YASARA refine

[JinyuanSun]

Of which YASARA version is required to run the refine.mcr scripts?

yasara -txt refine.mcr modelin='AF-Q9ZV05-F1-model_v1.cif' modelout='refined.cif'

I ran the script but got an error:

Macro>AF-Q9ZV05-F1-model_v1.cif - ERROR - Unknown command, syntax error or undefined Yanaconda variable just before line 2. If there is no typing mistake, this is either a WHAT IF command (type WHATIF first), or you need a newer version of YASARA to run this command. Get an update from www.yasara.org/update.
 Error 724 occurred, the macro has been stopped.

[drlemmus]

We use a very new version of YASARA dynamics. Which version do you have?

[JinyuanSun]

Version 15.3.8, I guess my YASARA is a little bit old. I try to find this bug line by line, and it seems that I cannot load the cif file using LoadCIF command:

>LoadCIF AF-Q9ZV05-F1-model_v1.cif, Center=No, Correct=No
 - ERROR - Unexpected characters found at 'Correct=No'. This error can also be caused by command arguments specified in an incorrect order.

>LoadCIF AF-Q9ZV05-F1-model_v1.cif                       
==============================
*** Open Babel Warning  in ExtractSpacegroup
  CIF Error: missing spacegroup description: defaulting to P1... (in data block:data_AF-Q9ZV05-F1)
==============================
*** Open Babel Error  in ExtractUnitCell
  CIF Error: missing a,b and c value - cannot interpret structure ! (in data block:data_AF-Q9ZV05-F1)
==============================
*** Open Babel Error  in Cartesian2FractionalCoord
  Lattice parameters are not available.
 - WARNING - This molecule is too large to be converted to YASARA's internal SMILES format, most likely the atoms need to be divided into multiple residues like proteins or DNA.
 - Molecule 1/1 (AF-Q9ZV05-F1-model_v1.cif) loaded as object 1 (0 atoms).

[drlemmus]

Indeed, it is seven years old, that could be part of the problem. The other problem it seems is that you may be trying to refine a model straight out of AlphaFill you need to create a model with just one transplant, otherwise the refinement will definitely go wrong.

[JinyuanSun]

OK. I solved this. It seems that this version just cannot take care of mmCIF, I have to use a PDB version. So I modified the macro script.

# refine_pdb.mcr: a YASARA macro energy minimize an AlphaFill model
# Runs the default YASARA energy minimization experiment. The returned model is protonated.  
#
# Version 0.01
#
# Minimum YASARA tier: YASARA dynamics 
#
# This script was created by Robbie P. Joosten (r.joosten@nki.nl)
# Reference: If you publish results (directly or indirectly) obtained by using this macro, please cite YASARA and (any of)
# these publications:
# 1) Maarten L. Hekkelman, Ida de Vries, Robbie P. Joosten, Anastassis Perrakis: "­AlphaFill: enriching AlphaFold models 
#    with  ligands and co-factors" (2022)
#
# Changelog:
# Version 0.01
# - First attempt.
#
# YASARA input variables:
# modelin  The mmCIF file of the Alphafill model
# modelout The minimised AlphaFill model
#
#Initialise
OnError Exit
Console off
Processors 8

#Check the YASARA version
if (Dynamics)==0
  Print "YASARA version too low, you need at least YASARA Dynamics"
  exit

#Load the model

LoadPDB (modelin), Center=No, Correct=No

#Setup the forcefield
Forcefield NOVA
Longrange None
Cutoff 10.5
Boundary Wall

#Do the energy minimization (default settings)
Experiment minimization
Experiment On

# Wait till end of experiment
Wait ExpEnd

#Write the PDB coordinate file
SavePDB 1, (modelout)

exit

And ran this command:

~/biosoft/yasara/yasara refine_pdb.mcr "modelin = 'refine_test.pdb'" "modelout = 'refined_.pdb'" -txt

The first error was because of a syntax error of YASARA command, I missed "" out of a variable assignment.