PyMOL Wiki - User contributions [en]

Intra rms

2007-09-18T11:52:45Z

Asceyman: /* USER EXAMPLES/COMMENTS */

===DESCRIPTION===
'''intra_rms''' calculates rms fit values for all states of an object over an atom selection relative to the indicated state. Coordinates are left unchanged. The rms values are returned as a python array.

===PYMOL API===
<source lang="python">
cmd.intra_rms( string selection, int state)
</source>

===PYTHON EXAMPLE===
<source lang="python">
from pymol import cmd
rms = cmd.intra_rms("(name ca)",1)
</source>

===USER EXAMPLES/COMMENTS===
[[Fit]], [[Rms]], [[Rms_Cur]] are finicky and only work when all atom identifiers match: segi, chain, resn, name, alt. If they don't then you'll need to use the alter command to change the identifiers to that they do -- typically that means clearing out the SEGI field, renaming chains, and sometimes renumbering.

I tried made two selections A, and D as

PyMOL>sel A, 1gh2 and n. CA and i. 65-99
Selector: selection "A" defined with 35 atoms.

PyMOL>sel D, 1kao and n. CA and i. 64-98
Selector: selection "D" defined with 35 atoms

which as you can see both yield 35 atoms. Now,
rms_cur A, D
won't work, due to the aforementioned reason. To fix this, one needs to do,
alter all,segi=""
alter all,chain=""
alter D, resi=str(int(resi)+1) # I don't actually use this line
and now
rms_cur A, D
should work.

===SEE ALSO===
[[Fit]], [[Rms]], [[Rms_Cur]], [[Intra_Fit]], [[Intra_Rms_Cur]], [[Pair_Fit]]

[[Category:Commands|intra_rms]]

Set name

2007-07-31T15:56:34Z

Asceyman:

===DESCRIPTION===
'''set_name''' can be used to change the name of an object or selection.

Not only can you simply rename an object or selection, but this command is also a powerful tool for those who deal with multiple structures in one file --- say a collection of NMR models. The user can execute the [[Split_States]] command and then rename the molecule of choice in the state of choice. For example, if one loads an NMR structure (with, say, 20 states) and aligns it to another structure, the balance of the alignment will (most likely) be off due to the weighting of the 19 other structures you probably don't see. To overcome this problem, one simply executes [[Split_States]] and then renames one of the states and then aligns that newly renamed object.

===USAGE===
set_name old_name, new_name

===PYMOL API===
<source lang="python">
cmd.set_name(string old_name, string new_name)
</source>

==User Comments/Examples===
<source lang="python">
cmd.set_name("example", "nicename")
</source>

[[Category:Commands|set_name]]

Load

2007-07-31T15:48:28Z

Asceyman: /* User Comments/Examples= */

===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===
<source lang="python">
load filename [,object [,state [,format [,finish [,discrete ]]]]]
</source>

===PYMOL API===
<source lang="python">
cmd.load( filename [,object [,state [,format [,finish [,discrete ]]]]] )
</source>

===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

===SEE ALSO===
[[:Category:Commands save |save]]

==User Comments/Examples===
<source lang="python">
cmd.load("xyz.pdb")
</source>

[[Category:Commands|load]]

Load

2007-07-31T15:46:13Z

Asceyman: /* PYMOL API */

Hide

2007-05-24T14:35:48Z

Asceyman: /* DESCRIPTION */

===DESCRIPTION===
'''hide''' conceals atom and bond representations for a certain selection or other graphical objects like distances.

The available representations are:
*lines
*spheres
*mesh
*ribbon
*cartoon
*sticks
*dots
*surface
*labels
*nonbonded
*nb_spheres

===USAGE===
hide representation [,object]
hide representation [,(selection)]
hide (selection)

===PYMOL API===
<source lang="python">
cmd.hide( string representation="", string selection="")
</source>

===EXAMPLES===
<source lang="python">
# hides all lines
hide lines,all

# hides all ribbons
hide ribbon

# hides all distances
hide dashes

# hides sticks in protA and all residues that aren't in the range of 40-65
hide sticks, protA and not i. 40-65
</source>

===SEE ALSO===
[[Cmd show]], [[Cmd enable]], [[Cmd disable]]

[[Category:Commands|hide]]

Hide

2007-05-24T14:34:49Z

Asceyman: /* EXAMPLES */

===DESCRIPTION===
'''hide''' conceals atom and bond representations for a certain selection.

The available representations are:
*lines
*spheres
*mesh
*ribbon
*cartoon
*sticks
*dots
*surface
*labels
*nonbonded
*nb_spheres

===USAGE===
hide representation [,object]
hide representation [,(selection)]
hide (selection)

===PYMOL API===
<source lang="python">
cmd.hide( string representation="", string selection="")
</source>

===EXAMPLES===
<source lang="python">
# hides all lines
hide lines,all

# hides all ribbons
hide ribbon

# hides all distances
hide dashes

# hides sticks in protA and all residues that aren't in the range of 40-65
hide sticks, protA and not i. 40-65
</source>

===SEE ALSO===
[[Cmd show]], [[Cmd enable]], [[Cmd disable]]

[[Category:Commands|hide]]

Hide

2007-05-24T14:26:55Z

Asceyman: /* USAGE */

===DESCRIPTION===
'''hide''' conceals atom and bond representations for a certain selection.

The available representations are:
*lines
*spheres
*mesh
*ribbon
*cartoon
*sticks
*dots
*surface
*labels
*nonbonded
*nb_spheres

===USAGE===
hide representation [,object]
hide representation [,(selection)]
hide (selection)

===PYMOL API===
<source lang="python">
cmd.hide( string representation="", string selection="")
</source>

===EXAMPLES===
<source lang="python">
# hides all lines
hide lines,all

# hides all ribbons
hide ribbon

# hides sticks in protA and all residues that aren't in the range of 40-65
hide sticks, protA and not i. 40-65
</source>

===SEE ALSO===
[[Cmd show]], [[Cmd enable]], [[Cmd disable]]

[[Category:Commands|hide]]