VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Feb 26 2018 - 10:32:33 CST

Hi Rune,

Have you tried getting the domains prefit independently into the density, either with COLORES from Situs or newer EM-fitting programs like GEMfitter or BCL::EM-Fit? Then MDFF can fix up some of the small structural changes, letting the other programs get you in the right ballpark. It sounds like you are trying to take a structure that is misaligned to the initial density, which is going to be needlessly slow to converge rather than starting from a density-structure pair that are properly aligned.

-Josh

On 02/26/2018 08:15 AM, Rune Thomas Kidmose wrote:

Hi Ryan,

thx for getting back.

Yes I have played a lot with the domain restraints feature as well, and for a few cases, as the one shown in the tutorial, it kinda works, but not for all.

In general, I find the way you have to specify the domains using beta and occupancy values, to be a very slow'ish procedure for larger PDB files with many domains. But that is a different story I guess.

Ruki

________________________________
Fra: Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu><mailto:ryanmcgreevy_at_ks.uiuc.edu>
Sendt: 26. februar 2018 14:47
Til: Rune Thomas Kidmose
Cc: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Emne: Re: vmd-l: MDFF rotation

Have you tried using domain restraints (an example is in the MDFF tutorial)? This should help the domain fit together rather than the usual piecemeal approach.

On Mon, Feb 26, 2018, 4:48 AM Rune Thomas Kidmose <rtk_at_mbg.au.dk<mailto:rtk_at_mbg.au.dk>> wrote:

Hi all,

I have been tinkering with MDFF for the past half year now, and I have accumulated a couple of questions, one of which is:

Is it possible to somehow make MDFF handle large rotations of the initial model when fitting to the target density? It seems MDFF progresses quite linearly in its fitting, so is there a way to tell it or help it rotate e.g. a domain?

I have come across a couple of cases where a domain clearly should be rotated significantly to fit the density, but MDFF just kept on pushing it into the density and then proceeded to fill the density by pulling in the domain. I am not thinking about iMDFF, where you manually interact with the model, which currently is the only way that worked for me.

I acknowledge that rotation during MDFF it is not a trivial problem to solve but maybe I have missed some thing?

Cheers

Ruki