From: Luba Simhaev (luba.simhaev0703_at_gmail.com)
Date: Wed Aug 13 2014 - 00:41:04 CDT

Thank you very much!!
I'll try to do that.

Luba

On Tue, Aug 12, 2014 at 7:31 PM, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
wrote:

> 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/
>>>
>>
>>
>