Render by Attribute for residues. However, ChimeraX does not. On reporting a problem, I was told to use attribute assignment files for kdHydrophobicity. I downloaded the file as .txt file with .defattr suffix. Then, following the instructions in the user guide, I tried to use the open command to start using the attribute file. But I was shown an error that no such file existed. I even changed the file location and checked with multiple directories, including where ChimeraX files are stored on my PC to try to open the file, but nothing has worked. Kindly provide clearer instructions on where to save and open the attribute assignment files.
Thank you.
Regards, Suhani Bhattacharyya
Dear Team Chimera,
Thank you for the information.
Regards, Suhani Bhattacharyya
On Wed, Aug 23, 2023, 22:01 Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Suhani Bhattacharyya, I don't know what filesystems are on your computer. Choose any location where you have permission to save and open files. If the file is named ending in ".defattr" you can use menu: File... Open, list all file types or just the defattr type, and browse to the location interactively to open it.
https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html
Example defattr files including the one for kdHydrophobicity:
https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html#examples
Besides the defattr file, we also provided a second (alternative) way to do this, a command file to make a custom preset for kdHydrophobicity assignment and coloring, see:
https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 23, 2023, at 6:41 AM, SUHANI BHATTACHARYYA via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Dear Team Chimera,
I am a second-year undergraduate student at IISER, Pune. I have been
using ChimeraX for some time. Earlier I have also used some older Chimera versions. They had the kdHydrophobicity under Render by Attribute for residues. However, ChimeraX does not.
On reporting a problem, I was told to use attribute assignment files for
kdHydrophobicity. I downloaded the file as .txt file with .defattr suffix. Then, following the instructions in the user guide, I tried to use the open command to start using the attribute file. But I was shown an error that no such file existed. I even changed the file location and checked with multiple directories, including where ChimeraX files are stored on my PC to try to open the file, but nothing has worked. Kindly provide clearer instructions on where to save and open the attribute assignment files.
Thank you.
Regards, Suhani Bhattacharyya
participants (2)
-
Elaine Meng -
SUHANI BHATTACHARYYA