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Difference between revisions of "Mcsalign"

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  conda install -c schrodinger pymol-psico
 
  conda install -c schrodinger pymol-psico
 
  conda install -c rdkit rdkit
 
  conda install -c rdkit rdkit
  conda install -c bioconda -c kalev csb
+
  conda install -c speleo3 csb
 +
 
 +
== Usage ==
 +
 
 +
mcsalign mobile, target [, mobile_state [, target_state
 +
    [, cycles [, timeout [, method ]]]]]
 +
 
 +
== Arguments ==
 +
 
 +
* '''mobile''' = str: atom selection of mobile object
 +
* '''target''' = str: atom selection of target object
 +
* '''mobile_state''' = int: object state of mobile selection {default: -1 = current state}
 +
* '''target_state''' = int: object state of target selection {default: -1 = current state}
 +
* '''cycles''' = int: number of weight-refinement iterations for weighted RMS fitting {default: 5}
 +
* '''timeout''' = int: MCS search timeout in seconds {default: 10}
 +
* '''method''' = indigo or rdkit {default: check availability}
  
 
== Example ==
 
== Example ==
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  import psico.mcsalign
 
  import psico.mcsalign
 
  mcsalign /3zcf//A/HEC, /4n8t//A/HEM
 
  mcsalign /3zcf//A/HEC, /4n8t//A/HEM
 +
 +
Align a set of small molecules to a reference
 +
 +
fetch ala ile arg trp met
 +
extra_fit *, ala, method=mcsalign
  
 
== See Also ==
 
== See Also ==
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* [[align]]
 
* [[align]]
 
* [[pair_fit]]
 
* [[pair_fit]]
 +
* [[LigAlign]]
  
 
[[Category:Script Library]]
 
[[Category:Script Library]]
 
[[Category:Structural_Biology_Scripts]]
 
[[Category:Structural_Biology_Scripts]]

Latest revision as of 05:01, 22 June 2020

Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.mcsalign

mcsalign aligns two small-molecule selections based on Maximum-Common-Substructure.

Installation

mcsalign is available from the psico package and requires rdkit and csb.

All dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c rdkit rdkit
conda install -c speleo3 csb

Usage

mcsalign mobile, target [, mobile_state [, target_state
    [, cycles [, timeout [, method ]]]]]

Arguments

  • mobile = str: atom selection of mobile object
  • target = str: atom selection of target object
  • mobile_state = int: object state of mobile selection {default: -1 = current state}
  • target_state = int: object state of target selection {default: -1 = current state}
  • cycles = int: number of weight-refinement iterations for weighted RMS fitting {default: 5}
  • timeout = int: MCS search timeout in seconds {default: 10}
  • method = indigo or rdkit {default: check availability}

Example

Align Cytochrome C and Hemoglobin based on their Heme moieties:

fetch 3zcf 4n8t, async=0
zoom /4n8t//A/HEM, animate=2, buffer=3

import psico.mcsalign
mcsalign /3zcf//A/HEC, /4n8t//A/HEM

Align a set of small molecules to a reference

fetch ala ile arg trp met
extra_fit *, ala, method=mcsalign

See Also