[PyMOL] Coordination bonds

[James Starlight]

Dear PyMol users!

Using present ->  ligand sites context menu I would like to display
possible non-covalent contacts between ions embedded within the
protein.
First I tried to rename ATOM to HETATM record corresponds to ions
however pymol still don't recognize ions as ligand.

Will be very thankful for any suggestions!

James

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Re: [PyMOL] coordination bonds

[Maia Cherney]

Thank you for your help. However, I have 4  Mg ions  in the au, so all 
Mg ions (and all coordinated ligands) got connected. I need only 
coordination for one Mg.

Maia

Nathaniel Echols wrote:
> On Sun, May 23, 2010 at 3:55 PM, Maia Cherney  > wrote:
>
> I would like to show coordination bonds between Mg ion and its ligands
> (oxygens) as broken lines, the distance of Mg-O bond is between
> 1.9-2.2 A.
>
>  
> dist elem mg, (all within 2.2 of elem mg) 
>
> Might need to try a slightly longer length to catch everything.
>
> -Nat
> 
>
> --
>
>   
> 
>
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Re: [PyMOL] coordination bonds

[Nathaniel Echols]

On Sun, May 23, 2010 at 6:33 PM, Maia Cherney  wrote:

> Thank you for your help. However, I have 4  Mg ions  in the au, so all Mg
> ions (and all coordinated ligands) got connected. I need only coordination
> for one Mg.
>

Then you need to qualify the selection with the residue number, and repeat
up to 4 times.  Same principle still applies, though:

dist (elem mg and resid 341), (all within 2.2 of (elem mg and resid 341))

this particular example may be unnecessarily verbose if the residue number
is unique.

-Nat
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Re: [PyMOL] coordination bonds

[Maia Cherney]

I found a similar command

dist 1, elem mg, elem o, 2.2

Nathaniel Echols wrote:
> On Sun, May 23, 2010 at 3:55 PM, Maia Cherney  > wrote:
>
> I would like to show coordination bonds between Mg ion and its ligands
> (oxygens) as broken lines, the distance of Mg-O bond is between
> 1.9-2.2 A.
>
>  
> dist elem mg, (all within 2.2 of elem mg) 
>
> Might need to try a slightly longer length to catch everything.
>
> -Nat
> 
>
> --
>
>   
> 
>
> ___
> 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

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Re: [PyMOL] coordination bonds

[Nathaniel Echols]

On Sun, May 23, 2010 at 3:55 PM, Maia Cherney  wrote:

> I would like to show coordination bonds between Mg ion and its ligands
> (oxygens) as broken lines, the distance of Mg-O bond is between 1.9-2.2 A.
>

dist elem mg, (all within 2.2 of elem mg)

Might need to try a slightly longer length to catch everything.

-Nat
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Re: [PyMOL] coordination bonds

[Maia Cherney]

I would like to show coordination bonds between Mg ion and its ligands 
(oxygens) as broken lines, the distance of Mg-O bond is between 1.9-2.2 A.

Maia



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