Hi Jason,
thanks for your hints.
I tried. All fine:
cmd.alter_state doesn't message the user also without a quite=1 option.
cmd.label makes the same.
I used (as suggested)
cmd.alter_state
cmd.label
'cmd.alter_state' appears not be the same than 'alter_state'
and so
'cmd.label' appears not be the same than 'label'.
I've got errors when I setted quite=1 options in
'alter_state' and in 'label'
So thanks for your hints.
Cheers
roberto
Tjha
alter_state
and
label
instead message the
the output window and don't suppor
If I set a quite=1 option in
alter_state
label
I get errors.
.. but probably you already know.
>----Messaggio originale----
>Da: jason.vertr...@schrodinger.com
>Data: 28/02/2011 6.36
>A: "rv...@libero.it"<rv...@libero.it>
>Cc: <pymol-users@lists.sourceforge.net>
>Ogg: Re: [PyMOL] labeling by a pseudoatom
>
>Hi Roberto,
>
>It's nice to see people learning how to script and putting PyMOL
>through its paces.
>
>> trying to use a pseudoatom as label I met several problems:
>>
>> 1) How to move the label (pseudoatom) to a target residue?
>> Is there a simple command to do?
>
>The easiest way would be to get the coordinates of the target residue,
>I'd choose the alpha carbon (replace "X" with your residue number):
>
># query residue X's alpha carbon, store the position in targetResPosition
>
>targetResPosition = cmd.get_atom_coords("resi X and n. CA")
>
># next, just assign that position to the pseudoatom:
>
>cmd.alter_state(1, "myPseudoAtom", "(x,y,z) = targetResPosition")
>
>
>> 2) How to change the label without messaging the user?
>> The 'label' command appears not have a 'quiet' option.
>
>This is interesting, and not what I'd expect from PyMOL, however it works:
>
># make a new text label as a Python string
>
>newLabel = "New Pseudoatom label"
>
># assign that label
>
>cmd.label("myPseudoAtom", "newLabel")
>
>Interestingly, PyMOL picks up the 2nd parameter as a variable name.
>Also, label does have a quiet option:
>
># assign that label, quietly
>
>cmd.label("myPseudoAtom", "newLabel", quiet=1)
>
>
>
>> 3) (less important) How to hide the pseudoatom?
>> I wish not have the pseudoatom listed among models in the GUI panel.
>
>To hide a pseudoatom (just the + symbol):
>
>hide nonbonded, myPseudoAtom
>
># or, just hide the labels
>
>hide labels, myPseudoAtom
>
># or, hide all
>
>hide everything, myPseudoAtom
>
>
>> 4) (less important) I need to execute all these operations by script (mdo
>> commands during a movie)
>> To simplify the movie I wish use only one mdo command
>>
>> def doAll()
>> .. all my script here ..
>>
>> extending the cmd just before the movie start
>>
>> cmd.extend('doAll', doAll)
>>
>> and clearing the cmd just at the end of the movie but I don't know
>> how.
>> Is there a way to clear a command?
>
>The mdo command takes a frame number and a string. For that frame it
>stores the string, and then applies it prior to setting the scene.
>PyMOL overwrites the string each time, so you need to cache all your
>commands for one frame and use the mdo command once per fram. Create
>a small class that stores all the mdo commands as one string. Then,
>when you want those command executed ask the class to call mdo on the
>given frame, using that long string. That might look something like:
>
>
>mcache 50, "show sticks"
>
>mcache 50, "as spheres, het"
>
>mcache 50, "show surface, poly within 10 or org"
>
>...
>
>store scenes, plan movie, etc.
>
>...
>
>mCacheApply 50
>
>I made something similar for making movie fades, just cache the string
>an apply it when necessary.
>
>Cheers,
>
>-- Jason
>
>--
>Jason Vertrees, PhD
>PyMOL Product Manager
>Schrodinger, LLC
>
>(e) jason.vertr...@schrodinger.com
>(o) +1 (603) 374-7120
>
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