Registered File Types

All file types that have been registered in Chimera can be opened from:

the system command line upon startup; the type can be specified by a suffix that is part of the filename or by prefix:filename, where prefix is not part of the filename (the default is Python)
the Command Line (using the command open); the type is specified as described above, except that the default is PDB
the Chimera Open File Dialog (File... Open) (except that Fetch by ID must be used for specifying NDB, PDB, or SCOP files by ID code)

If a tool-specific type of file is opened, the associated tool will be executed or started (if it has not been started already).

Registered File Types
type	prefix	suffix	contents	associated Chimera tool (if any)
Aligned FASTA	afasta:	.afasta .afa .fasta .fa	sequence alignment	Multalign Viewer
Aligned NBRF/PIR	pir:	.pir	sequence alignment	Multalign Viewer
APBS potential	apbs:	.dx	electrostatic potential calculated with Adaptive Poisson-Boltzmann Solver (APBS)	Volume Viewer
BILD	bild:	.bild .bld	graphical objects
BRIX or DSN6	dsn6:	.brix .omap	crystallographic density map used by O	Volume Viewer
CCP4 or MRC	mrc:	.ccp4 .mrc	crystallographic or EM density map	Volume Viewer
Chimera commands	cmd: com:	.cmd .com	commands (and optionally, comment lines starting with #)
Chimera demo source	demo:	.src	instructions to Chimera and explanatory text for the demo viewer	Demos
Chimera markers	markers:	.cmm	markers placed in 3D	Volume Path Tracer
Chimera web data	chimerax:	.chimerax	instructions on data files to open, commands and code to execute (can have a Chimera demo embedded)
Clustal ALN	aln:	.aln .clustal .clustalw .clustalx	sequence alignment	Multalign Viewer
CNS or XPLOR	xplor:	.cns .xplor	unformatted ASCII density map	Volume Viewer
DelPhi or GRASP potential	delphi:	.phi	electrostatic potential calculated with DelPhi (the academic version; see also DelPhiController) or GRASP	Volume Viewer
DOCK scoring grids	dock:	.bmp .cnt .nrg	DOCK (versions 4, 5) bump, contact, and energy scoring grids (suffixes not interchangeable; gridname.bmp required for reading gridname.cnt and/or gridname.nrg)	Volume Viewer
Gaussian cube grid	cube:	.cube .cub	orbitals, electron densities, other	Volume Viewer
Gaussian formatted checkpoint	fchk: gaussian:	.fchk	molecular structure
GCG RSF	rsf:	.rsf	sequence alignment	Multalign Viewer
gOpenMol (see conversion instructions)	gopenmol:	.plt	orbitals, electron densities, other	Volume Viewer
GRASP surface	graspsurf:	.srf	molecular surface generated by DelPhi (the academic version; see also DelPhiController) or GRASP
MD Movie metafile	md: movie:		specification of trajectory format and filenames	MD Movie
Mol2	mol2:	.mol2	molecular structure
MPOSE	mpose:	.mpose	superposition and affine model from the separate program MPOSE	MPOSE
MS surface	dms: ms:	.dms .ms	dot molecular surface
MSF	msf:	.msf	sequence alignment	Multalign Viewer
NDB	ndb:		nucleic acid structure (PDB format but identified by NDB ID)
NetCDF	netcdf:	.nc	3D data	Volume Viewer
PDB	pdb:	.pdb .pdb1 .ent	molecular structure
Priism	priism:	.xyzw	3D light and EM data	Volume Viewer
Purdue image format	pif:	.pif	EM density map	Volume Viewer
PROFEC	profec:	.dat	interaction free energy grid from PROFEC (in AMBER versions 6 and 7)	Volume Viewer
Python	python: py: chimera:	.py .pyc .pyo .pyw	Python code
SCOP	scop:		protein domain structure (PDB format but identified by SCOP domain ID)
Situs map	situs:	.sit	EM density map	Volume Viewer
SPIDER	spider:	.spi	EM density map	Volume Viewer
Stockholm	pfam: hmmer:	.pfam .sto	sequence alignment	Multalign Viewer
TOM toolbox map	tom_em:	.em	EM density map	Volume Viewer
UHBD potential, binary	uhbd:	.grd	electrostatic potential calculated with the University of Houston Brownian Dynamics (UHBD) program	Volume Viewer
VRML	vrml:	.vrml .wrl	graphical objects
XYZ	xyz:	.xyz	molecular structure

UCSF Computer Graphics Laboratory / January 2006