variables from "coor helix"

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variables from "coor helix" #38578 12/16/22 02:45 AM
Joined: Dec 2018 Posts: 17 J jamesmao OP Forum Member
OP jamesmao Forum Member 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

Re: variables from "coor helix"

jamesmao #38579 12/16/22 02:55 PM

Joined: Sep 2003

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39 59 56 N, 77 06 07 W

rmv

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rmv

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Joined: Sep 2003

Posts: 8,650

Likes: 26

39 59 56 N, 77 06 07 W

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

Re: variables from "coor helix" jamesmao #38580 12/16/22 03:53 PM
Joined: Dec 2018 Posts: 17 J jamesmao OP Forum Member
OP jamesmao Forum Member J Joined: Dec 2018 Posts: 17	thank you very much!

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