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.

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

Molecular Structures and Related Data
Electrostatic Potential (associated tool: Electrostatic Surface Coloring)
Volume Data (associated tool: Volume Viewer)
Sequence Alignments (associated tool: Multalign Viewer)
Command Scripts
Generic 3D Objects

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