Input 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
CASTp CASTp:
castp:
structure and precomputed pocket measurements
(data to fetch from the from the Computed Atlas of Surface Topography of proteins specified by 4-character PDB ID with chain ID optionally appended, for example 2gsh.A; not all PDB entries are in the database; measurements will be displayed in a pocket list)
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)
MDL MOL/SDF mol:
sdf:
.mol
.sdf
molecular structure
ModBase modbase: modeled protein structure
(comparative models in PDB format to fetch from ModBase specified by SwissProt, TrEMBL, GenPept or PIR accession code; associated information will be shown in a list)
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 pdb: .pdb
.pdb1
.ent
molecular structure
PDBID pdbID: molecular structure
(PDB format; file to fetch specified by 4-character PDB ID)
PQSID pqsID: predicted biological unit structure
(file to fetch from the from the Protein Quaternary Structure server specified by 4-character PDB ID; predictions are not available for all PDB entries; some entries have multiple predictions, and for those, multiple files will be retrieved)
PubChem CID (input) PubChem:
pubchem:
small molecule structure
(3D structure SDF fetched from the Pub3D database provided by the CICC)
SCOP scop: protein domain structure
(PDB format; file to fetch specified by SCOP domain ID)
SMILES (input) SMILES:
smiles:
small molecule structure
(SMILES string converted to 3D structure SDF using the smi23d web service provided by the CICC)
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 coordinate xyz: .xyz molecular structure


Electrostatic Potential (can also be handled as volume data)
Associated tool: Electrostatic Surface Coloring
type prefix suffix contents
APBS potential apbs: .dx electrostatic potential calculated with Adaptive Poisson-Boltzmann Solver (APBS)
DelPhi or GRASP potential delphi: .phi electrostatic potential calculated with DelPhi (the academic version; see also DelPhiController) or GRASP
UHBD grid, binary uhbd: .grd electrostatic potential calculated with University of Houston Brownian Dynamics (UHBD)


Volume Data (see also electrostatic potential)
Associated tool: Volume Viewer
type prefix suffix contents
BRIX or DSN6 density map dsn6: .brix
.omap
crystallographic density map used by O
CCP4 density map ccp4: .ccp4
.map
electron density map
Chimera map
(based on the hierarchical data format HDF5)
cmap: .cmap
.cmp
electron density map
CNS or XPLOR density map xplor: .cns
.xplor
unformatted ASCII density map
DOCK scoring grid 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)
EDSDIFFID edsdiffID: electron density difference map (fo-fc)
(file to fetch from the Electron Density Server specified by 4-character PDB ID; not all PDB entries have maps available)
EMAN HDF map
(based on the hierarchical data format HDF5)
emanhdf: .hdf
.h5
electron density map
Gaussian cube grid cube: .cube
.cub
orbitals, electron densities, other
gOpenMol grid
(see conversion instructions)
gopenmol: .plt orbitals, electron densities, other
Image stack
(formats supported by PIL)
images: .tif
.tiff
.png
(etc.)
series of grayscale images in multiple files or a single multipage file
IMOD map
(MRC map with signed 8-bit mode interpreted as unsigned)
imodmap: .rec electron density map
MRC density map mrc: .mrc electron density map
NetCDF generic array netcdf: .nc 3D data
Priism microscope image priism: .xyzw 3D light or EM data
Priism time series priism_t: .xyzt time series of 3D light or EM data
(also starts Volume Series)
PROFEC free energy grid profec: .profec interaction free energy grid from PROFEC (in AMBER versions 6 and 7)
Purdue image format pif: .pif electron density map
Situs map file situs: .situs
.sit
electron density map
SPIDER volume data spider: .spi electron density map
TOM toolbox EM density map tom_em: .em electron density map


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
Selex selex:
pfam:
.selex
.slx
.pfam
sequence alignment
Stockholm sth:
hmmer:
.sth
.sto
sequence alignment


Command Scripts
type prefix suffix contents
Chimera commands com:
cmd:
.com
.cmd
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 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)


Generic 3D Objects
type prefix suffix contents
Bild bild: .bild
.bld
graphical objects
Chimera markers markers: .cmm markers placed in 3D
(associated tool: Volume Tracer)
IMOD segmentation imod: .imod
.mod
EM segmentation meshes and contours
VRML vrml: .vrml
.wrl
graphical objects

UCSF Computer Graphics Laboratory / March 2008