Registered File Types

Ways to open registered file types in Chimera:

In the Chimera and system command lines, the file 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. Suffixes (filename extensions) also control which files are listed in the Open File dialog when the File type is set to a specific type.

In the tables below, registered file types are grouped by data type:

When a tool-specific type of file is opened, the associated tool will execute or start.

Molecular Structures and Related Data
type prefix suffix contents
CIF/mmCIF cif:
mmcif:
.cif molecular structure
CIFID cifID: molecular structure
(mmCIF format; file to fetch specified by 4-character PDB ID)
Gaussian
formatted checkpoint
fchk:
gaussian:
.fchk molecular structure
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
(associated tool: MD Movie)
Mol2 mol2: .mol2 molecular structure
MS surface dms:
ms:
.dms
.ms
dot molecular surface
NDB ndb: nucleic acid structure
(PDB format; file to fetch specified by NDB ID)
PDB
(see Intro to PDB Format)
pdb: .pdb
.pdb1
.ent
molecular structure
PDBID pdbID: molecular structure
(PDB format; file to fetch specified by 4-character PDB ID)
SCOP scop: protein domain structure
(PDB format; file to fetch specified by SCOP domain ID)
VIPERdb viper: .vdb icosahedral virus capsid structure
(PDB format, in the Virus Particle Explorer database coordinate system; capsid automatically constructed with Multiscale Models)
VIPERID viperID: icosahedral virus capsid structure
(PDB format; file to fetch specified by Virus Particle Explorer database ID; capsid automatically constructed with Multiscale Models)
XYZ xyz: .xyz molecular structure


Command Scripts
type prefix suffix contents
Chimera commands cmd:
com:
.cmd
.com
Chimera commands
(locations of files opened by a command file can be specified relative to the command file's location, or with absolute pathnames)
Chimera demo source demo: .src instructions to Chimera and explanatory text for the demo viewer
(associated tool: Demos)
Chimera web data chimerax: .chimerax instructions on data files to open, commands and code to execute (can have a Chimera demo embedded)
Python python:
py:
chimera:
.py
.pyc
.pyo
.pyw
Python code
(locations of files opened by a Python script can be specified relative to the script's location, or with absolute pathnames)


Sequence Alignments (associated tool: Multalign Viewer)
type prefix suffix contents
Aligned FASTA afasta: .afasta
.afa
.fasta
.fa
sequence alignment
Aligned NBRF/PIR pir: .ali
.pir
sequence alignment
Clustal ALN aln: .aln
.clustal
.clustalw
.clustalx
sequence alignment
GCG RSF rsf: .rsf sequence alignment
MSF msf: .msf sequence alignment
Pfam pfam: .pfam sequence alignment
Stockholm sth:
hmmer:
.sth
.sto
sequence alignment


Generic 3D Objects
type prefix suffix contents
BILD bild: .bild
.bld
graphical objects
Chimera markers markers: .cmm markers placed in 3D
(associated tool: Volume Path Tracer)
VRML vrml: .vrml
.wrl
graphical objects


Volume Data (associated tool: Volume Viewer)
type prefix suffix contents
APBS potential apbs: .dx electrostatic potential calculated with Adaptive Poisson-Boltzmann Solver (APBS)
BRIX or DSN6 dsn6: .brix
.omap
crystallographic density map used by O
CCP4 or MRC mrc: .ccp4
.mrc
crystallographic or EM density map
CNS or XPLOR xplor: .cns
.xplor
unformatted ASCII density map
DelPhi or GRASP potential delphi: .phi electrostatic potential calculated with DelPhi (the academic version; see also DelPhiController) or GRASP
DOCK scoring grids dock: .bmp
.cnt
.nrg
DOCK (versions 4, 5, 6) bump, contact, and energy scoring grids
(suffixes not interchangeable; gridname.bmp required for reading gridname.cnt and/or gridname.nrg)
EDSID edsID: electron density map
(file to fetch from the Electron Density Server specified by 4-character PDB ID; not all PDB entries have maps available)
Gaussian cube grid cube: .cube
.cub
orbitals, electron densities, other
gOpenMol
(see conversion instructions)
gopenmol: .plt orbitals, electron densities, other
NetCDF netcdf: .nc 3D data
Priism priism: .xyzw 3D light and EM data
PROFEC profec: .profec interaction free energy grid from PROFEC (in AMBER versions 6 and 7)
Purdue image format pif: .pif EM density map
Situs map situs: .sit EM density map
SPIDER spider: .spi EM density map
TOM toolbox map tom_em: .em EM density map
UHBD potential, binary uhbd: .grd electrostatic potential calculated with the University of Houston Brownian Dynamics (UHBD) program

UCSF Computer Graphics Laboratory / September 2006