Hi Jason,
sorry for last message ..
To label a residue by an mdo command cmd.mdo(int frame, string command) I can
pass as command one among these strings:
1) 'label %s, "%s %s"' % (..)
works fine but prints a message (I don't want) to the output window
1+) 'label %s, "%s %s", quiet=1' % (..)
doesn't work, I get a
SyntaxError: can't assign to literal
2) 'cmd.label("%s", "\'%s %s\'")' % (..)
works fine and doesn't print a message to the output window (is my
choise)
2+) 'cmd.label("%s", "\'%s %s\'", "quiet=1")' % (..)
doesn't work, pyMOL crashes
A similar behaviour I've got about alter_state and cmd.alter_state()
So the 'label ..' command appears not having a 'quiet' option and appears not
being the same than 'cmd.label ..'
This was strange to me and (hoping I didn't make a mistake in the script) I
was curious to know the raison of this behaviour if simple to tell. If not,
please don't care: I solved (thanks to you) my problem and so you can skip my
request.
Thanks a lot.
Cheers
Roberto
>----Messaggio originale----
>Da: jason.vertr...@schrodinger.com
>Data: 01/03/2011 18.29
>A: "rv...@libero.it"<rv...@libero.it>
>Ogg: Re: Re: [PyMOL] labeling by a pseudoatom
>
>Hi Roberto,
>
>I'm not sure what you're asking here. Can you please rephrase this.
>
>Also, are you trying "quite=1" or "quiet=1".
>
>Cheers,
>
>-- Jason
>
>On Tue, Mar 1, 2011 at 2:17 AM, rv...@libero.it <rv...@libero.it> wrote:
>> 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
>>>
>>
>>
>>
>
>
>
>--
>Jason Vertrees, PhD
>PyMOL Product Manager
>Schrodinger, LLC
>
>(e) jason.vertr...@schrodinger.com
>(o) +1 (603) 374-7120
>
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