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)
CATH cath: protein domain structure
(PDB format; file to fetch specified by CATH domain ID)
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
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
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 Pub3D database of modeled structures using a web service provided by the CICC at Indiana University)
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 smi23d web service provided by the CICC 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 calculated with Adaptive Poisson-Boltzmann Solver (APBS);
the APBS tool in Chimera runs this program via web service provided by the NBCR
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)
*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, scalar (not vector) amira: .am scalar field data
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
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
(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
MacMolPlt grid
(3D surfaces)
macmolplt: .mmp 3D surface data
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
.vol
electron density map
TOM toolbox EM density map tom_em: .em electron density map
Visualization Toolkit (VTK) structured points, ASCII vtk: .vtk values on a grid


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 and search interface
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
AutoPack results apr: .apr collections of 3D objects from AutoPack
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
Segger segmentation
(based on the hierarchical data format HDF5)
segger: .seg segmentation surfaces and grouping hierarchy, pointer to corresponding volume data file
(associated tool: Segment Map)
Sphgen spheres sph: .sph spheres from the DOCK accessory program sphgen
STL surface stl: .stl triangle-based format (binary) native to stereolithography CAD software from 3D Systems®
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 / September 2014