[Chimera-users] Combine atom-spec non-alphanumeric no-nunderscore character error

[Ahmad Khalifa]

Thanks Elaine, but after I combine using the syntax that you mentioned, I
get the entire molecule and not the chains that I selected.

I also tried selecting the that chains that I want to combine from
different models, and used "combine sel", I got the same result.

On Wed, Jan 30, 2019 at 6:21 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ahmad,
> Commas separate items at the main symbol level # (model) : (residue) @
> (atom).  They cannot be used to separate items at the sub-levels with dots
> after those symbols   #. (submodel)  :. (chain ID)  @.  (atom alternate
> location).
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy
> >
>
> I agree it can be confusing.  In our next-gen program ChimeraX we only use
> the dot for submodels, and chain has its own symbol.
> Best,
> Elaine
>
> > On Jan 30, 2019, at 2:18 PM, Ahmad Khalifa <underoath006 at gmail.com>
> wrote:
> >
> > Thanks, I will try that, but quickly, I often use commas with selection
> and it works fine, what's the difference between the commas and the colons?
> >
> > On Wed, Jan 30, 2019 at 4:03 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Ahmad,
> > The specification is wrong for two reasons:
> > (1) need colon instead of comma, for example #1:.k:.e
> > (2) you would need to either remove the space between the two models or
> put quotes around the whole thing like "#1:.k:.e #2:.k:.e"
> >
> > However, more important is that “combine” will include all the atoms in
> the whole models even if you only specify some chains. It says this in the
> second paragraph:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
> >
> > So what you really wanted to do is to delete all the other atoms before
> you combine the two models, something like
> >
> > select #1:.k:.e #2:.k:.e
> > delete ~sel
> > combine #1,2
> >
> > (also make sure you really have models #1 and #2, since the first model
> is #0 and you might need to use #0 and #1 instead… check in the Model
> Panel, opened from Favorites menu)
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Jan 30, 2019, at 11:23 AM, Ahmad Khalifa <underoath006 at gmail.com>
> wrote:
> > >
> > > I'm trying to combine a few chains from different models. I'm using:
> combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure
> why my selection isn't working!
> > >
> > > Regards.
> >
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>
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