[Chimera-users] Writing models in PDB only working via model panel, not via drop-down menu (UCSF Chimera 1.3)

[Elaine Meng]

Hi Junha,
Well, marker models are not exactly the same as atomic models, so it’s not exactly a bug, just inconsistent implementation. Keep in mind that you lose some of the information (colors, radii, labels) when saving markers as PDB, so it’s not clear whether allowing it is good or not, which may be why we allow it one place and not the other.  The main  menu  File… Save PDB only lists regular atomic models, whereas the Model Panel also lists the marker model as a choice to save.  You can also use the “write” command to save a marker model to PDB, if you don’t want to use the Model Panel.

However, if you want to keep the color/radius/label information in the marker model, you should save it as a marker model (.cmm) using the File menu of the Volume Tracer tool (in menu under Tools… Volume Data).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 10, 2018, at 2:45 AM, Jun Ha Song <junhasong at berkeley.edu> wrote:
> 
> Dear RBVI,
> 
> I noticed that I could not write .cmm marker sets in UCSF Chimera as PDB file via drop down menu from main window, but that I could write it as PDB via Model Panel's side menu. Is this a bug?
> 
> Best,
> Junha Song.
> <WritePDB01.png><WritePDB02.png>