Ways to open registered file types in Chimera:
In the tables below, registered file types are grouped by data type:
type | prefix | suffix | contents |
---|---|---|---|
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) |
|
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 Intro to PDB Format) |
pdb: | .pdb .pdb1 .ent |
molecular structure |
PDBID | pdbID: | molecular structure
(PDB format; file to fetch specified by 4-character PDB ID) |
|
SCOP | scop: | protein domain structure
(PDB format; file to fetch specified by SCOP domain ID) |
|
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 | xyz: | .xyz | molecular structure |
type | prefix | suffix | contents | |
---|---|---|---|---|
Chimera commands | cmd: com: |
.cmd .com |
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 source | 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) |
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 |
Pfam | pfam: | .pfam | sequence alignment |
Stockholm | sth: hmmer: |
.sth .sto |
sequence alignment |
type | prefix | suffix | contents |
---|---|---|---|
BILD | bild: | .bild .bld |
graphical objects |
Chimera markers | markers: | .cmm | markers placed in 3D
(associated tool: Volume Path Tracer) |
VRML | vrml: | .vrml .wrl |
graphical objects |
type | prefix | suffix | contents |
---|---|---|---|
APBS potential | apbs: | .dx | electrostatic potential calculated with Adaptive Poisson-Boltzmann Solver (APBS) |
BRIX or DSN6 | dsn6: | .brix .omap |
crystallographic density map used by O |
CCP4 or MRC | mrc: | .ccp4 .mrc |
crystallographic or EM density map |
CNS or XPLOR | xplor: | .cns .xplor |
unformatted ASCII density map |
DelPhi or GRASP potential | delphi: | .phi | electrostatic potential calculated with DelPhi (the academic version; see also DelPhiController) or GRASP |
DOCK scoring grids | 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) |
|
Gaussian cube grid | cube: | .cube .cub |
orbitals, electron densities, other |
gOpenMol (see conversion instructions) |
gopenmol: | .plt | orbitals, electron densities, other |
NetCDF | netcdf: | .nc | 3D data |
Priism | priism: | .xyzw | 3D light and EM data |
PROFEC | profec: | .profec | interaction free energy grid from PROFEC (in AMBER versions 6 and 7) |
Purdue image format | pif: | .pif | EM density map |
Situs map | situs: | .sit | EM density map |
SPIDER | spider: | .spi | EM density map |
TOM toolbox map | tom_em: | .em | EM density map |
UHBD potential, binary | uhbd: | .grd | electrostatic potential calculated with the University of Houston Brownian Dynamics (UHBD) program |