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dcor in correl
#37312 01/29/19 11:35 AM
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Nadia Offline OP
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Hi all,

I am trying to calculate the distance correlation between protein domains using correl according to the recommended syntax, for ex.:
correl maxt 5000 maxa 4 maxs 6
enter a atom XYZ sele ires 1 .and. type CA end
enter b atom XYZ sele ires 20 .and. type CA end
traj firstu 31 nunit 2
dcor a b
end
However, "dcor" is not recognized ("unrecognized command") (I am using version 41b2). Can anybody help? Thanks.

Re: dcor in correl
Nadia #37313 01/29/19 05:05 PM
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The DCOR command was not added until c42b1.


Rick Venable
computational chemist

Re: dcor in correl
Nadia #37314 01/30/19 08:40 AM
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Thank you, I tried with c44 and everything works now.

Re: dcor in correl
Nadia #37316 02/01/19 10:23 AM
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Hi Rick, to follow up on dcor with correl, I have another question:

I am using the dcor function without any problems but wondering whether my setup is appropriate. Currently, I copy my .crd to a comparison set using "coor copy comp"
then use the lines below to calculate dcor between two protein domains.
My question is: is the "orient mass sele" with respect to one (in this case, transmembrane) domain meaningful, or should I be using the entire protein? Should I orient with "mass" or without, and should I be using all backbone atoms? I guess these are physics questions, but maybe you can help. Thank you.
______________________________________________________
correl maxt 5000 maxa 1000 maxs 6
enter a atom XYZ sele @domain1 end
enter b atom XYZ sele @domain2 end
! reorient each frame with respect to Transmembrane domain
traj firstu 32 nunit 1 orient mass sele tmd end
dcor a b

Re: dcor in correl
Nadia #37319 02/02/19 05:28 PM
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I've always tended to use backbone atoms C,CA,N of fairly conserved structural motifs (helices, sheets, turns) for alignments, but I'm not familiar enough with DCOR to suggest the best strategy for this case.

Run some tests comparing the results without the ORIENT option, and ORIENT with and w/o the MASS keyword.


Rick Venable
computational chemist

Re: dcor in correl
Nadia #37320 02/03/19 09:11 PM
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OK, sounds good! I will run those comparisons.
Thank you!


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