On Fri, Oct 8, 2010 at 1:04 PM, Tyler Glembo <tglembo.asu.edu> wrote:
> Thank you for the advice. I used ambmask with the ":GLY.CA|.CB" mask and
> it
> chose all the correct atoms. However, the output from ptraj is still:
>
> Atom selection follows :1-19.CA
>
> ,:20-40,CA,:41-55,CA,:56-81,CA,:82-90,CA,:91-151,CA,:152-170,CA,:171-178,CA,:179-203,CA,:204-239,CA
> :240-249,CB
>
> Is there a known issue with ptraj's output of what atoms are masked? Is
> there a good way within ptraj to see whether or not it is masking the
> correct atoms besides the simple output?
>
>
The output should mean :1-19.CA,:20-40.CA,:41-55.CA, etc. Generally
speaking, if you see an atom name without an "." but a "," in front of it,
try to replace that "," with ".". You can also check to see if the number of
atoms conforms with it. Hopefully this bug will be fixed soon.
> > > > >
> > > > > ":GLY .CA | !:GLY .CB"
> > > > >
> >
> "(:ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PRO,PHE,SER,TYR,THR,TRP,VAL
> > > > > .CB) & (:GLY .CA)"
> > > > >
> > > > > However, the output that I get from ptraj is as follows:
> > > > >
> > > > > Atom selection follows :1-19.CA
> > > > >
> >
> ,:20-40,CA,:41-55,CA,:56-59,CB,:61-81,CA,:82-90,CA,:91-151,CA,:152-170,CA,:171-178,CA,:179-197,CB
> > > > > :199-203,CA,:204-239,CA,:240-246,CB,:248,CB,:249.CB
> > > > >
>
It seems a little wierd for me that your first two atom masks reported the
above atom selection.
I think the first atom mask ":GLY .CA | !:GLY .CB" means ":GLY.CA| !(:GLY.CB)",
which is just " !(:GLY.CB)". That should be all atoms except ":GLY.CB". You
could in stead use ":GLY.CA| !:GLY&.CB", which means "(:GLY.CA) | ((!:GLY) &
(.CB))". Please note that whitespaces are OK as long as the whole atom mask
is enclosed by a pair of quotation marks which is required if whitespaces
are included. Whitespaces will be stripped before mask interpretation.
Your second atom mask should yield no atoms because the "&" means
intersection. If you replace the "&" with a "|", you should get what you
want.
Best,
Jianyin Shao
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Received on Fri Oct 08 2010 - 21:00:03 PDT
