Hi,
I just wanted to chime in and add to what Folmer said.
Your selection syntax was close, but not quite correct, you are missing
a slash.
Following you example, you would do /2hyy//A/600 where 600 is the
residue id of the ligand.
But in general, I would recommend using the syntax that Folmer suggested
wherein you spell out the selections. In addition to being more
readable, you can make more powerful and complex selections.
To answer your second question, you can check out the PyMOL Cheat Sheet
which has a nice summary of commands. It is available here:
http://www.pymolwiki.org/index.php/CheatSheet
It's not necessarily completely up to date though. The wiki page
indicates that it was last updated in 2008. Perhaps one of the devs
could comment on any changes.
Matt Baumgartner
On 01/06/2015 04:34 AM, Folmer Fredslund wrote:
Hi Brenton,
It seems 2HYY only has that one (type of) ligand present?
so:
fetch 2hyy
as cartoon
show sticks, organic
color black, elem c and organic
remove not chain a
gives me a cartoon representation of the protein, with a stick
representation of the ligand. There are 4 copies of the complex in the
asymmetric unit and they have chain ID's A-D, so the last command
removes all atoms except the ones in chain a.
I am personally more comfortable with this kind of selections, instead
of the 2hhy/something/something/something
In case you want to keep all molecules, but just select on of the
ligands, you could do something like:
select ligandA, organic and chain a and resname STI
Hope this helps,
Folmer
2015-01-06 9:40 GMT+01:00 Brenton Horne <brentonho...@ymail.com
<mailto:brentonho...@ymail.com>>:
Hi,
I know I must be getting annoying, although I must say this
mailing list and its users have been very helpful for me so thank
you all. My question this time is how do I select specific
ligands? Like I am using PDB ID 2HYY and I'd like to set the
imatinib (STI600) ligand as the only visible ligand, plus I'd like
to colour it according to the CPK scheme, except with carbons
coloured black. Now I've tried:
select 2hyy/A/STI
based on the Selection Algebra
<http://pymolwiki.org/index.php/Selection_Algebra> page on PyMOL
Wiki but this returned the result:
Selector: selection "sele" defined with 0 atoms.
ps. is there are any PDF document showing complete up-to-date
command-line syntax for PyMOL because I think this will really
help me. PyMOL Wiki I find generally only gives a snippet of the
command-line syntax for a given topic. Plus I generally find the
really general format of the syntax (e.g.,
show reprentation [,object]
) with the square brackets PyMOL sometimes shows is confusing to
me, unless it's accompanied by an example of how that code appears
for a specific example.
Thanks for your time,
Brenton
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