you can also do this with a chempy model, takes 2 seconds on my machine.
python
from pymol import cmd
from chempy import Atom, models
model = models.Indexed()
for x in range(20):
for y in range(20):
for z in range(20):
atom = Atom()
atom.coord = [x,y,z]
model.add_atom(atom)
cmd.load_model(model, 'fake')
python end
Cheers,
Thomas
Jason Vertrees wrote, On 12/08/10 18:32:
> Hi Björn,
>
> If you need that many points, then I suggest you fake a PDB or XYZ
> file. If you could make the 5670 points in PyMOL, then it'll probably
> be easiest to modify the script to simply write out a PDB/XYZ file and
> then load that file. Here's some template code to get you started.
> This code will create an XYZ file of 8000 carbons in a 20x20x20 box.
> It takes about 0.1s to run on my machine. Modify as necessary.
>
>
> # in PyMOL, start a python block
> python
>
> # no boding on load
> cmd.set("connect_mode", 1)
>
> # open a file
> f = open("fake.xyz", 'wb')
>
> # write a tiny header
> f.write("8000\n");
> f.write("FAKE\n")
>
> # write the 20x20x20 box
> i=0
> for x in range(20):
> for y in range(20):
> for z in range(20):
> f.write("C\t%f\t%f\t%f\n" % (x,y,z))
> f.close()
>
> # load the fake XYZ file
> cmd.load("fake.xyz")
>
> # end the python block
> python end
>
> Cheers,
>
> -- Jason
>
>
>
>
> On Wed, Dec 8, 2010 at 3:59 AM, Bjoern-oliver Gohlke
> <[email protected]> wrote:
>> Hi Jason,
>>
>> at first thanks for your answer.
>> I know the generating of individual object. But I need all pseudoatoms in
>> one object. Is their any way to merge the individual objects into one??
>> Hope for answer.
>>
>> kind regards
>> Björn
>>
>>
>> p.s. In this way:
>> cmd.pseudoatom('grid', pos=[i,j,k], color='white')
>> the calculation of 5670 gridpoints needs ca. 8hours
>>
>> Zitat von Jason Vertrees <[email protected]>:
>>
>>> Hi Björn,
>>>
>>> The command you're issuing,
>>>
>>>> cmd.pseudoatom('grid', pos=[i,j,k], color='white')
>>> is asking PyMOL to create an object called 'grid' -- which on
>>> subsequent calls will just append the pseudoatoms to original 'grid'
>>> object created from the first call. If you want, say 10, individual
>>> objects then please try specifying original objects names:
>>>
>>> for x in range(10):
>>> cmd.pseudoatom('grid'+str(x), pos=[i,j,k], color='white')
>>>
>>> This will create objects "grid0", "grid1", ..., "grid9" as separate
>>> objects.
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>>
>>> On Fri, Dec 3, 2010 at 4:11 AM, Bjoern-oliver Gohlke
>>> <[email protected]> wrote:
>>>> Hi,
>>>>
>>>> I would like to generate a bounding box (grid) of pseudoatoms.
>>>> I do this by the following command:
>>>>
>>>> cmd.pseudoatom('grid', pos=[i,j,k], color='white')
>>>>
>>>> My problem is, that from step to step, the algorithm slow down. I
>>>> think that in each step pymol build up a new object. But he should
>>>> only expand the object with the next pseudoatom.
>>>> Know anybody a way to fix this problem?
>>>>
>>>> Thanks,
>>>> Björn
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>
>>>
>>> --
>>> Jason Vertrees, PhD
>>> PyMOL Product Manager
>>> Schrodinger, LLC
>>>
>>> (e) [email protected]
>>> (o) +1 (603) 374-7120
>>>
>>
>
>
>
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