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003 Helper Macros

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Jordy Homing Lam edited this page Apr 12, 2020 · 16 revisions

Before we proceed to the research facilities of ICM, we need to introduce on some useful macros that make life easier.

Useful Tables

Similar to DataFrames in Pandas Python, ICM can iterate on Table objects to facilitate control. Of course, they can be built from scratch assigning Parray,Sarray,Iarray, ... , some macros can avoid the tedious process. Usually, the tables were intended as a calculation of properties, but the structure/data of these tables can be reused in other calculations.

  • Pairwise Distances

calc_short_distance_table a_//ca&a_/510:533 5.0

  • Headers: []
  • This macro calculate all nC2 pairwise distances within atom selection and only record pairs that are within 5.0 angstrom.
  • Facilitate assignment of drestraints e.g. of a local helix calc_short_distance_table a_//ca&a_SH/&a_/510:533 5.0
  • Residue Table calcResTable Res( a_5w0pNoT506End.PTH1R ) a_NULL./

Protein Modelling

  • Chain Extension by Sequence

if(String( aln_1 )=="align" )s_out = "align" if(String( aln_1 )!="align" )s_out = Name( aln_1 alignment ) buildModel1 sp_Q03431_PTH1R_HUMAN a_5w0pNoT506End.PTH1R ( no )? Obj( a_5w0pNoT506End.PTH1R ) : a_NONE. s_out 100 0 5 1 no yes { "nh3+" , "coo-" }

  • This is an extremely powerful ICM macro. Basically, what it does is that it takes sp_Q03431_PTH1R_HUMAN as template sequence, a_5w0pNoT506End.PTH1R as template model, aln_1 as alignment between model the sequence and output a model with padded N- and/or C- terminus extended by an assigned number of residues e.g. (0,5).
  • The output model topology is guaranteed valid. We may then optimise the model accordingly.
  • It can also pair with other functionalities (e.g. EM density restraints) to extend model one residue per chain at a time. And of course, extended single chain models can be re-assembled and incorporate the rest of the multi-chain model.
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