Re: [PyMOL] selection help + align question

[Jules J. <jo...@he...>]

Hi,

I've written a script for aligning all structures loaded against your 
structure of choice:


def __init__(self):
     cmd.extend('allalign',allAlign)

def allAlign(id='xxxx'):
     """Aligns all models in a list to the
         specified model where 'xxxx' is the model id you want to 
align 	 all others against. Written by Jules Jacobsen 
(jac...@eb...). Feel free to do whatever you like with this code."""
     id = id.lower()
     pdbList = cmd.get_names()

     for entry in pdbList[:]:
         entry = entry.strip()
         if entry not in id:
             cmd.do('align %s, %s\n'%(entry,id))

     cmd.do('zoom %s'%(id))
     cmd.do('show cartoon, %s'%(id))


just save the section above as a seperate file ie allalign.py and put it 
in the PyMOL\modules\pmg_tk\startup directory.

the script is run using the command 'allalign x' where x is the model 
you wish to align all others against.

This is one of my first teetering steps into Python so if anyone can 
suggest a better way of writing it i'd be keen to hear....

Jules



Douglas Kojetin wrote:
> Thanks for that one; it works as advertised.
> 
> Another question:  if I have 10 different structures read into PyMOL, 
> what is the best (most accurate) method for aligning the structures as 
> an ensemble?  Currently, I'm aligning all to the first structure read in 
> (i.e. 2>1, 3>1, etc.) using a for loop and the 'align' command.  Since 
> the structures have different sequences, I cannot use 'intra_fit', etc., 
> is that right?  Are there any other commands or methods of aligning that 
> might be easy to script?
> 
> Thanks,
> Doug
> 
> 
> On Jan 20, 2005, at 2:12 PM, Warren DeLano wrote:
> 
>> Doug,
>>
>> Setwise logical ANDs and ORs are tricky at first.  In this case, you 
>> want to
>> create a new set that contains atoms in a1 *or* a2.  There aren't any 
>> atoms
>> that are in both a1 and a2 which is why you're ending up with an empty
>> object.
>>
>> create one, a1 or a2
>>
>>> -----Original Message-----
>>> I'm having some problems with selection syntax w/ multiple objects.
>>> I've loaded four different PDB files (in sequence & structure):
>>>
>>>     load 1.pdb, a1
>>>     load 2.pdb, a2
>>>     load 3.pdb, b1
>>>     load 4.pdb, b2
>>>
>>> I wanted to create two new selections:
>>>
>>>     one = a1 & a2
>>>     two = b1 & b2
>>>
>>> I've tried many different combinations of PyMOL selection
>>> syntax, but I cannot get the objects to add to the same
>>> selection (using 'create' or
>>> 'select'):
>>>
>>>     create one, a1 + a2
>>>     create one, a1 and a2
>>>     create one, object a1 + object a2
>>>     create one, a*
>>>
>>>  From what I've read in the manual, I think these commands
>>> are not working because they actually work to select atoms
>>> that are the same between a1 & a2.  The manual says it
>>> 'selects atoms included in both s1 and s2'.
>>>
>>> Any clues or hints?
>>>
>>> Thanks,
>>> Doug
>>>
> 
> 
> 
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