[chimerax-users] listing all-by-all atom distances

Tue Jun 15 11:44:20 PDT 2021

Yes! Exactly !
Thank you

El mar, 15 de jun. de 2021 a la(s) 15:38, Elaine Meng (meng at cgl.ucsf.edu)
escribió:

> Hi Juliana,
> Sure, you can do that, and it's not necessary to bother with selecting or
> naming the selection.  You can specify using only the atom-atom center
> distances (instead of VDW overlap) with the "distanceOnly" option of the
> ChimeraX contacts command.  Example:
>
> contacts  (#1/B:19 & sidechain) restrict (#1/A & sidechain) distanceOnly 6
> log true
>
> See options in the "contacts" help
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
>
> Yes being more specific when you ask a question always helps!
>
> I hope this was what you needed,
> Elaine
>
> > On Jun 15, 2021, at 11:12 AM, Juliana Glavina via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Thank you Elaine !
> > Sorry I didn't cc the list before.
> >
> > I think I need to be a little bit more specific. I am doing the
> following:
> >
> > open 1ycr
> > name frozen pocket1 (#1/B:19 & sidechain) @<6 & (#1/A & sidechain)
> >
> > and I want to list the distances between the atoms of sel1 and sel2 that
> are lower than 6A
> > I could use contacts, but it includes things that are over 6A.
> >
> > Thank you!
> > Juliana
> >
> > El mar, 15 de jun. de 2021 a la(s) 14:59, Elaine Meng (meng at cgl.ucsf.edu)
> escribió:
> > Of course, if you only want to use alpha-carbons instead of all atoms of
> all residues, you could define the atom sets that way, e.g.
> >
> > name frozen blah #1/A:100-200 at ca
> > contacts #1/A:55 at ca restrict blah overlap -1000 log true
> >
> > Also, I was using named selection because you asked about it.  You do
> not need to use a named selection.  Instead you can just specify both atom
> sets in "contacts," e.g.
> >
> > contacts #1/A:55 at ca restrict #1/A:100-200 at ca overlap -1000 log true
> >
> > Elaine
> >
> > > On Jun 15, 2021, at 10:48 AM, Elaine Meng via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> > >
> > >
> > >> On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina at gmail.com>
> wrote:
> > >>
> > >> Hi Elaine,
> > >> I am trying to calculate the distance between one residue and a set
> of residues (within a name selection). I couldn't do this in Chimera either
> and I couldn't find the answer online.
> > >> Thanks!
> > >> Juliana
> > >
> > > Hi Juliana,
> > > (We recommend using the chimerax-users address CC'd here for
> questions, so that the Q & A will be archived and searchable.)
> > >
> > > One way to do it in ChimeraX is with the "contacts" command or
> Contacts tool.  In this case you aren't necessarily using it to find
> contacts, but instead to measure and list atom-atom distances.
> > >
> > > You say "residues" but really all the distances are measured from atom
> to atom. You will get all by all distances between two sets of atoms, where
> the first set is your first residue and the second set is all the residues
> in your named selection.
> > >
> > > In ChimeraX, you can name the current selection or some other
> specification with the "name" command.  To name the current selection
> "blah" it would be command:
> > >
> > > name frozen blah sel
> > >
> > > See "name" help:
> > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html>
> > >
> > > Then if you want to measure all atom-atom distances between (1) atoms
> in residue 55 of chain A of model 1 and (2) your named selection "blah" and
> show them in the Log, you could use a command something like
> > >
> > > contacts #1/A:55 restrict blah overlap -1000 log true
> > >
> > > The large negative overlap value is used to force measuring all the
> distances even if the atoms are 1000 Angstroms apart, instead of the usual
> behavior of finding only the contacts.  The Log will have lines like the
> following, where the last column is the distance between atomic centers:
> > >
> > > 1728 contacts
> > >    atom1          atom2       overlap  distance
> > > /A BGC 310 C6  /A TYR 10 CE2    0.018    3.622
> > > /A BGC 310 O6  /A HIS 152 NE2   -0.134    2.834
> > > /A BGC 310 O4  /A TRP 183 CG    -0.202    3.272
> > > /A BGC 310 C3  /A TRP 183 CE3   -0.253    3.893
> > > /A BGC 310 C2  /A PHE 16 CD1    -0.323    3.963
> > > /A BGC 310 C5  /A HIS 152 NE2   -0.360    3.880
> > > /A BGC 310 C6  /A HIS 152 NE2   -0.366    3.886
> > > /A BGC 310 O4  /A TRP 183 CD2   -0.424    3.494
> > > /A BGC 310 C5  /A TRP 183 CE2   -0.429    3.919
> > > /A BGC 310 O6  /A HIS 152 CD2   -0.490    3.710
> > > /A BGC 310 C3  /A TRP 183 CZ3   -0.495    4.135
> > > /A BGC 310 O4  /A TRP 183 CD1   -0.499    3.719
> > > /A BGC 310 O6  /A HIS 152 CE1   -0.556    3.776
> > > /A BGC 310 C5  /A TRP 183 NE1   -0.596    4.116
> > > [...]
> > >
> > > The lines are in order of largest VDW overlap which is similar to
> shortest distance but not exactly the same.  If you save to text file you
> can then sort by column, for example, by the second residue number to group
> those together, or by the distance.
> > >
> > > The "contacts" command has a lot of options including saving results
> to text file, as detailed here:
> > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
> > >
> > > You can do the same thing in Chimera, name selection and use
> "findclash" but the exact commands and their syntax are slightly different.
> > >
> > > I hope this helps,
> > > Elaine
> > >
>
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