[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] COOT RSR

[Schreuder, Herman /DE]

Hi Paul,

For me, dummy waters are waters placed in very early models, where it is not 
yet clear whether the density belongs to a water, a rearranged side chain or a 
ligand. In the course of the refinement process, it becomes clear to which 
category the density really belongs. Especially for larger rebuilding, I find 
it helpful to use such waters.

A real water is for me a nicely defined, hydrogen bonded water in a 
well-refined structure. However, in this stage one does not need any RSR 
anymore.

Best regards,
Herman

Von: CCP4 bulletin board  Im Auftrag von Paul Emsley
Gesendet: Montag, 22. November 2021 22:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] COOT RSR




What's the difference between a dummy water and a real one?

Paul


On 22/11/2021 14:34, Schreuder, Herman /DE wrote:
Dear Paul,

I agree with Oliver and Norbert, in the early phases of refinement, when a lot 
of rebuilding has to be done, the coot RSR is not very helpful and in general I 
leave it to buster do refine the rebuilt regions. Knowing now that (dummy) 
waters may be the culprit, I will remove them. However, it would be much more 
convenient if the  repulsions with water molecules would not be taken into 
account.

Thank you,
Herman

Von: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> 
Im Auftrag von Norbert Straeter
Gesendet: Sonntag, 21. November 2021 12:24
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: Re: [ccp4bb] COOT RSR

Dear Paul,

I agree to Oliver. In situations where you want to fit a "dummy water" to a 
difference density peak (to determine distances to the environment) or try the 
fit of solvent molecules to yet unexplained density, it would be nice to first 
obtain an optimal fit and next think about the environment and possible bumps 
and partial occupancy. I had this problem already several times, that I could 
not get a good fit because of the model repulsions. Even if two partially 
occupied waters are at closed distance the repulsions appear to be active in 
RSR. It is not about the old method being better.

Best wishes,

Norbert



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Re: [ccp4bb] AW: [ccp4bb] COOT RSR

[Norbert Straeter]

Dear Paul,

with "dummy water" I refer to a water molecule, which I place at the center of 
a (usually positive) difference electron density peak to be able to measure the 
distances to the environment and decide, what the density actually might be. I 
do that quite often. It could also be any other atom, of course.

Best wishes,

Norbert



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Re: [ccp4bb] AW: [ccp4bb] COOT RSR

[Paul Emsley]

What's the difference between a dummy water and a real one?

Paul


On 22/11/2021 14:34, Schreuder, Herman /DE wrote:


Dear Paul,

I agree with Oliver and Norbert, in the early phases of refinement, 
when a lot of rebuilding has to be done, the coot RSR is not very 
helpful and in general I leave it to buster do refine the rebuilt 
regions. Knowing now that (dummy) waters may be the culprit, I will 
remove them. However, it would be much more convenient if the 
repulsions with water molecules would not be taken into account.


Thank you,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von 
*Norbert Straeter

*Gesendet:* Sonntag, 21. November 2021 12:24
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] COOT RSR

Dear Paul,

I agree to Oliver. In situations where you want to fit a "dummy water" 
to a difference density peak (to determine distances to the 
environment) or try the fit of solvent molecules to yet unexplained 
density, it would be nice to first obtain an optimal fit and next 
think about the environment and possible bumps and partial occupancy. 
I had this problem already several times, that I could not get a good 
fit because of the model repulsions. Even if two partially occupied 
waters are at closed distance the repulsions appear to be active in 
RSR. It is not about the old method being better.


Best wishes,

Norbert



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[ccp4bb] AW: [ccp4bb] COOT RSR

[Schreuder, Herman /DE]

Dear Paul,

I agree with Oliver and Norbert, in the early phases of refinement, when a lot 
of rebuilding has to be done, the coot RSR is not very helpful and in general I 
leave it to buster do refine the rebuilt regions. Knowing now that (dummy) 
waters may be the culprit, I will remove them. However, it would be much more 
convenient if the  repulsions with water molecules would not be taken into 
account.

Thank you,
Herman

Von: CCP4 bulletin board  Im Auftrag von Norbert Straeter
Gesendet: Sonntag, 21. November 2021 12:24
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] COOT RSR

Dear Paul,

I agree to Oliver. In situations where you want to fit a "dummy water" to a 
difference density peak (to determine distances to the environment) or try the 
fit of solvent molecules to yet unexplained density, it would be nice to first 
obtain an optimal fit and next think about the environment and possible bumps 
and partial occupancy. I had this problem already several times, that I could 
not get a good fit because of the model repulsions. Even if two partially 
occupied waters are at closed distance the repulsions appear to be active in 
RSR. It is not about the old method being better.

Best wishes,

Norbert



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[ccp4bb] AW: [ccp4bb] coot problems to decrease R FREE

[Herman . Schreuder]

Dear Peter,

First a common misconception: your goal should be to get the best possible fit 
of your model to your electron density maps. Rfree is only an indicator, 
telling you whether you are moving in the right direction.

So in coot, you should look for places where your model does not fit the 
electron density very well and correct them. Things to look for are peaks 
(positive and negative) in the electron density maps. Here I use the default of 
+/- 3 sigma. You should also look for parts of your model with weak or bad 
electron density, as well as uninterpreted electron density. Good parts usually 
have density above the 1.5 sigma level, but for weak parts, you could go down 
to ~0.6 sigma. Below that, you get into the noise/artefact level.

Things to do are fitting side chains in different orientations, flipping 
peptides, removing disordered loops with no or very bad density, fitting extra 
residues where there is extra density etc. In certain cases, you may have to 
rebuild complete loops. You are done with your refinement when you see nothing 
any more that could be improved.

Good luck!
Herman


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ??
Gesendet: Montag, 21. April 2014 02:34
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] coot problems to decrease R FREE

Dear all,

I'm a novice of coot and ccp4. Now I'm doing refinement using both refmac5 and 
coot.Here are some problems I'm facing. Really hope you can give me some 
suggestions.

1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of refmac5 
I got R factor which is 0.26 and R FREE which is 0.31. My question is what the 
final R factor and R FREE should be after several rounds of refinement by 
refmac5 and coot.

2、At which map level（e/A3 or rmsd）should I refine the data by coot?


3、Can you give me some tips and strategies about how to use coot to decrease R 
free? now I just use some basic tricks such as fit density and Ramachandran 
plot to refine the data.


Best regards,


Peter Chen

[ccp4bb] AW: [ccp4bb] coot

[Stefan Gerhardt]

Hi Zheng

I think, it's much easier to go this way:
Coot -> Extensions -> NCS -> Copy NCS Chain or Copy NCS Residue Range

Cheers
Stefan

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Zheng
Zhou
Gesendet: Montag, 28. Februar 2011 12:13
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] coot

Hi, Stefanie

Are those 6 molecules related by NCS? If so, you can model one first, and
use transform_coords_molecule (imol, rtop) to generate others.

I used to do this five times for a pentamer:

output_pdb='template'
for i in range (2,6):
transform_coords_molecule (1, [[x1, y1, z1, x2, y2, z2, x3, y3, z3],
[a, b, c]])
filename=output_pdb+str(i)+'.pdb'
save_coordinates (1, filename)

I think you can write all the the tranformation matrix out instead of the
loop if they differ significantly. Others may have more experience.

Best,

Joe

On Mon, Feb 28, 2011 at 6:32 PM, FREITAG-POHL S.
 wrote:
> Hello everybody,
>
> Currently I am refining my 6 x 220 amino acid structure and I was 
> wondering if COOT is automatically writing a kind of protocol what I 
> am changing in my pdb file when I am fitting-in new residues or mutate 
> amino acids. If so where can I find it?
>
> Thanks a lot,
>
> Stefanie
>
> Dr. Stefanie Freitag-Pohl
> Durham University
> Chemistry Dept
> South Road
> Durham.  DH1 3LE
> Tel:  0191 3342143
> Email: stefanie.freitag-p...@durham.ac.uk
>
>
>