[Chimera-users] Script to minimise the binding site

[Miro Moman]

Hello,

I would like to minimise the binding site including ligands, cofactors and
water molecules.

I have the following script:
___

runCommand("open " + pdbpath + pdbid + "_chimera.pdb")

runCommand("findclash 'ligand | solvent' test '~ligand | ~solvent'
overlapCutoff -1.0 hbondAllowance 0.0 intraMol false selectClashes true")

runCommand("sel up")
runCommand("namesel tomin")

runCommand("minimize spec tomin fragment true cache true prep true freeze
:@ca cgsteps 0")

runCommand("write format pdb #0 " + pdbpath + pdbid + "_min.pdb")
runCommand("write format mol2 #0 " + pdbpath + pdbid + "_min.mol2")
___

I am facing two issues:

1) Water molecules are deleted by prep. Is there as way of preventing this.
I have tried creating a custom preferences file like:

echo "{'AddCharge': {'charge method': 'Gasteiger'}," >
${DIR}/chimera_preferences
#echo " 'DockPrep': {'delete solvent': 'false'}," >
${DIR}/chimera_preferences
echo " 'DockPrep': {'incomplete side chains': 'rotamers'}}" >>
${DIR}/chimera_preferences

However, the second option is not recognised. Does it exist and, if so,
what would be the correct syntax?

2) The second problem is that the selection is ignored and every atom
except CAs is minimised.

Another option I have tried be setting prep to false and running it
beforehand:

models = chimera.openModels.open(pdbpath + pdbid + "_chimera.pdb")
prep(models, delSolvent=False)

But, again, if I do this, the selection is also ignored.

Best,

Miro


--
Edelmiro Moman, PhD
South Ural State University - SUSU
Южно-Уральский государственный университет - ЮУрГУ
Phone: +7 902 614 73 77
E-mail: miromoman at gmail.com
https://www.linkedin.com/in/edelmiro-moman-3a9979a/
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