[Chimera-users] Script to minimise the binding site

[Eric Pettersen]

> On Dec 18, 2018, at 10:54 AM, Miro Moman <miromoman at gmail.com> wrote:
> 
> 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?

In your preferences file, look for the string “memorized settings”.  Under that grouping there should be a ‘delSolvent’ entry whose value (for your case) should be 0.  If your preference file is missing those strings then you haven’t followed Elaine’s instructions for memorizing settings correctly.

> 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.

Did you try the simple examples that Elaine provided?  Did they work for you?  If they did, how do they differ from what you’re doing?

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> 
> 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 <mailto:miromoman at gmail.com>
> https://www.linkedin.com/in/edelmiro-moman-3a9979a/ <https://www.linkedin.com/in/edelmiro-moman-3a9979a/>
>    
> 
> On Tue, 18 Dec 2018, 23:21 Elaine Meng <meng at cgl.ucsf.edu <mailto: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 <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 <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 <mailto: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 <mailto:miromoman at gmail.com>
> > https://www.linkedin.com/in/edelmiro-moman-3a9979a/ <https://www.linkedin.com/in/edelmiro-moman-3a9979a/>
> > 
> > 
> > On Tue, 18 Dec 2018 at 12:47, Miro Moman <miromoman at gmail.com <mailto: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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