filter.dccm() clarification
Issue #640
resolved
Greetings,
I've been comparing cross-correlation plots after using filter.dccm() with and without a contact map. I notice that including a contact map (with every other option the same) actually results in more non-zero correlations on the plot. This makes me think I'm misunderstanding the purpose of including a contact map at this step. I thought that the contact criteria filter out certain long-range correlations between residues that are not actually in contact. Shouldn't filtering with a contact map result in equal or fewer non-zero correlations than filtering without the contact map?
Comments (2)
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- changed status to resolved
Not a bug. Closed because the use has no response
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Hi,
If you have only one 'DCCM' to filter, then yes, it should have fewer non-zero values with contact map. But, if you have multiple 'DCCMs', the calculation will be very different between with and without contact map. In some cases, using a cmap may result in more non-zero values. See
help(filter.dccm)
for more details.Let me know which case you are. Also, it would be helpful if you could upload an example for us to reproduce your problem.