VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 17 2015 - 11:08:40 CST

Hi,
  You should be able to load MRC formatted density maps via
the "CCP4, MRC Density Map" option under the "Determine File Type"
chooser in the file loading window.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 18, 2015 at 01:04:40AM +0800, Kevin C Chan wrote:
> Thanks so much for the reply.
>
> Your guess is right, I'm in fact using the potential map generated by
> griddx command. However what was because I have used it for my previous
> (not yet trimmed) structure and CCC calculations and it seems fine as I got
> values of 0.7~0.8. I'm confused why the sign reverses, which indicates a
> rather bad correlation, simply because I trimmed the system (of cause I run
> new MDFFs for the trimmed ones).
>
> I'm willing to try my very original density map instead however it has .mrc
> as extension and I didn't find it available in the plugin's input list.
>
> Thanks in advance,
>
> Kevin
>
> Sent from my iPhone
>
> On 18 Feb, 2015, at 00:19, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu
> <javascript:_e(%7B%7D,'cvml','ryanmcgreevy_at_ks.uiuc.edu');>> wrote:
>
> The threshold is based on the map simulated from your structure. When you
> calculate the correlation, are you sure that you are comparing to the
> density map, and not the potential map (the map you fit to during mdff,
> created with the griddx command)? In cases of such bad correlation, my
> first guess is that you are using the potential instead of the density
> during analysis.
>
> On Mon Feb 16 2015 at 9:42:31 PM Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk
> <javascript:_e(%7B%7D,'cvml','cchan2242-c_at_my.cityu.edu.hk');>> wrote:
>
> > Dear Users,
> >
> > I am now using mdff plugin to analyse my mdff results.
> >
> > I am using a quite crude density map (as it is trimmed from a much bigger
> > one) in which there are much unoccupied density areas. As the unoccupied
> > areas are few angstroms away from my structure, I hope they won???t affect
> > much. Therefore I resort to local ccc calculations. I have chosen threshold
> > of 0.5 (and waiting for results of 0.2) however it still gives a very bad
> > ccc, say -0.7 to -0.8. I am curious that the threshold was referred to the
> > given density map or the simulated one from my input structure? If it is
> > the given one, then the bad ccc values come from the unoccupied areas in
> > the simulated map, right?
> >
> > Thanks in advance,
> >
> > Kevin
> > PhD Candidate
> > Department of Physics and Material Science
> > City University of Hong Kong
> > ukevi_at_gmx.hk <javascript:_e(%7B%7D,'cvml','ukevi_at_gmx.hk');>
> >
> > 

-- 
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/