Re: [PyMOL] How to get the coordinates of the center of a group of atoms?
Dear Jason,
Thank you for you quick reply!
And This problem is solved!
Yours,
Zhang Cun
On Thu, Apr 29, 2010 at 9:31 PM, Jason Vertrees
wrote:
> Hi Cun,
>
> That's a good start. Just a couple things needs to be changed.
> First, frames don't track coordinates, states do. Frames are for
> movies; states are for coordinates. Next, instead of using center,
> use the origin command with the state parameter specified. Here's
> example code for 1NMR a multi-state protein, adjust his for your
> application:
>
> python
> cmd.fetch("1nmr", async=0)
> coord=[]
> for i in range(1,cmd.count_states()+1):
> cmd.origin("i. 1-24", state=i)
> coord.append(cmd.get_position())
> print coord
> python end
>
> Cheers,
>
> -- Jason
>
> On Thu, Apr 29, 2010 at 8:58 AM, Cun Zhang wrote:
>> hi,
>> I have a pdb file with serveral frames, I hope to get the trajectory
>> of the center of a selected group of atoms.
>> I use the following commands, but return the same coord.
>>
>> cmd.load("a.pdb")
>> coord=[]
>> for i in range(cmd.count_frames()):
>> cmd.frame(i+1)
>> cmd.center('id 1-24')
>> coord.append(cmd.get_position())
>>
>>
>> What should I do?
>>
>> Thank you!
>>
>> Zhang Cun
>>
>> --
>> Blog: http://www.edwardpku.com/cun
>>
>> --
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
--
Blog: http://blog.4message.net
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Re: [PyMOL] How to get the coordinates of the center of a group of atoms?
Hi Cun,
That's a good start. Just a couple things needs to be changed.
First, frames don't track coordinates, states do. Frames are for
movies; states are for coordinates. Next, instead of using center,
use the origin command with the state parameter specified. Here's
example code for 1NMR a multi-state protein, adjust his for your
application:
python
cmd.fetch("1nmr", async=0)
coord=[]
for i in range(1,cmd.count_states()+1):
cmd.origin("i. 1-24", state=i)
coord.append(cmd.get_position())
print coord
python end
Cheers,
-- Jason
On Thu, Apr 29, 2010 at 8:58 AM, Cun Zhang wrote:
> hi,
> I have a pdb file with serveral frames, I hope to get the trajectory
> of the center of a selected group of atoms.
> I use the following commands, but return the same coord.
>
> cmd.load("a.pdb")
> coord=[]
> for i in range(cmd.count_frames()):
> cmd.frame(i+1)
> cmd.center('id 1-24')
> coord.append(cmd.get_position())
>
>
> What should I do?
>
> Thank you!
>
> Zhang Cun
>
> --
> Blog: http://www.edwardpku.com/cun
>
> --
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
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[PyMOL] How to get the coordinates of the center of a group of atoms?
hi,
I have a pdb file with serveral frames, I hope to get the trajectory
of the center of a selected group of atoms.
I use the following commands, but return the same coord.
cmd.load("a.pdb")
coord=[]
for i in range(cmd.count_frames()):
cmd.frame(i+1)
cmd.center('id 1-24')
coord.append(cmd.get_position())
What should I do?
Thank you!
Zhang Cun
--
Blog: http://www.edwardpku.com/cun
--
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