Re: [PyMOL] Details of the morph interpolation?

[Thomas Holder]

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)  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.


--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Numpy in incentive pymol

[Thomas Holder]

Hi Filip,

Incentive PyMOL includes numpy and scipy. However, the 1.8.0.0 release on 
Windows was missing some dlls, that's why "import numpy" fails. The 1.8.0.7 
update fixes that.

Cheers,
  Thomas

On 30 May 2016, at 06:44, Filip Leonarski  wrote:

> Hi,
> 
>I have a question - is it possible to have numpy and scipy available in 
> pymol 1.8 incentive version. I have some plugins that worked perfectly well 
> with pymol 1.7, however after upgrade to 1.8 they fail on "import numpy" step.
> 
> Thanks,
> Filip
> 
> -- 
> Filip Leonarski, PhD
> IBMC/CNRS
> 15 rue René Descartes
> 67084 Strasbourg Cedex

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] Map issue

[Filip Leonarski]

Hi,

I'm trying to access electron density maps from PyMol. Everything is
fine, when the map is orthorombic. I take map extremities with get_extend
and compare them with shape of array accessed via get_volume_field .
However when map is non-orthorombic I need to shuffle between
fractional/real coordinates. And here is the problem:

I have a map calculated exactly for the unit cell. However map_extend
provides values around 1% smaller. Why can it be?

Thanks,
Filip


-- 
Filip Leonarski, PhD
IBMC/CNRS
15 rue René Descartes
67084 Strasbourg Cedex
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net