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Handle n<param>
parameter assignment logic internally?
#369
Comments
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Did this get patched already @joaomcteixeira or is it still relevant? |
No. It is an open discussion, still. Currently, users need to provide |
I thought this should be implemented, changed it to discussion to better reflect the current state of things. |
n<param>
parameter assignment logic internallyn<param>
parameter assignment logic internally?
@amjjbonvin, when you have time let us know your opinion here. |
Looking at the discussion I think this all makes sense |
As long as that parameter is written to the CNS input files it does not need to be defined by the user.
But it is required for the CNS scripts to work properly
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Currently we have some parameters that represent the number of segments/residues for a given functionality;
nfle1
: Number of fully flexible segmentsnseg1
: Number of semi-flexible segmentsnhisd
: Number of HISD residuenhise
: Number of HISE residuenumc2sym
: Number of C2 symmetry restraintsnumc3sym
: Number of C3 symmetry restraintsnumc4sym
: Number of C4 symmetry restraintsnumc5sym
: Number of C5 symmetry restraintsnumc6sym
: Number of C6 symmetry restraintsnums3sym
: Number of S3 symmetry restraintsnumncs
: Number of non-crystallographic symmetry restraintsThese are defined by the user, then the number of these parameters must match the number of segments defined.
If this logic is handled internally (without user intervention), we both remove a possible fault point and simplify the integration with the web interface.
Besides that,
nsegN
is polymorphic and can be a bit confusing for users:To alleviate that we can add a new parameter but still write
nsegN
since its needed for CNSSimilarly
nfleN
:We can also alleviate that with adding a new parameter but still write
nfleN
since its needed for CNS that can even account for the full flexibilityAdditionaly
ranair
is a boolean, but it should be a choiceand then
nrair_N
should be handled internallyThe text was updated successfully, but these errors were encountered: