[PyMOL] Selective valency on bond

[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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[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

Post by 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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[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

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
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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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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