Thank you for the reply, Thomas. I have a few items in reply:
1) I have not yet tried to change the refinement settings, but (for
educational purposes, if nothing else) I would like to know what it is that
this particular command that you typed, does: PyMOL> refine(5, "mout",
sculpt_field_mask=(0xFFF & ~0x60)). I haven't found any online
documentation for sculpt_field_mask.
2) Thank you for showing me how to fix atoms by typing
PyMOL> flag fix, (selection), set
before I call the morph command. Now how does one UNfix the atoms in the
selection? Navigating Build>Scultping>Clear memory does not do it. Do I
really need to exit the session to accomplish the reset (which is what
worked for me)?
3) I encountered a warning message about the match command when I type:
PyMOL> morph mout, sele1, sele2, refinement=0
(where sele1 and sele2 both have 4 iron ions each, each labeled 'FE')
The result is several lines that say 'Match-Warning: unknown residue type
'FE' (using X).' No Fe ions are used/observed in the interpolation. If,
however, I type:
PyMOL> morph mout, sele1, sele2, match=in, refinement=0
then the Fe ions do appear as part of the interpolation. Why does the
'align' argument (which is default for 'match') ignore the Fe?
Thank you for your time, Thomas.
Regards,
Emily.
On Tue, May 31, 2016 at 4:44 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:
> Hi Emily,
>
> PyMOL's morphing performs two steps: (1) RigiMOL, and (2) refinement of
> non-backbone atoms by sculpting. The second part can be skipped with
> "refinement=0".
>
> Unfortunately, there is no RigiMOL publication or method documentation.
>
> The sculpting refinement tries to avoid clashes and maintain the local
> sidechain geometry, based on start and end conformation as references. You
> are right that sculpting doesn't consider the Ramachandran plot or a real
> energy force field. But it does consider clashes (it has a VDW term). Check
> "Build > Sculpting > ...", the bottom part of that submenu lists some of
> the available terms. The corresponding numerical values can be found here:
> https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Sculpt.h
>
> The "morph" command refinement uses all sculpting terms. You could
> customize that, e.g. exclude VDW repulsion, like this:
>
> PyMOL> morph mout, sele1, sele2, refinement=0
> PyMOL> from epymol.rigimol import refine
> PyMOL> refine(5, "mout", sculpt_field_mask=(0xFFF & ~0x60))
>
> You can also "fix" atoms, e.g. all non-polymer atoms, like free ions,
> which tend to bounce around as a result of the refinement:
>
> PyMOL> morph mout, sele1, sele2, refinement=0
> PyMOL> from epymol.rigimol import refine
> PyMOL> flag fix, (not polymer), set
> PyMOL> refine(5, "mout")
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> On 30 May 2016, at 12:43, Emilia C. Arturo (Emily) <ec...@drexel.edu>
> wrote:
>
> > Hello.
> >
> > I would like to know more about the type of interpolation that is done
> when morph is called, and what calculations are done at each refinement
> cycle. Is there a literature reference or previous forum discussion to
> which you can point me?
> >
> > From my sifting through the internet, I settled on the likelihood that
> refinement is done using the "molecular sculpting" algorithm that has been
> employed since at least this discussion took place in 2002:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00359.html
> > In other words, refinement is not done on the basis of energy
> differences, Ramachandran plot, interatomic clashes, or other problems with
> geometry that could arise at each interpolation step.
> >
> > Is that correct? If so, is there a way to customize the refinement
> that's done?
> >
> > I am using MacPyMOL version 1.7.6.2.
> >
> > Regards,
> >
> > Emily.
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
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die tomorrow." - Maria Mitchell
"Success is going from failure to failure without losing your enthusiasm."
- Anon.
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