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

[Elaine Meng]

Hi Ahmad,
In my first reply (and in the manual page), I already told you that “combine” would give the whole models.

In the second part of that reply, I gave commands to select and DELETE the unselected parts before you use “combine.”

See previous reply below or at <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-January/015390.html> 

Best,
Elaine

> On Feb 1, 2019, at 7:27 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> 
> 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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