VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 12 2014 - 10:01:41 CDT

Hi,
  If the map is in a DX file, it is trivial to rewrite the header of the
DX file with newly translated/rotated basis vectors. In principle, applying
the inverse transformations to the map that one would have applied to the
structure should enable the map to be (very roughly) docked to a structure
without changing the overall orientation or translation of the structure.
A little Tcl script could be used to manipulate the header of a DX file
to accomplish the needed rotations and translations of the map.
Perhaps Ryan can comment about whether that would be easy to link
to the MDFF tools or not.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 12, 2014 at 07:21:59AM +0000, Tristan Croll wrote:
> Ah. Then things are a little more challenging.
> One option: VMD's .dx maps are in the openDX format. There's free software
> available for that at [1]www.opendx.org - I would guess (though I've never
> had need to check) that would include translation and rotation tools.
>
>
> On 12 Aug 2014, at 4:44 pm, "Luba Simhaev" <[2]luba.simhaev0703_at_gmail.com>
> wrote:
>
> Thank you for your replies.
> This is a little bit more complicated, since the simulated system
> contains not only the water box but also a membrane. Which means that
> prior to MDFF simulations I used the initial docked protein structure
> (to the denstiy map) for placing it in a membrane (according to the
> membrane protein tutorial in VMD). As a result the orientation of the
> protein system and the density map are changed.
> Thanks,
> Luba
>
> On Tue, Aug 12, 2014 at 5:09 AM, Ryan McGreevy
> <[3]ryanmcgreevy_at_ks.uiuc.edu> wrote:
>
> Oops, looks like I may have misinterpreted your question. If your
> problem is, as Tristan suggests, an issue of having an unaligned map
> and structure then you indeed need to do an initial docking either
> manually or with a tool like Situs as the tutorial suggests.
>
> On Mon, Aug 11, 2014 at 8:13 PM, Tristan Croll
> <[4]tristan.croll_at_qut.edu.au> wrote:
>
> Personally, I'd do it the other way around. Desolvate your
> structure, fit it into the map (either by moving it manually in VMD
> or using a package like Situs), save your coordinates, re-solvate
> and go from there.
>
>
>
> From: [5]owner-vmd-l_at_ks.uiuc.edu [mailto:[6]owner-vmd-l_at_ks.uiuc.edu]
> On Behalf Of Luba Simhaev
> Sent: Monday, 11 August 2014 7:23 PM
> To: [7]vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: MDFF simulations
>
>
>
> Hello,
>
>
>
> I would like to know how can I fit the target density map into the
> simulated box in a case that they are rotated with respect to each
> other?
>
>
>
> I saw in the tutorial that it's not supported by VMD. Maybe there is
> another way?
>
>
>
> Thanks!
>
>
>
> Regards,
>
> Luba
>
> References
>
> Visible links
> 1. http://www.opendx.org/
> 2. mailto:luba.simhaev0703_at_gmail.com
> 3. mailto:ryanmcgreevy_at_ks.uiuc.edu
> 4. mailto:tristan.croll_at_qut.edu.au
> 5. mailto:owner-vmd-l_at_ks.uiuc.edu
> 6. mailto:owner-vmd-l_at_ks.uiuc.edu
> 7. mailto:vmd-l_at_ks.uiuc.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/