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#38578 12/16/22 02:45 AM
Joined: Dec 2018
Posts: 17
J
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J
Joined: Dec 2018
Posts: 17
Dear all,

After "coor helix", the output is something like this:

Quote
CHARMM selection followed (Default)

Helix analysis using the Chothia, Levitt, and Richardson algorithm.
J.Mol.Biol. Vol.145, pp215-250 (1981).
MOMENTS FOR HELIX 1
153.16470609 -13.00068170 45.11089577
173.60842007 24.41487973
18.94533703

MOMENTS for helix 1 0.92162 164.81056 179.98628
AXIS for helix 1 -0.29282 -0.15543 0.94345
CENTER for helix 1 14.78493 85.76448 89.77356
BEGIN for helix 1 17.67454 87.29829 80.46354
END for helix 1 11.92578 84.24683 98.98541

Helix analysis using the Aqvist algorithm.
Computers & Chemistry Vol.10, pp97-99, (1986).

HELIX AXIS: -0.299669 -0.166771 0.939354
Perp. vector to origin: 34.505343 96.563124 28.151416
Estimated number of significant digits: 9

I need the values of "CENTER" (14.78493 85.76448 89.77356 in this case). Can I obtain their values through internal variables?

I have tried ?XCEN and ?XAVI. "?XCEN ?YCEN ?ZCEN" have the values "34.505343 96.563124 28.151416", and "?XAXI ?YAXI ?ZAXI" have the values "-0.299669 -0.166771 0.939354" in this case.

Thank you very much.

James

Joined: Sep 2003
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Likes: 24
rmv Online Content
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Online Content
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The documentation in subst.info appears to be wrong. From source/manip/helix.F90

Code
         call set_param('ROTA',RHOANG)
         !axis and begin vector substitution
         ! first one
         ! axis
         call set_param('FXAV',AVEC(1,1))
         call set_param('FYAV',AVEC(2,1))
         call set_param('FZAV',AVEC(3,1))
         ! 2nd axis and 3rd axis
         call set_param('FXA2',CU(4,1))
         call set_param('FYA2',CU(5,1))
         call set_param('FZA2',CU(6,1))
         call set_param('FXA3',CU(7,1))
         call set_param('FYA3',CU(8,1))
         call set_param('FZA3',CU(9,1))
         ! begin
         call set_param('FXBE',BVEC(1,1))
         call set_param('FYBE',BVEC(2,1))
         call set_param('FZBE',BVEC(3,1))
         ! end
         call set_param('FXEN',EVEC(1,1))
         call set_param('FYEN',EVEC(2,1))
         call set_param('FZEN',EVEC(3,1))
         ! center
         call set_param('FXCE',RBAR(1,1))
         call set_param('FYCE',RBAR(2,1))
         call set_param('FZCE',RBAR(3,1))
         ! boundary
         CALL set_param('FLBO',LDOT(1))
         CALL set_param('FUBO',UDOT(1))
         !
         call set_param('FXPR',PRVEC(1,5,1))
         call set_param('FYPR',PRVEC(2,5,1))
         call set_param('FZPR',PRVEC(3,5,1))

The internal variables for the center would appear to be ?FXCE ?FYCE ?FZCE


Rick Venable
computational chemist

Joined: Dec 2018
Posts: 17
J
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OP Offline
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J
Joined: Dec 2018
Posts: 17
thank you very much!


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