puzzle: How to select all residues not containing C-beta atoms?

[Oliver Beckstein]

Hi,

I have a purely academic question: how do I neatly select "all residues that do not contain a C-beta atom" using MDAnalysis?

For standard proteins these are the Gly.

The best I could come up with was "byres (name CA and not (around 1.7 name CB))" but that includes the fragile fudge of an estimated maximum bonding distance of ~1.7 Å between CA and CB (which is larger than the ~1.4 Å C-C I would have expected):

from MDAnalysis import Universe
from MDAnalysis.tests.datafiles import PSF, DCD
u = Universe(PSF, DCD)

sel = u.selectAtoms("byres (name CA and not (around 1.7 name CB))")
ref = u.selectAtoms("resname GLY")

sel.residues[:] == ref.residues[:]

#>>> True

Does anyone have any better ideas; the naive

u.selectAtoms("not name CA").residues

does not work because you pick up ALL other atoms (e.g. the N in Gly) and hence you get all residues.

(As a curious side observation: sel[:] == ref[:] returns False.)

Oliver

--
Oliver Beckstein * orbe...@gmx.net
skype: orbeckst * orbe...@gmail.com

[Elizabeth Denning]

Hi Oliver,

why not just say "protein and not resname GLY" ?
Maybe I'm misunderstanding something subtle but that seems the easiest
way to me.

~Elizabeth

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[Oliver Beckstein]

On 24 Apr, 2013, at 09:56, Elizabeth Denning wrote:

> Hi Oliver,
>
> why not just say "protein and not resname GLY" ?
> Maybe I'm misunderstanding something subtle but that seems the easiest way to me.

As I said it really is an academic question and is more about how expressibe is the selection syntax that we have.

(But maybe I want to apply this to strange residues or non-protein residues (e.g. all lipids that do not contain N) where I don't know the answer beforehand.)

Oliver

[Naveen Michaud-Agrawal]

Unfortunately, I think you need disjunction on the level of residues, so you could do something like:

sel = u.selectAtoms("(byres name CA) and not (byres name CB)")

but that would give you the disjunction of those two sets of atoms. Does this work?:

sel = u.selectAtoms("byres ((byres name CA) and not (byres name CB))")

Naveen

-----------------------------------
Naveen Michaud-Agrawal

[Naveen Michaud-Agrawal]

or maybe this:

u.selectAtoms("(byres name CA) and not (byres name CB)").residues

--
-----------------------------------
Naveen Michaud-Agrawal

[Oliver Beckstein]

Hi Naveen,

both

u.selectAtoms("byres ((byres name CA) and not (byres name CB))")

u.selectAtoms("(byres name CA) and not (byres name CB)").residues

work. Good idea to do this at the residue level.

(Playing with the selections also compelled me to file Issue 135...)

Thanks,
Oliver

p.s.: see http://becksteinlab.physics.asu.edu/pages/courses/2013/SimBioNano/15/MDAnalysis/first_steps.html#exercises-2 for where your solution ended up...

[Naveen Michaud-Agrawal]

By the way, exercise 1 on that page has a typo - 

"e.g. 150-160) are missing from the structure then the selection will simply give you residues 100-149 and 151-200"

should be

"e.g. 150-160) are missing from the structure then the selection will simply give you residues 100-149 and 161-200"

Also, you should make solutions hidden by default with the ability to click them open :)

I've attached a modified version of that html file - see what i did with exercise 2.1 and 2.2

On Wed, Apr 24, 2013 at 4:15 PM, Naveen Michaud-Agrawal <naveen.mic...@gmail.com> wrote:

Cool, glad to see MDAnalysis is still going strong! :)

--
-----------------------------------
Naveen Michaud-Agrawal

[Oliver Beckstein]

On 24 Apr, 2013, at 13:35, Naveen Michaud-Agrawal wrote:

> By the way, exercise 1 on that page has a typo -
>
> "e.g. 150-160) are missing from the structure then the selection will simply give you residues 100-149 and 151-200"
>
> should be
>
> "e.g. 150-160) are missing from the structure then the selection will simply give you residues 100-149 and 161-200"

Thanks, corrected.

>
> Also, you should make solutions hidden by default with the ability to click them open :)
>
> I've attached a modified version of that html file - see what i did with exercise 2.1 and 2.2

That's a very good idea – ideally implemented as a new role in sphinx :-). Maybe one could use some of the stuff mentioned in http://stackoverflow.com/questions/8151729/how-to-show-and-hide-code-in-sphinx-doc