pymol-users

[PyMOL] how to count all the Polar contacts

[天元 <422...@qq...>]

Dear PyMol users! I'm analysing polar contacts by "preset:technical". I got so many yellow bar measurements that I can't count the number.  IS there any else way to count the number of all polar contacts ? Thanks for help, Merlin

Re: [PyMOL] how to count all the Polar contacts

[Sampson, J. <Jar...@ny...>]

Hi Merlin -

Try limiting the distances shown to those between atoms in specific selections using the `distance` command.  For example, to show H-bonds to solvent, disable the “my_obj_pol_conts” object created by the technical preset and use the command:

distance my_dist, my_obj and not solvent, my_obj and solvent, cutoff=3.5

Make sure to specify a cutoff or you’ll get every pair of polar atoms between your selections.

Hope that helps.

Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On May 27, 2014, at 3:33 AM, 天元 <422...@qq...<mailto:422...@qq...>> wrote:


Dear PyMol users!


I'm analysing polar contacts by "preset:technical". I got so many yellow bar measurements that I can't count the number.

IS there any else way to count the number of all polar contacts ?

Thanks for help,


Merlin

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Re: [PyMOL] how to count all the Polar contacts

[T. N. <tn...@ca...>]

Hi,

And you can use get_raw_distances script at
http://www.pymolwiki.org/index.php/Get_raw_distances
to get detailed information about contacts.

Best regards,

Takanori Nakane

On 2014-05-27 15:24, Sampson, Jared wrote:
> Hi Merlin -
> 
> Try limiting the distances shown to those between atoms in specific
> selections using the `distance` command. For example, to show H-bonds
> to solvent, disable the “my_obj_pol_conts” object created by the
> technical preset and use the command:
> 
> distance my_dist, my_obj and not solvent, my_obj and solvent,
> cutoff=3.5
> 
> Make sure to specify a cutoff or you’ll get every pair of polar
> atoms between your selections.
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
>  --
>  Jared Sampson
>  Xiangpeng Kong Lab
>  NYU Langone Medical Center
>  http://kong.med.nyu.edu/ [2]
> 
> On May 27, 2014, at 3:33 AM, 天元 <422...@qq...> wrote:
> 
>> Dear PyMol users!
>> 
>> I'm analysing polar contacts by "preset:technical". I got so many
>> yellow bar measurements that I can't count the number.
>> 
>> IS there any else way to count the number of all polar contacts ?
>> 
>> Thanks for help,
>> 
>> Merlin
>> 
> ------------------------------------------------------------------------------
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>> companies.
>> Download your FREE open source Enterprise Search Engine today!
>> Our experts will assist you in its installation for $59/mo, no
>> commitment.
>> Test it for FREE on our Cloud platform anytime!
>> 
> http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk_______________________________________________
>> [1]
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:
>> http://www.mail-archive.com/pym...@li...
> 
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> [1]
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