Re: [PyMOL] using a pseudoatom for distance measurement

[M. F. <far...@gm...>]

Thanks a lot for the tip and explaining the whole thing, Jared. I learned a
lot from that. It worked but here is why I had a problem at the beginning
(and tried the command I emailed), still same problem persists.

I had tried similar command on one of the models after splitting the pdb
file (split_states pdbfile, ) and it was not working.
>split_states pdbfile,
>pseudoatom test, pdbfile_0001 and chain A and resi 100 and n.
cg+cd1+ce1+cz+ce2+cd2, color=tv_blue


Now, I tried exactly what you mentioned. After splitting the states it
doesn't work, but when I don't do split_states, the same command works and
creates a pseudoatom. The problem is that the NMR structure I have been
doing split_states on is an average structure of 20 models. So, I need to
create the pseudoatom on one of the 20 structure models ( the closest to
the average or the lowest energy). It is not a big deal for now because for
these two residues all the 20 structure are very similar but I still wonder
why isn't it possible!

I mean it would make more sense that the command doesn't work on the
average structure, because it doesn't refer to a real coordinate in the
file and it can take any of the twenty models, but when it knows which
model to take, it is more probable to work because it refers to the right
coordinates. Any comments on that?

Cheers
Mary


On Mon, May 5, 2014 at 4:17 PM, Sampson, Jared <Jar...@ny...>wrote:

>  Hi Mary -
>
>  There are a couple problems here.  First, you’re giving the pseudoatom
> command a positional argument out-of-order (and after keyword parameters).
>  Keyword parameters can appear in any order, but only if you use the
> keyword.  Otherwise, you must list them in the order specified by the
> function.  So, you either need to use the keyword and enclose the selection
> in quotes (selection=“n. …”) or simply move it to its proper position, like
> this:
>
>  pseudoatom test, n. cg+cd1+ce1+cz+ce2+cd2, resi=100, color=tv_blue
>
>
>  For the full order of arguments, see
> http://www.pymolwiki.org/index.php/Pseudoatom or type `help pseudoatom`
> on the PyMOL command line.
>
>  Second, your current selection is going to use any atom named
> cg+cd1…etc. in the entire session, not just in your single Phe residue.
>  This is because the resi=100 and color=tv_blue are used to determine the
> properties of the new pseudoatom, and not to determine or refine the
> selection.  If you want to use the ring of Phe 100 only, the selection
> argument needs to include that information.  If you have more than one
> object or chain that includes resi 100, you will also need to specify that.
>
>  So I’m guessing what you probably want is something along the lines of
> (replacing “myobject” and “A” with appropriate values):
>
>  pseudoatom test, myobject and chain A and resi 100 and n.
> cg+cd1+ce1+cz+ce2+cd2, color=tv_blue
>
>
>  which will create a tv_blue-colored pseudoatom in the center of the ring
> of residue 100.
>
>  Hope that helps.
>
>  Cheers,
> Jared
>
>  --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
> On May 4, 2014, at 2:12 PM, M. Faridounnia <far...@gm...> wrote:
>
>   Hi there,
>
> I want to measure the distance and angle between an aromatic ring
> (phenylalanin and a residue backbone) like this:
> http://www.pymolwiki.org/index.php/File:Pseu1.png
>
>  I learned from here that I need to make a pseudoatom but I cannot make it
> work.
>
>  I tried
> pseudoatom test, resi=100, color=tv_blue, n. cg+cd1+ce1+cz+ce2+cd2
>
>  and some other ways! I don't know how should I choose the write atoms
> and make the pseudoatom. After this probably distance and angle measurement
> would be straightforward.
>
>  Best regards
> Mary
>
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