From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Tue Aug 12 2014 - 11:31:31 CDT

I am attaching an example script for translating/rotating a dx file. For
this method, you will need an initial structure which is properly aligned
to the map and your target structure (the one you want your map to be
aligned to). You set up an atomselection for each and use vmd's 'measure
fit' command to get the 4x4 translation matrix which when applied to the
initial structure, would overlap the two. You then apply the matrix to the
origin/delta vectors that are found in the header of your DX file. You
then replace those vectors with the ones obtained after translation.

On Tue, Aug 12, 2014 at 10:17 AM, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
wrote:

> 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/
>>
>
>