[Chimera-users] Script to minimise the binding site

[Miro Moman]

Thanks, however:

1) I checked the default preferences file and cannot find any line about
water deletion, in spite of the fact that I deselected this iption on the
GUI numerous times. Chimera remembers the choice until I close the session.
Is there a transient preferences file?

2) Regarding "fragment true", it does not work for me. I am guessing that
it could be because my selection is distance-dependent. Spec doesn't seem
to be working either, only freeze does.

So, I am able to accomplish what I want. Only that it takes longer.

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/


On Tue, 18 Dec 2018, 23:21 Elaine Meng <meng at cgl.ucsf.edu wrote:

> Hi Miro,
> (1)Turn off option to remove waters.  If you use the Minimize GUI and turn
> on "Memorize options chosen in subsequent dialogs” and then in the Dock
> Prep GUI turn off the option to remove waters, that should be remembered in
> your preferences.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html
> >
>
> (2) from “spec” description: "However, energy calculations will include
> the entire molecule models containing the specified atoms, unless fragment
> true is also used.”
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>
>
> (3) I tried a simple test case with “fragment true” vs. omitting that
> option and I got different energies, so as far as I can tell it is
> working.  The calculation was slower with the option omitted, since more
> atoms were involved.
>
> open 1zik
> sel @ca & :.b
> addh
> addcharge
> mini spec 'sel’  fragment true cache true prep false freeze '@CA | ~sel'
> nsteps 10
>
> ….gave  Potential energy: -1001.525464
>
> open 1zik
> sel @ca & :.b
> addh
> addcharge
> mini spec 'sel'  cache true prep false freeze '@CA | ~sel' nsteps 10
>
> …gave Potential energy: -581.897083
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Dec 18, 2018, at 3:01 AM, Miro Moman <miromoman at gmail.com> wrote:
> >
> > 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
>
>
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