pymol-users

[PyMOL] visualize mode

[Command L. <g4c...@gm...>]

Hi all,
when visualizing motion or modes (like NMA), is it possible to show the
velocities as small arrows on all the moving atoms? B-values are not an
option, since I want to see the 3D motion of the atoms. Thanks

Re: [PyMOL] visualize mode

[Osvaldo M. <alo...@gm...>]

Hi,

Do you want to do something similar to porcupine plots? If so, check the
porcupine function in this Ipython notebook
<https://github.com/aloctavodia/SBioA/blob/master/English/04_Comparing_structures.ipynb>
.

Cheers,
Osvaldo.

On Thu, Jun 18, 2015 at 5:07 PM, Command Line <g4c...@gm...>
wrote:

Hi all,
> when visualizing motion or modes (like NMA), is it possible to show the
> velocities as small arrows on all the moving atoms? B-values are not an
> option, since I want to see the 3D motion of the atoms. Thanks
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
​

Re: [PyMOL] visualize mode

[Command L. <g4c...@gm...>]

Hi, that works for me. Albeit I would be more happy if there would be an
option directly inside pymol. Anyway, thanks.

2015-06-18 16:30 GMT-05:00 Osvaldo Martin <alo...@gm...>:

> Hi,
>
> Do you want to do something similar to porcupine plots? If so, check the
> porcupine function in this Ipython notebook
> <https://github.com/aloctavodia/SBioA/blob/master/English/04_Comparing_structures.ipynb>
> .
>
> Cheers,
> Osvaldo.
>
> On Thu, Jun 18, 2015 at 5:07 PM, Command Line <g4c...@gm...>
> wrote:
>
> Hi all,
>> when visualizing motion or modes (like NMA), is it possible to show the
>> velocities as small arrows on all the moving atoms? B-values are not an
>> option, since I want to see the 3D motion of the atoms. Thanks
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
> ​
>

Re: [PyMOL] visualize mode

[Emilio X. E. <emi...@gm...>]

Hi
What about Modevectors?

http://www.pymolwiki.org/index.php/Modevectors

Emilio

On Fri, Jun 19, 2015 at 10:23 AM, Command Line <g4c...@gm...> wrote:
> Hi, that works for me. Albeit I would be more happy if there would be an
> option directly inside pymol. Anyway, thanks.
>
> 2015-06-18 16:30 GMT-05:00 Osvaldo Martin <alo...@gm...>:
>>
>> Hi,
>>
>> Do you want to do something similar to porcupine plots? If so, check the
>> porcupine function in this Ipython notebook.
>>
>> Cheers,
>> Osvaldo.
>>
>> On Thu, Jun 18, 2015 at 5:07 PM, Command Line <g4c...@gm...>
>> wrote:
>>>
>>> Hi all,
>>> when visualizing motion or modes (like NMA), is it possible to show the
>>> velocities as small arrows on all the moving atoms? B-values are not an
>>> option, since I want to see the 3D motion of the atoms. Thanks
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...