Re: [ccp4bb] Refmac use - water addition

2020-09-14 Thread Christian Roth 
Hi Luca,
as Eleanor mentioned, in the i2 interface there is in the option menu an
add water button. That will automatically run the coot find waters script
similar to the old interface.  Paul did use some very sensible values to
look for blobs, which might be waters. These ones are used (basically the
same defaults if you press the interactive find waters button in Coot
alone).  Afterwards there is another quick 5 cycle refmac run to refine
position and B-values of the added waters.
The R value is the R work. If the value does not reach the given values
during the refinement process, the  additional water picking step is
skipped. The R value is based on your experience and one has to take
resolution, status of the model etc. into account. It is often not helpful
to add waters at an early stage of model building and refinement when R
values are hight or the model is very incomplete.
Does that make sense?

Best
Christian

On Sat, Sep 12, 2020 at 8:38 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> 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=1
>>
>>
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>> available at https://www.jiscmail.ac.uk/policyandsecurity/
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>>
>>
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Re: [ccp4bb] Refmac use - water addition

2020-09-12 Thread 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=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/
>
>
>
>
>
>
>
>
>
> --
>
>
> To unsubscribe from the CCP4BB list, click the following link:
>
>
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Re: [ccp4bb] Refmac use - water addition

2020-09-12 Thread 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=1 
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB 
> , a mailing list hosted by 
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Re: [ccp4bb] Refmac use - water addition

2020-09-12 Thread 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=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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[ccp4bb] Refmac use - water addition

2020-09-12 Thread 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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