Input File Types

Ways to open registered file types in Chimera:

with File... Open (local files), Fetch by ID (files to be fetched from databases)
from the Chimera Command Line, using the command open (default type PDB)
from the system command line at the time of Chimera startup

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:

Molecular Structures and Related Data (see also MD Movie and ViewDock)
Electrostatic Potential (associated tool: Electrostatic Surface Coloring)
Volume Data (associated tool: Volume Viewer)
Sequence (associated tool: Multalign Viewer)
Command Scripts
Other 3D Objects

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
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 (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 / December 2014