Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

[Paul Emsley]

On 14/03/2018 10:40, Eleanor Dodson wrote:

Use words!!!



I am nonplussed.

Is that what you meant?

Paul.



On 14 March 2018 at 00:56, Paul Emsley > wrote:

On 13/03/2018 20:12, Ana Luísa Moreira de Carvalho wrote:

You can find the tool “Fixed Atoms” in the Refinement Toolbar (the side 
menu). Just click Fix Atom
and then click the atom(s) you wish to fix. It won’t move in real space 
refinement or in regularisation.



That's right, Ana Luísa.

And for the record, it's often useful to move fixed atoms. Use Ctrl 
Left-mouse click and drag. So Fixed
Atoms move when nothing else moves and stay still when everything else 
refines. Paradoxical maybe, but
useful. I use it when I have to assert my authority over recalcitrant atoms.

Paul.

Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

[Eleanor Dodson]

Use words!!!

Eleanor

On 14 March 2018 at 00:56, Paul Emsley  wrote:

> On 13/03/2018 20:12, Ana Luísa Moreira de Carvalho wrote:
>
>> You can find the tool “Fixed Atoms” in the Refinement Toolbar (the side
>> menu). Just click Fix Atom and then click the atom(s) you wish to fix. It
>> won’t move in real space refinement or in regularisation.
>>
>
>
> That's right, Ana Luísa.
>
> And for the record, it's often useful to move fixed atoms. Use Ctrl
> Left-mouse click and drag. So Fixed Atoms move when nothing else moves and
> stay still when everything else refines. Paradoxical maybe, but useful. I
> use it when I have to assert my authority over recalcitrant atoms.
>
> Paul.
>

Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

[Paul Emsley]

On 13/03/2018 20:12, Ana Luísa Moreira de Carvalho wrote:
You can find the tool “Fixed Atoms” in the Refinement Toolbar (the side menu). Just click Fix Atom and then 
click the atom(s) you wish to fix. It won’t move in real space refinement or in regularisation.



That's right, Ana Luísa.

And for the record, it's often useful to move fixed atoms. Use Ctrl Left-mouse click and drag. So Fixed 
Atoms move when nothing else moves and stay still when everything else refines. Paradoxical maybe, but 
useful. I use it when I have to assert my authority over recalcitrant atoms.


Paul.

Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

[Ana Luísa Moreira de Carvalho]

You can find the tool “Fixed Atoms” in the Refinement Toolbar (the side menu). 
Just click Fix Atom and then click the atom(s) you wish to fix. It won’t move 
in real space refinement or in regularisation.
Cheers!

> On 13 Mar 2018, at 19:46, Steve Chou  wrote:
> 
> Dear Coot developers and CCP4 list subscribers,
> 
> The density of my map is not perfect. However, I know where a specific atom 
> should be located. Every time I did real space fitting, the atom and the 
> associated chemical groups in the whole ligand ran away. Is there a way to 
> fix the position of this atom, and let the force field drive the fitting of 
> the rest of the atoms in the ligand?
> Many thanks in advance!
> Steve
> 
> -- 
> Steve Chou
> 
> 

Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA
***
Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
Dep. Quimica, FCT-UNL
2829-516 Caparica
Portugal
Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
Fax: 00351212948550
http://docentes.fct.unl.pt/almc 
http://sites.fct.unl.pt/xtal 
https://orcid.org/-0002-3824-0240/print
***

Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

[Eleanor Dodson]

Yes - you can "FixAtom"  - I cant remember which menu it is under - real
space rene I think.. Will check tomorrow

Eleanor

On 13 March 2018 at 19:46, Steve Chou  wrote:

> Dear Coot developers and CCP4 list subscribers,
>
> The density of my map is not perfect. However, I know where a specific
> atom should be located. Every time I did real space fitting, the atom and
> the associated chemical groups in the whole ligand ran away. Is there a way
> to fix the position of this atom, and let the force field drive the fitting
> of the rest of the atoms in the ligand?
> Many thanks in advance!
> Steve
>
> --
> Steve Chou
>
>
>

[ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

[Steve Chou]

Dear Coot developers and CCP4 list subscribers,

The density of my map is not perfect. However, I know where a specific atom
should be located. Every time I did real space fitting, the atom and the
associated chemical groups in the whole ligand ran away. Is there a way to
fix the position of this atom, and let the force field drive the fitting of
the rest of the atoms in the ligand?
Many thanks in advance!
Steve

-- 
Steve Chou