UCSF Chimera2 User Guide
UCSF Chimera2 is the successor program to UCSF Chimera,
here termed “Chimera1.”
- General:
- Tools:
- Commands:
- color
- color atomic models, cartoons, molecular surfaces
- colordef
- define a color name
- surface
- create and display molecular surfaces
- Command-Related:
Many more commands exist, but are not yet documented in detail.
Some are in an experimental state and could be changed significantly or
omitted from later versions of Chimera2.
Several current commands are listed below.
The help command can be used to show brief descriptions
of specific commands or all commands in the Log
(for example, help style or help all).
Some commands are much the same as the corresponding Chimera1 commands,
except for the specification differences noted above.
- open
- open local file or fetch from repository
- first model is #1
- default for 4-character ID is to fetch mmCIF; use pdb: prefix
to fetch PDB, emdb: to fetch from EMDB, eds: to fetch
from EDS
- close
- close model
- list
- list current models
- style
(with options stick, ball, sphere)
- display/~display
- ribbon/~ribbon
- view
- bring everything into view
- lighting
(with options including soft for ambient occlusion, flat
for ambient-only, full with shadows, default)
- set
(with options including bgColor and silhouette)
- delete
- exit or quit
- sym
- sasa
- buriedarea
- contacts
- volume
- same as Chimera1
volume
- vop
- same as Chimera1
vop
- vseries
- same as Chimera1
vseries
- molmap
- same as Chimera1
molmap
- movie
- same as Chimera1
movie
- crossfade
- move
- similar to Chimera1
move
- turn
- similar to Chimera1
turn
- roll
- similar to Chimera1
roll
- stop
- stop all motion, like Chimera1
freeze
- wait
- same as Chimera1
wait
- title
- static annotation like Chimera1
2dlabels, with some of the same options
- perframe
- similar to Chimera1
perframe
- save
- material
- camera
- oculus
- pdbimages
- batch-render images of molecular assemblies defined in mmCIF files
(see examples)
UCSF Chimera2 documentation is copyrighted © by the
Regents of the University of California, 2015.
All rights reserved.