Writing models in PDB only working via model panel, not via drop-down menu (UCSF Chimera 1.3)
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.
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@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>
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@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@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>
participants (2)
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Elaine Meng -
Jun Ha Song