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 <faridoun...@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
------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos. Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
------------------------------------------------------------
This email message, including any attachments, is for the sole use of the
intended recipient(s) and may contain information that is proprietary,
confidential, and exempt from disclosure under applicable law. Any unauthorized
review, use, disclosure, or distribution is prohibited. If you have received
this email in error please notify the sender by return email and delete the
original message. Please note, the recipient should check this email and any
attachments for the presence of viruses. The organization accepts no liability
for any damage caused by any virus transmitted by this email.
=================================
------------------------------------------------------------------------------
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
