VMD-L Mailing List
From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Tue Feb 17 2015 - 11:24:58 CST
How are you trimming the density? Make sure that any operation you do on
the density map is done on the actual density, not the potential, and that
includes any trimming or manipulation. The only thing you should do with
the potential file is use it as the grid during MDFF. Also be careful with
how you are running 'mdff griddx'. This command will convert a density to
a potential, but if you run the command on a potential, it will 'turn it
back into' a density.
On Tue Feb 17 2015 at 11:04:47 AM Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
> 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
> Thanks in advance,
> Sent from my iPhone
> On 18 Feb, 2015, at 00:19, Ryan McGreevy <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>
>> 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,
>> PhD Candidate
>> Department of Physics and Material Science
>> City University of Hong Kong