From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Mon Feb 26 2018 - 12:58:53 CST

You can try smoothing the target density map prior to fitting, which will
remove the sharp "wells" in the data and make the earlier stages of fitting
faster and less prone to becoming stuck. You can do this with the VMD
plugin `volutil`. After an initial fitting to the smoothed map, you can run
a subsequent MDFF with the original.

On Mon, Feb 26, 2018 at 9:13 AM Rune Thomas Kidmose <rtk_at_mbg.au.dk> 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>
> *Sendt:* 26. februar 2018 14:47
> *Til:* Rune Thomas Kidmose
> *Cc:* 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> 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
>>
>>
>>