Bell: 2 revisions

2014-10-20T15:32:16Z

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PietroGattiLafranconi: download link added

2014-09-22T15:43:54Z

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2014-09-22T15:38:19Z

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{{Infobox script-repo
|type = script
|download = TBC
|author = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
|license = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
}}

== Introduction ==
Quick and simple script to replace B-factor values in a PDB structure.

New B-factors are provided in an external .txt file, one per line.

By default, the script will also redraw the selected molecule as cartoon putty and colour by B-factor

== Usage ==
loadBfacts mol, [startaa, [source, [visual Y/N]]]

== Required Arguments ==
* '''mol ''' = any object selection (within one single object though)

== Optional Arguments ==
* '''startaa''' = number of amino acid the first value in 'source' refers to (default=1)
* '''source''' = name of the file containing new B-factor values (default=newBfactors.txt)
* '''visual''' = redraws structure as cartoon_putty and displays bar with min/max values (default=Y)

== Limitations ==
For its very nature, this script is not suitable for complex cases in which only some B-factors are to be replaced, or on complex selections. In such cases, [http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ data2bfactor.py] is a better choice.

B-factors have to be entered one per line, with no labels or amino acid ID. They will replace values of a continuous stretch of amino acids of equal length (or shorter) starting from the position provided with 'startaa'.

'newBfactors.txt' looks like
2
0
0
3
7
...

== Examples ==
<source lang="python">
PyMOL>loadbfacts 1LVM
</source>
[[File:LoadBfacts1.png|450px|example #1]]

<source lang="python">
PyMOL>loadbfacts 1LVM and chain a, startaa=135
</source>
[[File:LoadBfacts02.png|450px|example #2]]

== The Code ==
<source lang="python">
from pymol import cmd, stored, math

def loadBfacts (mol,startaa=1,source="newBfactors.txt", visual="Y"):
"""
Replaces B-factors with a list of values contained in a plain txt file

usage: loadBfacts mol, [startaa, [source, [visual]]]

mol = any object selection (within one single object though)
startaa = number of first amino acid in 'new B-factors' file (default=1)
source = name of the file containing new B-factor values (default=newBfactors.txt)
visual = redraws structure as cartoon_putty and displays bar with min/max values (default=Y)

example: loadBfacts 1LVM and chain A
"""
obj=cmd.get_object_list(mol)[0]
cmd.alter(mol,"b=-1.0")
inFile = open(source, 'r')
counter=int(startaa)
bfacts=[]
for line in inFile.readlines():
bfact=float(line)
bfacts.append(bfact)
cmd.alter("%s and resi %s and n. CA"%(mol,counter), "b=%s"%bfact)
counter=counter+1
if visual=="Y":
cmd.show_as("cartoon",mol)
cmd.cartoon("putty", mol)
cmd.set("cartoon_putty_scale_min", min(bfacts),obj)
cmd.set("cartoon_putty_scale_max", max(bfacts),obj)
cmd.set("cartoon_putty_transform", 0,obj)
cmd.set("cartoon_putty_radius", 0.2,obj)
cmd.spectrum("b","rainbow", "%s and n. CA " %mol)
cmd.ramp_new("count", obj, [min(bfacts), max(bfacts)], "rainbow")
cmd.recolor()

cmd.extend("loadBfacts", loadBfacts);
</source>

[[Category:Script_Library]]
[[Category:Biochemical_Scripts]]
[[Category:Coloring]]
[[Category:Structural_Biology_Scripts]]

← Older revision	Revision as of 15:32, 20 October 2014
(No difference)

@@ Line 1: / Line 1: @@
 {{Infobox script-repo
 |type      = script
-|download  = TBC
+|download  = [http://dx.doi.org/10.6084/m9.figshare.1176991 figshare]
 |author    = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
 |license   = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]

Load new B-factors - Revision history

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