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Define selection of atoms with WMAIN
#37723 11/25/19 11:01 AM
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pmj Offline OP
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Hi!

I would like to add weighting to selection of the atoms, but I am not sure how to do it.

I have tried with:

define fit sele .byres. prop wmain .eq. 1 .and. .not. hydrogen end

define fit sele .byres. (prop wmain .eq. 1 .and. .not. hydrogen) end

define fit sele (.byres. (prop wmain .eq. 1 )) .and. .not. hydrogen end

But none of the atoms have been selected.

Thank you

Re: Define selection of atoms with WMAIN
pmj #37724 11/25/19 12:20 PM
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These are all syntactically correct.

Do you have heavy atoms with 1(exactly) in the WMAIN array?
You can check with:
SCALar WMAIN SHOW SELECT .NOT. HYDROGEN END

If you suspect a rounding error you can try with .AE. instead of .EQ. in you selection.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Define selection of atoms with WMAIN
lennart #37725 11/25/19 01:27 PM
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pmj Offline OP
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Dear Lennart,

it was not exactly 1 so I suppose that is why it could not be read.

What I would also like to understand what does WMAIN column precisely represents and how is it obtained? I have never used it before.

Thanks

Re: Define selection of atoms with WMAIN
pmj #37726 11/25/19 02:38 PM
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I think it could be read, but the values were not equal to 1...

WMAIN is used for a variety of things. When you read a PDB file the B-factors are read into WMAIN. Several CHARMM commands put results in WMAIN or use WMAIN as a weighting array (this is then mentioned in the documentation); the user can access it e.g. using SCALar commands.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  BRBrooks, lennart, rmv 

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