[Chimera-users] Transfer of the selection from reference to the ensemble

[Eric Pettersen]

Hi Gleb,
	You should be reporting these via Help->Report A Bug rather than sending them to the entire chimera-users list.  Please resubmit this using Report A Bug.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jun 29, 2016, at 4:19 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> So the question is now related only to force-field optimization of the
> ensemble via Chimera. Assuming that I have several pdb snapshots
> consisted of protein in deffrent conformation (taken from the gromos
> force field after md done in gromacs) with the ions put to the binding
> pockets- now I need to make quick optimization of this ensemble. In my
> case just for the minimization using latest Amber ff aplied on those
> ensemble Chimera produced error related to assigning of the hydrogens
> (probably due to the mismatching between previous ff and amber however
> the same error in case if I remove all hydrogens prior to
> optimisation):
> 
>  Args: ()
> Traceback (innermost last):
>  File "/opt/UCSF/Chimera64-1.11rc/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py",
> line 1747, in __call__
>    return apply(self.func, args)
>  File "/opt/UCSF/Chimera64-1.11rc/share/chimera/baseDialog.py", line
> 449, in command
>    getattr(s, buttonFuncName(txt))()
>  File "/opt/UCSF/Chimera64-1.11rc/share/chimera/baseDialog.py", line 704, in OK
>    self.Apply()
>  File "/opt/UCSF/Chimera64-1.11rc/share/AddH/gui.py", line 302, in Apply
>    initiateAddHyd(self.molList.getvalue(), addFunc=method, okCB=self.cb, **kw)
>  File "/opt/UCSF/Chimera64-1.11rc/share/AddH/unknownsGUI.py", line
> 274, in initiateAddHyd
>    addFunc(models, **kw)
>  File "/opt/UCSF/Chimera64-1.11rc/share/AddH/__init__.py", line 543,
> in hbondAddHydrogens
>    inIsolation=inIsolation, **protSchemes)
>  File "/opt/UCSF/Chimera64-1.11rc/share/AddH/__init__.py", line 554,
> in hbondAddHydrogens
>    idatmType, hisNs, coordinations, inIsolation)
>  File "/opt/UCSF/Chimera64-1.11rc/share/AddH/hbond.py", line 237, in
> addHydrogens
>    hbonds = findHBonds(mlist, distSlop=recDistSlop, angleSlop=recAngleSlop)
>  File "/opt/UCSF/Chimera64-1.11rc/share/FindHBond/base.py", line 574,
> in findHBonds
>    (donorAtom, donorHyds) + args):
> TypeError: accPhiPsi() takes exactly 8 arguments (10 given)
> 
> TypeError: accPhiPsi() takes exactly 8 arguments (10 given)
> 
>  File "/opt/UCSF/Chimera64-1.11rc/share/FindHBond/base.py", line 574,
> in findHBonds
>    (donorAtom, donorHyds) + args):
> 
> Any alternative suggestions?
> 
> Gleb
> 
> 
> 2016-06-28 16:01 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
>> Dear Pymol Users!
>> 
>> Within the Pymol session I have 2 loaded superimposed objects:
>> 1) one experimental pdb consisted of protein with co-factors (ligand
>> and metals);
>> 2) ensemble of 20 MD snapshots of the same protein (superimposed on
>> each others) without any cofactors;
>> 
>> For my particular task  I need
>> 1) to copy the selection (which include metals and ligand atoms) from
>> the reference structure to each model of the MD ensemble (via Pymol),
>> 2) make quick geometrical optimization of side-chains (I guess it
>> better to do it using Chimera) within the active side of each model
>> from MD ensemble
>> 3) perform post-processing - analysis of the distances between
>> cofactors and optimized side-chains of each MD conformers to obtain
>> statistical distribution of averaged distances (I guess it better to
>> do it via some MD software like Gromacs).
>> 
>> I will be very thankful for any suggestions for practical realization
>> of those steps!
>> 
>> 
>> 
>> James
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160629/659dac76/attachment.html>