Re: [PyMOL] Selective valency on bond

2016-06-14 Thread Thomas Holder 
Hi Patrick and Andreas,

"valence" is actually a bond-level setting, so you don't need to create 
individual objects. This should work:

set_bond valence, 1, organic

Cheers,
  Thomas

On 14 Jun 2016, at 10:01, Andreas Warnecke <4ndreas.warne...@gmail.com> wrote:

> The easiest way to deal with this is setting the valence or valence_mode 
> individually for the object.
> 
> set valence, 0, object1
> set valence, 1, object2
> 
> Cheers,
> 
> Andreas
> 
> On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick  
> wrote:
> Dear PyMol users,
> 
> I have a crystal structure of my protein with an unnatural amino acid 
> present. This amino acid has a double bond within it, which I would like to 
> display as such. However I would like the surrounding protein  side chains to 
> not show double bond character. Is this possible at all?
> 
> So far, I can either keep valence mode set to '0' and see no double bonds 
> across the whole protein, or set to '1' and see all of the double bonds, 
> which I don't want.
> 
> My question is, is it possible to selectively 'set valency' onto a single 
> bond, or is it a global command which is not capable of this fine-tuning? I 
> am using MacPyMol if this makes a difference at all?
> 
> Thanks for your help,
> Patrick

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Selective valency on bond

2016-06-14 Thread Andreas Warnecke 
The easiest way to deal with this is setting the valence or valence_mode
individually for the object.

set valence, 0, object1
set valence, 1, object2

Cheers,

Andreas

On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick 
wrote:

> Dear PyMol users,
>
> I have a crystal structure of my protein with an unnatural amino acid
> present. This amino acid has a double bond within it, which I would like to
> display as such. However I would like the surrounding protein  side chains
> to not show double bond character. Is this possible at all?
>
> So far, I can either keep valence mode set to '0' and see no double bonds
> across the whole protein, or set to '1' and see all of the double bonds,
> which I don't want.
>
> My question is, is it possible to selectively 'set valency' onto a single
> bond, or is it a global command which is not capable of this fine-tuning? I
> am using MacPyMol if this makes a difference at all?
>
> Thanks for your help,
> Patrick
>
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> patterns at an interface-level. Reveals which users, apps, and protocols
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> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
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[PyMOL] Selective valency on bond

2016-06-14 Thread McIntyre, Patrick 
Dear PyMol users,

I have a crystal structure of my protein with an unnatural amino acid present. 
This amino acid has a double bond within it, which I would like to display as 
such. However I would like the surrounding protein  side chains to not show 
double bond character. Is this possible at all?

So far, I can either keep valence mode set to '0' and see no double bonds 
across the whole protein, or set to '1' and see all of the double bonds, which 
I don't want. 

My question is, is it possible to selectively 'set valency' onto a single bond, 
or is it a global command which is not capable of this fine-tuning? I am using 
MacPyMol if this makes a difference at all?

Thanks for your help,
Patrick 
--
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patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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