VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Tue Aug 12 2014 - 10:17:34 CDT

I do actually have a script for making translating and rotating DX files
easier. I am trying to track it down and will send it as soon as I find
the script.

On Tue, Aug 12, 2014 at 10:01 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>