Re: [PyMOL] Is there a way to "count" hydrogen bond interactions?

Hi Celestine,

Did you run the "get_raw_distances.py" script first? You can do that by:

run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py

Or better: Download it to your computer and run it from there ("run" command or "File > Run Script..." from the menu).

After running the script, you can use the "get_raw_distances" command.

Cheers,
  Thomas

> On May 19, 2017, at 2:26 PM, Chi Celestine <chi...@ph...> wrote:
> 
> Hi Thomas,
> I am also interesting in getting bond distances between two pairs of molecule. I tried running the commands to suggested but I get an error message e.g 
> When I tried the following (see below) the fist command was well executed but the second gave an error message “ SyntaxError: invalid syntax”
> 
> I got a similar error message when I tried to execute  this command D = get_raw_distances("distname”)  as well 
> 
> 
> Sincerely,
> Celestine 
> 
> Example
> fetch 2xwu, async=0
> 
> 
> 
> # interface polar contacts
> distance iface_hbonds, chain A, chain B, mode=2
> 
> 
> 
> # dump (model,index) information
> get_raw_distances iface_hbonds
> 
>  
> -------------------------------------------------
> Celestine Chi, PhD
> ETH Zürich 
> Laboratory for Physical Chemistry
> Vladimir-Prelog-Weg 2 HCI F 222
> CH-8093 Zürich
> Email: chi...@ph...
> tele: 004144 63 37510
> 
>> On May 19, 2017, at 1:16 PM, Thomas Holder <tho...@sc...> wrote:
>> 
>> Hi Ahmad,
>> 
>> Unfortunately there is no proper API for this. But I can think of two approaches. Note that the results can differ because the two method do slightly different h-bond detection!
>> 
>> 1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection. Example:
>> 
>> sele1 = "chain A & (donors | acceptors)"
>> sele2 = "chain B & (donors | acceptors)"
>> radius = 3.5
>> D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
>> print("number of h-bonds:", len(D))
>> 
>> 1) Use "cmd.distance" and the "get_raw_distances" script. Example:
>> 
>> run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
>> 
>> sele1 = "chain A"
>> sele2 = "chain B"
>> radius = 3.5
>> cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
>> D = get_raw_distances("distname")
>> print("number of h-bonds:", len(D))
>> 
>> See also:
>> https://pymolwiki.org/index.php/Get_raw_distances
>> https://pymolwiki.org/index.php/Distance
>> https://pymolwiki.org/index.php/Find_pairs
>> 
>> Hope that helps.
>> 
>> Cheers,
>>  Thomas
>> 
>>> On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <und...@gm...> wrote:
>>> 
>>> I know I can can find the hydrogen bond interactions between a
>>> selection and surrounding residues within a certain radius. I would
>>> like to find a way to retrieve the actual count of those interactions
>>> per residue. How can I do it in the API?
>>> 
>>> Regards.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.