Hi,
This mask:
(:11.CD<:5.5)&:Na+
means "Select all residues within 5.5 Ang. of atom CD from residue 11)
AND those residues must be named Na+". If you also want the specified
residue you have to include it in the mask somehow, e.g.
(:11.CD<:5.5)&(:Na+|:11)
Another possibility that might work for you is the 'closest' command
after selecting your Na+ ions as solvent.
Hope this helps,
-Dan
On Wed, Jul 18, 2018 at 1:37 PM, Kenneth Huang <khuang8.student.gsu.edu> wrote:
> Hi all,
>
> I'm seeing some odd behavior with mask when searching for ions around a residue- specifically, when I try to search for Na+ ions around one residue with the command
>
> mask "(:11.CD<:5.5)&:Na+" maskout maskout_E11-Na+.dat
>
> The output looks like it's searching for Na+ to Na+ instead of the specified residue to Na+?
>
> #Frame AtomNum Atom ResNum Res MolNum
> 8 3269 Na+ 210 Na+ 63
> 17 3243 Na+ 184 Na+ 37
> 18 3243 Na+ 184 Na+ 37
> 19 3243 Na+ 184 Na+ 37
> 35 3223 Na+ 164 Na+ 17
>
> Trying a variation of the command by just picking up on anything that isn't protein within a 5.5 radius-
>
> mask "(:11.CD<:5.5)&!:1-104" maskout maskout_E11-Na+.dat
>
>
> Seems to reproduce the exact same results, so I'm not sure if it's actually working as intended, or a bug?
>
>
> Best,
>
> Kenneth
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Received on Fri Jul 20 2018 - 07:30:02 PDT
