[Chimera-users] Some UCSF Chimera marker (.cmm) bonds written as pseudobonds in pdb

[Elaine Meng]

Hi Junha,
If I understand correctly, they are not written as pseudobonds, it is just how they are interpreted when the file is read back in.  Since PDB format is meant for “real” atoms and bonds, Chimera detects abnormal bond lengths and decides that they must be pseudobonds rather than bonds.   If you don’t want them shown that way in Chimera, stick with the cmm (marker) format.  The cmm format also saves more things like colors and radii.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles>

Or, if you are writing PDB for some other purpose (some other program?) I don’t think you need to worry too much how they are displayed in Chimera.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Nov 20, 2018, at 8:40 AM, Jun Ha Song <junhasong at berkeley.edu> wrote:
> 
> Dear RBVI,
> I have UCSF Chimera marker set made by Volume Traver, and I used "Write PDB" in the model panel to transfer the .cmm file as .pdb file.
> 
> However, when I opened newly created .pdb file, only about 4.3% of bonds were being shown as bonds, and the rest were being shown as pseudobonds. Is there any reason for this phenomenon?
> Best,
> Junha.
> <UCSF CHimera WritePDB Bonds difference.png>