[Chimera-users] Script to minimise the binding site

[Miro Moman]

A quick update:

runCommand("sel #0 & ligand zr<6 | #0 & solvent zr<6")
runCommand("minimize spec 'sel' fragment true cache true prep false freeze
'@CA | ~sel' nsteps 100 cgsteps 10")

Freezing the unselected atoms works. However, my impression is that "spec"
and "fragment" have no effect whatsoever and that the total energy is
computed at each iteration.


--
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/


On Tue, 18 Dec 2018 at 12:47, Miro Moman <miromoman at gmail.com> wrote:

> 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/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20181218/9ea91cee/attachment.html>