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 <faridounnia@gmail.com> 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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