VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Mon Feb 23 2015 - 03:59:03 CST

Thanks for all the replies.

John,
I know that we could load mrc files and I do it all the time to check
fittings. I was just not sure whether the plugin mdff check can read mrc.
Turns out it does.

Ryan and Tristan,
I understand directly trimming the potential is bad but what I was
interested in is how my system response to separate MDFF for each dimer in
vacuum and will soon return to the original 4-dimer big system so I think
it is fine. Thanks for the reminder anyway.

I have used the very original mrc file instead and it works fine giving
reasonable ccc. However what I could not understand is why my previous
calculation gave a negative value (with similar magnitude). As Tristan has
mentioned, the griddx map might be inverted. However what I have done is
just trimmed the original potential file (griddx) and I always load it into
VMD to check fitting and found no weirdness.
​So in what manner my griddx is inverted?

Thanks in advance,

Kevin

On Wed, Feb 18, 2015 at 6:13 AM, Tristan Croll <tristan.croll_at_qut.edu.au>
wrote:

> If I understand correctly, your CCC is fine. The griddx map is inverted
> (zero becomes 1 and vice versa), which means it's now *anti*correlated to
> your structure. -1 is perfect anti-correlation, +1 is perfect correlation,
> and 0 is no correlation.
>
> Cheers,
>
> Tristan
>
>
>
> Tristan Croll
> Lecturer
> Faculty of Health
> School of Biomedical Sciences
> Institute of Health and Biomedical Engineering
> Queensland University of Technology
> 60 Musk Ave
> Kelvin Grove QLD 4059 Australia
> +61 7 3138 6443
>
> This email and its attachments (if any) contain confidential information
> intended for use by the addressee and may be privileged. We do not waive
> any confidentiality, privilege or copyright associated with the email or
> the attachments. If you are not the intended addressee, you must not use,
> transmit, disclose or copy the email or any attachments. If you receive
> this email by mistake, please notify the sender immediately and delete the
> original email.
>
>
>
> On 18 Feb 2015, at 4:05 am, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
> 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> 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>
> 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
>>
>>