VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue Aug 12 2014 - 02:21:59 CDT

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 www.opendx.org<http://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" <luba.simhaev0703_at_gmail.com<mailto: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 <ryanmcgreevy_at_ks.uiuc.edu<mailto: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 <tristan.croll_at_qut.edu.au<mailto: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: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> [mailto:owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>] On Behalf Of Luba Simhaev
Sent: Monday, 11 August 2014 7:23 PM
To: vmd-l_at_ks.uiuc.edu<mailto: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