atom.select() residues that are inserts

[Mark Sun]

atom.select() does not appear to enable the selection of a single residue that is an insert.

So selecting just by the chain & resno ends up selecting more than one residue.

[Lars Skjærven]

Hi Mark, Thanks for reporting. We've been discussing if we should include an insert argument in the atom.select function. What do you and others think about the following addition:

> pdb = read.pdb("1fuj")
> pdb = trim(pdb, chain="A")

# inserts at resi 186 (default behavior)
> sele = atom.select(pdb, resno=186, insert=NULL)
> pdb$atom$insert[ sele$atom ]
 [1] NA  NA  NA  NA  NA  NA  NA  "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "B"
[20] "B" "B" "B" "B" "B" "B" "B" "B" "B" "B"

# specify insert = NA
> sele = atom.select(pdb, resno=186, insert=NA)
> pdb$atom$insert[ sele$atom ]
[1] NA NA NA NA NA NA NA

# specify insert = "A"
> sele = atom.select(pdb, resno=186, insert="A")
> pdb$atom$insert[ sele$atom ]
 [1] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A"

[Xinqiu Yao]

I agree. Also, both NA and '' (empty string) can be used for 'non-inserted' residues.

[Lars Skjærven]

so that

atom.select(pdb, resno=186, insert="")

# equals to 
atom.select(pdb, resno=186, insert=NA)

?

[Xinqiu Yao]

Yes, I think so. What do you think?

[Barry Grant]

Sure - sounds good. Though what is the new default for insert then?

[Lars Skjærven]

Updated function in commit https://bitbucket.org/Grantlab/bio3d/commits/c14466a8c7a66adad689e39e26df2b9cfa7e5c4e (sorry I didn't see your comment before pushing the commit).

Default value is insert = NULL which will select both inserts and non-insert residues.

> pdb$atom[ atom.select(pdb, "calpha", resno=186, insert="")$atom, 1:8]
     type eleno elety  alt resid chain resno insert
1260 ATOM  1260    CA <NA>   PRO     A   186   <NA>


> pdb$atom[ atom.select(pdb, "calpha", resno=186, insert=NA)$atom, 1:8]
     type eleno elety  alt resid chain resno insert
1260 ATOM  1260    CA <NA>   PRO     A   186   <NA>


> pdb$atom[ atom.select(pdb, "calpha", resno=186, insert=NULL)$atom, 1:8]
     type eleno elety  alt resid chain resno insert
1260 ATOM  1260    CA <NA>   PRO     A   186   <NA>
1267 ATOM  1267    CA <NA>   ARG     A   186      A
1278 ATOM  1278    CA <NA>   ARG     A   186      B

# same as
> pdb$atom[ atom.select(pdb, "calpha", resno=186, insert=c(NA, "A", "B"))$atom, 1:8]
     type eleno elety  alt resid chain resno insert
1260 ATOM  1260    CA <NA>   PRO     A   186   <NA>
1267 ATOM  1267    CA <NA>   ARG     A   186      A
1278 ATOM  1278    CA <NA>   ARG     A   186      B

> pdb$atom[ atom.select(pdb, "calpha", resno=186, insert=c("A", "B"))$atom, 1:8]
     type eleno elety  alt resid chain resno insert
1267 ATOM  1267    CA <NA>   ARG     A   186      A
1278 ATOM  1278    CA <NA>   ARG     A   186      B

[Xinqiu Yao]

Great. Thanks a lot!

[Mark Sun]

I agree with setting insert = NULL as the default.

Thanks for committing the fix. You guys are super fast at responding to requests / bugs, that it is impressive.