[ccp4bb] Refmac use - water addition

[Luca Mazzei]

Dear CCP4 people, 

I am approaching in these days to the new CCP4i2 interface and, in particular, 
to REFMAC. Can anyone quickly explain what the factor R, that must be chosen in 
order to automatically add water molecules, is? How can I relate this value 
with the previous DELFWT and FWT map values?

Thanks,

Luca 

Luca Mazzei - PhD
Department of Pharmacy and Biotechnology
University of Bologna
Viale Giuseppe Fanin, 40 - 40127
Bologna - Italy



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Re: [ccp4bb] Refmac use - water addition

[Jon Cooper]

Hello, I'm not totally up-to-the minute with this but I didn't know that refmac 
itself added waters so maybe it's another program in an i2 pipeline, or 
something. However, I know another excellent refinement program that does ;-) 
and an excellent graphics program that does, too ;-0

In the past, we have added well-defined water molecule when the R-factor goes 
into the mid-to-low thirties, or lower.

Anything above 2 sigma in a delta-F map making sensible H-bonds is likely to be 
real but you can lower that cutoff a bit (~1.5) if your resolution is not 
brilliant.

Glad to be corrected on this.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

 Original Message 
On 12 Sep 2020, 11:06, Luca Mazzei wrote:

> Dear CCP4 people,
>
> I am approaching in these days to the new CCP4i2 interface and, in 
> particular, to REFMAC. Can anyone quickly explain what the factor R, that 
> must be chosen in order to automatically add water molecules, is? How can I 
> relate this value with the previous DELFWT and FWT map values?
>
> Thanks,
>
> Luca
>
> Luca Mazzei - PhD
> Department of Pharmacy and Biotechnology
> University of Bologna
> Viale Giuseppe Fanin, 40 - 40127
> Bologna - Italy
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] Refmac use - water addition

[Luca Mazzei]

Dear Jon,

thanks for your answer. Maybe I have been too quick in writing my last message. 
The point is that with the old CCP4 interface, I would have been able to run 
Coot-findwaters to automatically add and remove water molecules at certain 
DELFWT and FWT rmsd tresholds, respectively, through REFMAC interface. Now, 
with the new interface, Coot-findwaters is not made explicit anywhere, and 
DELFWT and FWT rmsd tresholds seem not to be changeable. There’s only "R lower 
than” that is surely what you say = Rfactor (%) lower than 30%. I would not 
want to create misunderstandings, I am just asking for things which are not 
clear to me (maybe given my limited experience), starting from the assumption 
that my knowledge in refinement, model building and, more in general, protein 
crystallography, can always improve. 

Thanks for the precious help,

Luca Mazzei

Luca Mazzei - PhD
Department of Pharmacy and Biotechnology
University of Bologna
Viale Giuseppe Fanin, 40 - 40127
Bologna - Italy



> Il giorno 12 set 2020, alle ore 17:55, Jon Cooper 
>  ha scritto:
> 
> Hello, I'm not totally up-to-the minute with this but I didn't know that 
> refmac itself added waters so maybe it's another program in an i2 pipeline, 
> or something. However, I know another excellent refinement program that does 
> ;-) and an excellent graphics program that does, too ;-0
> 
> In the past, we have added well-defined water molecule when the R-factor goes 
> into the mid-to-low thirties, or lower. 
> 
> Anything above 2 sigma in a delta-F map making sensible H-bonds is likely to 
> be real but you can lower that cutoff a bit (~1.5) if your resolution is not 
> brilliant.
> 
> Glad to be corrected on this.
> 
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
> 
> 
> 
> 
> 
>  Original Message 
> On 12 Sep 2020, 11:06, Luca Mazzei < luca.mazz...@unibo.it> wrote:
> 
> Dear CCP4 people,
> 
> I am approaching in these days to the new CCP4i2 interface and, in 
> particular, to REFMAC. Can anyone quickly explain what the factor R, that 
> must be chosen in order to automatically add water molecules, is? How can I 
> relate this value with the previous DELFWT and FWT map values?
> 
> Thanks,
> 
> Luca
> 
> Luca Mazzei - PhD
> Department of Pharmacy and Biotechnology
> University of Bologna
> Viale Giuseppe Fanin, 40 - 40127
> Bologna - Italy
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB 
> , a mailing list hosted by 
> www.jiscmail.ac.uk , terms & conditions are 
> available at https://www.jiscmail.ac.uk/policyandsecurity/ 
> 




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Re: [ccp4bb] Refmac use - water addition

[Eleanor Dodson]

You don’t say quite how you are doing this. There is an option in the i2
pipeline to add waters using coot when the r factor falls below some
assigned value.
This is done using COOT.
One can debate whether it is a useful option or whether the user would be
better o open COOT and supervise the water search..
Eleanor

On Sat, 12 Sep 2020 at 16:56, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello, I'm not totally up-to-the minute with this but I didn't know that
> refmac itself added waters so maybe it's another program in an i2 pipeline,
> or something. However, I know another excellent refinement program that
> does ;-) and an excellent graphics program that does, too ;-0
>
> In the past, we have added well-defined water molecule when the R-factor
> goes into the mid-to-low thirties, or lower.
>
> Anything above 2 sigma in a delta-F map making sensible H-bonds is likely
> to be real but you can lower that cutoff a bit (~1.5) if your resolution is
> not brilliant.
>
> Glad to be corrected on this.
>
> Best wishes, Jon Cooper.
>
> jon.b.coo...@protonmail.com
>
>
>
>
>
>  Original Message 
> On 12 Sep 2020, 11:06, Luca Mazzei < luca.mazz...@unibo.it> wrote:
>
>
> Dear CCP4 people,
>
>
> I am approaching in these days to the new CCP4i2 interface and, in
> particular, to REFMAC. Can anyone quickly explain what the factor R, that
> must be chosen in order to automatically add water molecules, is? How can I
> relate this value with the previous DELFWT and FWT map values?
>
>
> Thanks,
>
>
> Luca
>
>
> Luca Mazzei - PhD
>
>
> Department of Pharmacy and Biotechnology
>
>
> University of Bologna
> 
>
>
> Viale Giuseppe Fanin, 40 - 40127
> 
>
>
> Bologna - Italy
> 
>
>
> 
>
>
> To unsubscribe from the CCP4BB list, click the following link:
>
>
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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>
>
>
>
>
>
>
> --
>
>
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