From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed Mar 02 2016 - 18:51:04 CST

You can reduce the time required for vmd to calculate the correlations by
only computing them for a subset of frames by using the -frames options of
mdff check. e.g., -frames 0:10:4999 would compute the correlation for every
10th frame, starting with the first and ending at the last, but you still
get a good idea of how the correlation progresses. Also, in the next VMD
release (1.9.3), mdff check -ccc will be much faster in general.

On Wed, Mar 2, 2016 at 6:06 PM Bylund, Tatsiana (NIH/NIAID) [F] <
tatsiana.bylund_at_nih.gov> wrote:

> Oh, it actually works now. I have 5'000 frames and it's slow.
>
> Thank you so much!!!!
>
>
> From: Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
> Date: Wednesday, March 2, 2016 at 12:28 AM
>
> To: "Bylund, Tatsiana (NIH/NIAID) [F]" <tatsiana.bylund_at_nih.gov>, "
> vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: how to analyze fitting structure into density map
>
> What version of VMD and what operating system are you using? Also, do you
> get any messages or errors in the VMD terminal (the one you started VMD in)
> when you run the command?
>
> On Tue, Mar 1, 2016 at 6:54 PM Bylund, Tatsiana (NIH/NIAID) [F] <
> tatsiana.bylund_at_nih.gov> wrote:
>
>> When I tried
>>
>> Mdff check –ccc ….
>>
>> It said calculating the cross correlation, but then no window appeared
>> and console got to the next command without making any output.
>>
>> Do you know where can be the problem?
>>
>> Thank you very much!
>>
>> Best regards,
>> Tatsiana
>>
>> From: Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
>> Date: Tuesday, March 1, 2016 at 12:09 PM
>> To: "Bylund, Tatsiana (NIH/NIAID) [F]" <tatsiana.bylund_at_nih.gov>, "
>> vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
>> Subject: Re: vmd-l: how to analyze fitting structure into density map
>>
>> As discussed in the tutorial, you can calculate a global cross
>> correlation between your structure and your density map using 'mdff check'
>> or mdff 'ccc'. This value will give you an idea of the quality of fit. You
>> can also use Timeline to calculate many local cross correlations which will
>> provide a finer level of analysis. Using Timeline for cross correlation is
>> discussed in the last section of the mdff tutorial.
>>
>> On Tue, Mar 1, 2016 at 10:45 AM Bylund, Tatsiana (NIH/NIAID) [F] <
>> tatsiana.bylund_at_nih.gov> wrote:
>>
>>> Dear all,
>>>
>>> I performed fitting of a protein structure into a density map. I
>>> followed mdff tutorial, but in my case I don't have the target structure,
>>> just the initial structure and target density map.
>>>
>>> Is there a way to analyze the results? Not sure how to compute rmsd
>>> since there is no target structure.
>>>
>>> Thank you very much!
>>>
>>> Best regards,
>>> Tatsiana
>>>
>>>