[Chimera-users] Curves+ output files

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 10 09:32:22 PST 2009

Hi Dave,
Those files stretch the definitions of "PDB" format -- the residue  
names are 5 characters, the atom names are in the wrong columns, and  
all the atoms in one file are named "H" and all the atoms in the other  
file are named "O"!

However, I realize many programs write nonstandard "PDB" formats to  
show various things and it is useful to view them.

The initial default display can be adjusted in the Preferences  
(Favorites... Preferences), category "New Molecules."  Change "smart  
initial display" to "false" and click Save if you want that to apply  
to later uses of Chimera.

Alternatively (instead of changing New Molecule preferences) you could  
create an alias to show nucleic acids as all atoms, for example with  
the command:

alias ^plain nuc side atom; ~ribbon nucleic acid

and in recent Chimera (v 1.5, so daily builds) that would be saved in  
your preferences file.  You could execute that alias with the command  
"plain", for example:

open 1bna

or by choosing it from the top-level Aliases menu.  That menu appears  
when "^" (start-of-line) aliases are defined in recent Chimera 1.5  

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 10, 2009, at 7:03 AM, David Chenoweth wrote:

> Problem solved! Sorry, but it seems all I needed to do was show the  
> atoms and bonds. Chimera is reading the file it just doesn't show  
> anything until you tell it to show atoms and bonds. Another surprise  
> with the new Chimera version is that it automatically displays my  
> nucleic acid files with slab bases, filled sugars, and a backbone  
> ribbon. Is there anyway to shut this off so I don't have to go in  
> and manually do it each time I open a nucleic acid structure?
> Thanks,
> Dave

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