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Difference between revisions of "Load"
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If an object is specified, then the file is loaded into that object. Otherwise, an object is created with the same name as the file prefix. | If an object is specified, then the file is loaded into that object. Otherwise, an object is created with the same name as the file prefix. | ||
| − | + | ||
===USAGE=== | ===USAGE=== | ||
<source lang="python"> | <source lang="python"> | ||
| − | load filename [,object [,state [,format [,finish [,discrete ]]]]] | + | load filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]] |
</source> | </source> | ||
===PYMOL API=== | ===PYMOL API=== | ||
<source lang="python"> | <source lang="python"> | ||
| − | cmd.load( filename [,object [,state [,format [,finish [,discrete ]]]]] ) | + | cmd.load( filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]] ) |
</source> | </source> | ||
===NOTES=== | ===NOTES=== | ||
| − | You can override the file extension by giving a format string: | + | *You can override the file extension by giving a format string: |
'pdb' : PDB, 'mmod' : Macromodel, 'xyz' : Tinker, 'cc1' : ChemDraw3D | 'pdb' : PDB, 'mmod' : Macromodel, 'xyz' : Tinker, 'cc1' : ChemDraw3D | ||
| Line 28: | Line 28: | ||
'pqr' : PQR (a modified PDB file with charges and radii) | 'pqr' : PQR (a modified PDB file with charges and radii) | ||
'mol2' : MOL2 | 'mol2' : MOL2 | ||
| − | |||
| − | |||
| − | |||
| − | ==User Comments/Examples=== | + | * A new feature has been added to load. You can specify an URL to a PDB and PyMOL will download it. This is a very handy feature for loading experimental/theoretical data from servers across the web. Just copy the link they give you and do, |
| + | <source lang="python"> | ||
| + | load http://www.theurl.com/path/toYourData | ||
| + | </source> | ||
| + | or you can open a remote file just from the command line | ||
| + | <source lang="bash"> | ||
| + | # load a PDB file; I placed one example file on the PyMOL Wiki | ||
| + | pymol http://www.pymolwiki.org/1rsy.pdb | ||
| + | |||
| + | # PyMOL can also handle the gzipped files on the PDB. :-) | ||
| + | pymol ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/00/pdb100d.ent.gz | ||
| + | </source> | ||
| + | |||
| + | ===User Comments/Examples=== | ||
| + | *Load xyz.pdb using the PyMOL API: | ||
<source lang="python"> | <source lang="python"> | ||
cmd.load("xyz.pdb") | cmd.load("xyz.pdb") | ||
</source> | </source> | ||
| + | |||
| + | * Loading multiple PDBs into one object with many states: | ||
| + | <source lang="python"> | ||
| + | load trj0001.pdb, mov | ||
| + | load trj0002.pdb, mov | ||
| + | load trj0003.pdb, mov | ||
| + | etc. | ||
| + | </source> | ||
| + | or, if you have too many states to do that by hand, | ||
| + | <source lang="python"> | ||
| + | for idx in range(1,1001):cmd.load("trj%04d.pdb"%idx,"mov") | ||
| + | </source> | ||
| + | or, you can use "glob" from Python, | ||
| + | <source lang="python"> | ||
| + | from glob import glob | ||
| + | lst = glob("trj*.pdb") | ||
| + | lst.sort() | ||
| + | for fil in lst: cmd.load(fil,"mov") | ||
| + | </source> | ||
| + | |||
| + | *Load a NAMD multi-PDB file. These are just concatenated PDB files. | ||
| + | <source lang="python"> | ||
| + | load NAMDtrajFile.pdb, multiplex=0 | ||
| + | </source> | ||
| + | |||
| + | * Hint: You can save some time & a lot of memory by loading the file and removing the atoms in a single-line compound statement (with a semicolon | ||
| + | after the load statement). | ||
| + | <source lang="python"> | ||
| + | load 1E3M.pdb; remove not A-C+F// | ||
| + | </source> | ||
| + | |||
| + | ===SEE ALSO=== | ||
| + | [[Save]] [[Load Traj]] | ||
| − | [[Category:Commands| | + | [[Category:Commands|Load]] |
| + | [[Category:States|Load]] | ||
Revision as of 14:13, 20 June 2009
DESCRIPTION
load reads several file formats. The file extension is used to determine the format. PDB files must end in ".pdb", MOL files must end in ".mol", Macromodel files must end in ".mmod", XPLOR maps must end in ".xplor", CCP4 maps must end in ".ccp4", Raster3D input (Molscript output) must end in ".r3d", PyMOL session files must end in ".pse", and pickled ChemPy models with a ".pkl" can also be directly read.
If an object is specified, then the file is loaded into that object. Otherwise, an object is created with the same name as the file prefix.
USAGE
load filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]]
PYMOL API
cmd.load( filename [,object [,state [,format [,finish [,discrete [,multiplex ]]]]]] )
NOTES
- You can override the file extension by giving a format string:
'pdb' : PDB, 'mmod' : Macromodel, 'xyz' : Tinker, 'cc1' : ChemDraw3D 'mol' : MDL MOL-file, 'sdf' : MDL SD-file 'xplor' : X-PLOR/CNS map, 'ccp4' : CCP4 map, 'callback' : PyMOL Callback object (PyOpenGL) 'cgo' : compressed graphics object (list of floats) 'trj' : AMBER trajectory (use load_traj command for more control) 'top' : AMBER topology file 'rst' : AMBER restart file 'cex' : Metaphorics CEX format 'pse' : PyMOL Session file 'pqr' : PQR (a modified PDB file with charges and radii) 'mol2' : MOL2
- A new feature has been added to load. You can specify an URL to a PDB and PyMOL will download it. This is a very handy feature for loading experimental/theoretical data from servers across the web. Just copy the link they give you and do,
load http://www.theurl.com/path/toYourData
or you can open a remote file just from the command line
# load a PDB file; I placed one example file on the PyMOL Wiki
pymol http://www.pymolwiki.org/1rsy.pdb
# PyMOL can also handle the gzipped files on the PDB. :-)
pymol ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/00/pdb100d.ent.gz
User Comments/Examples
- Load xyz.pdb using the PyMOL API:
cmd.load("xyz.pdb")
- Loading multiple PDBs into one object with many states:
load trj0001.pdb, mov
load trj0002.pdb, mov
load trj0003.pdb, mov
etc.
or, if you have too many states to do that by hand,
for idx in range(1,1001):cmd.load("trj%04d.pdb"%idx,"mov")
or, you can use "glob" from Python,
from glob import glob
lst = glob("trj*.pdb")
lst.sort()
for fil in lst: cmd.load(fil,"mov")
- Load a NAMD multi-PDB file. These are just concatenated PDB files.
load NAMDtrajFile.pdb, multiplex=0
- Hint: You can save some time & a lot of memory by loading the file and removing the atoms in a single-line compound statement (with a semicolon
after the load statement).
load 1E3M.pdb; remove not A-C+F//