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ardie Offline OP
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Dear all,
Maybe this is a very basic question. How to show the index of the atoms in selection?
For example, if I define atomcore by:
define atomcore sele .byres. resname prot .around. 4.0 end

Can charmm print the atom index in atomcore? Thank you.

Ardie.

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rmv Online Content
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I'm not sure about how to print the index itself. I'm fairly certain the indices will be in PSF order, however. The command

COOR PRINT SELE ATOMCORE END

should print the atoms in the correct order.


Rick Venable
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ardie Offline OP
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Thanks Rick, "COOR PRINT SELE ATOMCORE END" dose work. It shows coordinates in such format:

992 99 TYR N -1.22150 9.15371 14.61750 PROT 75 21.53000
993 99 TYR HN -2.06295 9.33654 14.11498 PROT 75 0.00000
994 99 TYR CA 0.02250 9.03071 13.82950 PROT 75 25.99000
995 99 TYR HA 0.52829 8.13688 14.16273 PROT 75 0.00000
996 99 TYR CB -0.23050 8.94971 12.29150 PROT 75 16.26000
997 99 TYR HB1 0.69665 9.20875 11.73707 PROT 75 0.00000
998 99 TYR HB2 -1.05326 9.63785 12.00233 PROT 75 0.00000
999 99 TYR CG -0.63250 7.54771 11.90750 PROT 75 23.92000
1000 99 TYR CD1 0.17850 6.46471 12.21150 PROT 75 13.64000
1001 99 TYR HD1 1.11792 6.62886 12.71832 PROT 75 0.00000


From the first column, I can get the wanted indices.

Thanks again.


Ardie

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Those are the sequential atom numbers, which can be used with the BYNUM atom selection. There is also the .SUBSET. feature, which uses the "index" within the selection, such that the following are equivalent--

SELECT BYNUM 992 END
SELECT ATOMCORE .SUBSET. 1 END


Rick Venable
computational chemist


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