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

[Jun Ha Song]

Dear Elaine Meng,

Thank you! Good to know why one menu was not working but the other one was.
I will use model panel from now on :)

Best,
Junha

On Mon, Sep 10, 2018 at 9:59 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180910/4bcde598/attachment.html>