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003 Helper Macros

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

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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