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.

The file types are grouped by data type below:

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

Molecular Structures and Related Data
file type prefix suffix contents
CASTp ID fetch CASTp:
castp:
structure and pocket measurements
(data to fetch from the from the Computed Atlas of Surface Topography of proteins (CASTp) database 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)
CASTp local .poc structure and pocket measurements
(previously saved results from the CASTp server specified by name.poc, which will also read name.pdb, name.pocInfo, name.mouth, and name.mouthInfo from the same location and display the measurements in a pocket list)
mmCIF cif:
mmcif:
.cif molecular structure
CIFID cifID: molecular structure
(mmCIF format; file to fetch specified by 4-character PDB ID)
EvalScore
summary file
score: .score model scores and associated filenames from protein structure prediction (used in CASP assessment)
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
Gromos87 gro: .gro molecular structure
(not read as a trajectory)
Maestro file maestro:
mae:
.mae molecular structure
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
(see also PQR)
pdb: .pdb
.pdb1
.ent
.pqr
molecular structure
PDBID pdbID: molecular structure
(PDB format; file to fetch specified by 4-character PDB ID)
PDB biounit biounitID: known or predicted biological assembly
(file(s) to fetch specified by 4-character PDB ID, optionally with “.N” appended to specify assembly N; otherwise, if the entry has multiple assemblies, multiple files will be retrieved)
PQSID pqsID: predicted biological unit
(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 PubChem3D database of modeled structures)
Rich Molecular Format
(based on the hierarchical data format HDF5)
rmf: .rmf
.rmf2info
hierarchical molecular structure, feature information, geometric markup
(associated data and controls will be shown in an RMF Viewer dialog)
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 NCI SMILES translator, or if that does not produce a structure, the smi23d web service provided by the cheminformatics group at Indiana University)
VIPERID viperID: icosahedral virus capsid structure
(PDB format; file to fetch specified by PDB 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
file type prefix suffix contents
APBS potential apbs: .dx electrostatic potential map from Adaptive Poisson-Boltzmann Solver (APBS);
see also the APBS tool in Chimera
DelPhi or GRASP potential delphi: .phi electrostatic potential map from DelPhi (the academic version; see also DelPhiController) or GRASP
UHBD grid, binary uhbd: .grd electrostatic potential map from University of Houston Brownian Dynamics (UHBD)
*Electrostatic potential maps can also be generated by using Coulombic Surface Coloring with the compute grid option
**Electrostatic potential isosurfaces are not displayed automatically, but can be shown with Volume Viewer or the volume command

Volume Data (see also electrostatic potential)
Associated tool: Volume Viewer
file type prefix suffix contents
Amira mesh amira: .am 3D data
BRIX or DSN6 map dsn6: .brix
.omap
electron density map
CCP4 map ccp4: .ccp4
.map
electron density map
Chimera map cmap: .cmap
.cmp
volume data from Chimera/ChimeraX
(based on the hierarchical data format HDF5)
CNS or XPLOR 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 emanhdf: .hdf
.h5
electron density map
(based on the hierarchical data format HDF5)
EMDBID emdbID: electron density map
(entry to fetch from the Electron Microscopy Data Bank; prefix emdbfitID will additionally fetch any corresponding PDB entries, but they may or may not be in the fit positions relative to the map)
Gaussian cube grid cube: .cube
.cub
orbitals, electron densities, other
gOpenMol grid gopenmol: .plt orbitals, electron densities, other
Image stack images: .tif
.tiff
.png
(etc.)
image stack
(grayscale image series in multiple files or a single multipage file, in formats supported by PIL)
IMAGIC map
(file reader courtesy of Ralf Schmidt and Michael Schatz, Image Science Software)
imagic: .hed
.img
density map
(the format consists of two files, filename.hed with header information and filename.img with the map values;
the format allows for multiple maps, but only the first will be read)
IMOD map imodmap: .rec electron density map
(MRC map with signed 8-bit mode interpreted as unsigned)
MacMolPlt grid macmolplt: .mmp 3D surfaces
MRC map mrc: .mrc electron density map
NetCDF generic array netcdf: .nc 3D data
Priism data 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 situs: .situs
.sit
electron density map
SPIDER map spider: .spi
.vol
electron density map
TOM toolbox map tom_em: .em electron density map
VTK PolyData vtk: .vtk lines, polygons from Visualization ToolKit [documentation PDF]


Sequence
Associated tool: Multalign Viewer
file 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
HSSP
(read-only)
hssp: .hssp sequence alignment
(other information not read; see HSSP database)
MSF msf: .msf sequence alignment
Selex selex:
pfam:
.selex
.slx
.pfam
sequence alignment
Stockholm sth:
hmmer:
.sth
.sto
sequence alignment
UniProt accession or ID (input) uniprot: protein sequence with feature annotations


Command Scripts
file 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;
for scripts with arguments,
see also runscript, startup option --script)


Other 3D Objects
file type prefix suffix contents
Bild bild: .bild
.bld
graphical objects
Chimera markers markers: .cmm markers placed in 3D
(associated tool: Volume Tracer)
COLLADA collada: .dae graphical objects
(geometry nodes define Chimera surface pieces)
IMOD segmentation imod: .imod
.mod
EM segmentation meshes and contours
Neuron trace
(SWC, see also the NeuroMorpho FAQ)
swc: .swc neuron reconstruction, such as from NeuroMorpho.Org
Segger segmentation segger: .seg segmentation surfaces and grouping hierarchy, pointer to corresponding volume data file; based on the hierarchical data format HDF5
(associated tool: Segger)
Sphgen spheres sph: .sph spheres from the DOCK accessory program sphgen
STereoLithography (binary) stl: .stl triangle-based format native to stereolithography CAD software
VIPERdb viper: .vdb icosahedral virus capsid structure
(PDB format, in the Virus Particle Explorer database coordinate system; capsid automatically constructed with Multiscale Models)
VRML vrml: .vrml
.wrl
graphical objects
(described in VRML geometry nodes)

UCSF Computer Graphics Laboratory / November 2020