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Error when running demo_ExperimentDesign.mcx example #7

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luisfabib opened this issue Apr 27, 2022 · 0 comments
Open

Error when running demo_ExperimentDesign.mcx example #7

luisfabib opened this issue Apr 27, 2022 · 0 comments

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@luisfabib
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The example demo_ExperimentDesign.mcx with the following script:

% MMMx Demo: Functionality of the ExperimentDesign module
%

# log

!ExperimentDesign

   import 2LZM T4L % load T4 lysozyme crystal structure
   
   import 2ADC RRM % load NMR structure of an RNA recognition motif

   sitescan mtsl T4L T4L_sites % sitescan for T4 Lysozyme, default set CILMSTV of residues 
      
   sitescan mtsl RRM RRM_sites I % sitescan for the protein part of the RRM, only isoleucine  
   
   sitescan iap-4tu RRM SL_sites u 1 0.1 % sitescan (only uracil) for the RNA part
   
   pairlist T4L_sites T4L T4L_pairs 15 80 % a site pair list for T4 lysozyme

   hetpairlist RRM_sites SL_sites RRM RRM_pairs 15 80 

   plot T4L_distributions pdf

   distributions mtsl T4L T4L_distribution
       68   131
       72   131
       75   131
       76   131
       79   131
       86   131
       89   131
      109   131
   .distributions

   plot RRM_distributions pdf
   
   distributions mtsl|iap-4tu RRM RRM_distribution
      RRM_pairs
   .distributions
   
   import 1BUY EPO % import what was once very popular in professional cycling
   
   sitescan mtsl EPO EPO_sites % perform site scan
   
   ENMpairs EPO_sites EPO EPO_enm_pairs 15 80 % score site pairs for elastic network modeling  

.ExperimentDesign

# report

results in the following error


Undefined function 'coor2dmat' for input arguments of type 'double'.

Error in score_enm_pairs (line 127)
dmat0 = coor2dmat(labels0); % label-to-label distance matrix for initial structure

Error in module_experiment_design (line 587)
            [c_entity,pairs] = score_enm_pairs(c_entity,sites,labels,cmd.fname,cmd.r_min,cmd.r_max);

Error in MMModel (line 101)
            [entity,module_exceptions,failed] = module_experiment_design(controller(module),logfid);

Error in MMMx (line 27)
exceptions = MMModel(control_file);
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