Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Xiao Lei]

I see. Thanks Eleanor!

On Thu, Dec 7, 2017 at 4:33 AM, Eleanor Dodson 
wrote:

> Rf_used is the R factor for the non-free reflections.
>
> If you do the plot the 4SSQ/L**2 is converted to As..
>
> E
>
> On 7 December 2017 at 11:50, Xiao Lei  wrote:
>
>> Thanks Eleanor, yes, I looked at that table and tried to find out the
>> Rfree and R, I know the 4SSQ/LL means column means resolution bins but I
>> did not know what column means Rfac (The Rf_free means Rfree I guess).
>>
>>
>> On Thu, Dec 7, 2017 at 2:58 AM, Eleanor Dodson <
>> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Dont you look at the graphs from the log file?
>>>
>>> This table gives you all sorts of information including R and Rfree in
>>> resolution shells..
>>>
>>> Eleanor
>>> Things for loggraph, R factor and
>>> others
>>>
>>>
>>> $TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
>>> $GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
>>> :Cycle   11.  and  v. resln :N:1,4,5,9,10:
>>> :Cycle   11. % observed v. resln :N:1,3:
>>> $$
>>> M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
>>> NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
>>> $$
>>>  0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2
>>> 539.4  0.59  0.62
>>>  0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5
>>> 412.9  0.57  0.58
>>>  0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6
>>> 431.4  0.57  0.57
>>>  0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3
>>> 455.8  0.59  0.59
>>>  0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2
>>> 354.8  0.55  0.54
>>>  0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1
>>> 304.8  0.57  0.54
>>>  0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5
>>> 229.6  0.60  0.58
>>>  0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8
>>> 195.7  0.52  0.50
>>>  0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4
>>> 170.1  0.59  0.56
>>>  0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1
>>> 144.9  0.61  0.57
>>>  0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1
>>> 115.1  0.57  0.53
>>>  0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5
>>> 110.5  0.60  0.58
>>>  0.1856963  99.12   116.693.8  0.55  0.53 390   113.4
>>> 96.3  0.54  0.53
>>>  0.1997194  99.09   100.779.4  0.55  0.54 405   106.4
>>> 84.0  0.55  0.53
>>>  0.2147427  99.1887.670.9  0.53  0.52 40088.9
>>> 71.3  0.53  0.52
>>>  0.2297702  98.6877.361.2  0.52  0.52 39580.2
>>> 61.7  0.54  0.53
>>>  0.2447963  98.9265.652.3  0.48  0.48 42865.5
>>> 53.7  0.54  0.54
>>>  0.2588198  98.4856.844.6  0.46  0.46 43753.5
>>> 43.6  0.49  0.49
>>>  0.2738375  98.6647.737.5  0.43  0.43 42848.0
>>> 37.6  0.47  0.48
>>>  0.2888611  98.2440.932.1  0.42  0.42 45041.8
>>> 32.1  0.50  0.50
>>> $$
>>>
>>>
>>>
>>> On 7 December 2017 at 01:07, Bernhard Rupp 
>>> wrote:
>>>
 You can find these numbers in the header of the output model coordinate
 file.



 BR



 *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
 Of *Xiao Lei
 *Sent:* Wednesday, December 6, 2017 2:40 PM
 *To:* CCP4BB@JISCMAIL.AC.UK
 *Subject:* [ccp4bb] How to find the Rfree and R in the highest
 resolution bin in Refmac 5?



 Dear All,

 I am asking how to find the Rfree and R in the highest resolution bin
 in Refmac 5 output?

 I used Refmac5 in refinement of protein structure at 3A resolution.
 Output of Refmac5 gives Rfee and R as:

   InitialFinal

R factor0.2900   0.2052

  R free0.3015   0.2639


 I'd also like to see the Rfree and R in the highest resolution bin. I
 checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
 with columns of Rf_free and WR_free, I searched in internet and still could
 not understand the Rf_free and WR_free label meaning.  I'd like to find
 something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
 value in the parenthesis).



 thanks ahead.





>>>
>>>
>>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Eleanor Dodson]

Rf_used is the R factor for the non-free reflections.

If you do the plot the 4SSQ/L**2 is converted to As..

E

On 7 December 2017 at 11:50, Xiao Lei  wrote:

> Thanks Eleanor, yes, I looked at that table and tried to find out the
> Rfree and R, I know the 4SSQ/LL means column means resolution bins but I
> did not know what column means Rfac (The Rf_free means Rfree I guess).
>
>
> On Thu, Dec 7, 2017 at 2:58 AM, Eleanor Dodson <176a9d5ebad7-dmarc-
> requ...@jiscmail.ac.uk> wrote:
>
>> Dont you look at the graphs from the log file?
>>
>> This table gives you all sorts of information including R and Rfree in
>> resolution shells..
>>
>> Eleanor
>> Things for loggraph, R factor and
>> others
>>
>>
>> $TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
>> $GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
>> :Cycle   11.  and  v. resln :N:1,4,5,9,10:
>> :Cycle   11. % observed v. resln :N:1,3:
>> $$
>> M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
>> NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
>> $$
>>  0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2
>> 539.4  0.59  0.62
>>  0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5
>> 412.9  0.57  0.58
>>  0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6
>> 431.4  0.57  0.57
>>  0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3
>> 455.8  0.59  0.59
>>  0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2
>> 354.8  0.55  0.54
>>  0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1
>> 304.8  0.57  0.54
>>  0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5
>> 229.6  0.60  0.58
>>  0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8
>> 195.7  0.52  0.50
>>  0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4
>> 170.1  0.59  0.56
>>  0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1
>> 144.9  0.61  0.57
>>  0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1
>> 115.1  0.57  0.53
>>  0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5
>> 110.5  0.60  0.58
>>  0.1856963  99.12   116.693.8  0.55  0.53 390   113.4
>> 96.3  0.54  0.53
>>  0.1997194  99.09   100.779.4  0.55  0.54 405   106.4
>> 84.0  0.55  0.53
>>  0.2147427  99.1887.670.9  0.53  0.52 40088.9
>> 71.3  0.53  0.52
>>  0.2297702  98.6877.361.2  0.52  0.52 39580.2
>> 61.7  0.54  0.53
>>  0.2447963  98.9265.652.3  0.48  0.48 42865.5
>> 53.7  0.54  0.54
>>  0.2588198  98.4856.844.6  0.46  0.46 43753.5
>> 43.6  0.49  0.49
>>  0.2738375  98.6647.737.5  0.43  0.43 42848.0
>> 37.6  0.47  0.48
>>  0.2888611  98.2440.932.1  0.42  0.42 45041.8
>> 32.1  0.50  0.50
>> $$
>>
>>
>>
>> On 7 December 2017 at 01:07, Bernhard Rupp 
>> wrote:
>>
>>> You can find these numbers in the header of the output model coordinate
>>> file.
>>>
>>>
>>>
>>> BR
>>>
>>>
>>>
>>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
>>> Of *Xiao Lei
>>> *Sent:* Wednesday, December 6, 2017 2:40 PM
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* [ccp4bb] How to find the Rfree and R in the highest
>>> resolution bin in Refmac 5?
>>>
>>>
>>>
>>> Dear All,
>>>
>>> I am asking how to find the Rfree and R in the highest resolution bin in
>>> Refmac 5 output?
>>>
>>> I used Refmac5 in refinement of protein structure at 3A resolution.
>>> Output of Refmac5 gives Rfee and R as:
>>>
>>>   InitialFinal
>>>
>>>R factor0.2900   0.2052
>>>
>>>  R free0.3015   0.2639
>>>
>>>
>>> I'd also like to see the Rfree and R in the highest resolution bin. I
>>> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
>>> with columns of Rf_free and WR_free, I searched in internet and still could
>>> not understand the Rf_free and WR_free label meaning.  I'd like to find
>>> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
>>> value in the parenthesis).
>>>
>>>
>>>
>>> thanks ahead.
>>>
>>>
>>>
>>>
>>>
>>
>>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Xiao Lei]

Thanks Eleanor, yes, I looked at that table and tried to find out the Rfree
and R, I know the 4SSQ/LL means column means resolution bins but I did not
know what column means Rfac (The Rf_free means Rfree I guess).

On Thu, Dec 7, 2017 at 2:58 AM, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dont you look at the graphs from the log file?
>
> This table gives you all sorts of information including R and Rfree in
> resolution shells..
>
> Eleanor
> Things for loggraph, R factor and
> others
>
>
> $TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
> $GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
> :Cycle   11.  and  v. resln :N:1,4,5,9,10:
> :Cycle   11. % observed v. resln :N:1,3:
> $$
> M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
> NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
> $$
>  0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2   539.4
> 0.59  0.62
>  0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5   412.9
> 0.57  0.58
>  0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6   431.4
> 0.57  0.57
>  0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3   455.8
> 0.59  0.59
>  0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2   354.8
> 0.55  0.54
>  0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1   304.8
> 0.57  0.54
>  0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5   229.6
> 0.60  0.58
>  0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8   195.7
> 0.52  0.50
>  0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4   170.1
> 0.59  0.56
>  0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1   144.9
> 0.61  0.57
>  0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1   115.1
> 0.57  0.53
>  0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5   110.5
> 0.60  0.58
>  0.1856963  99.12   116.693.8  0.55  0.53 390   113.496.3
> 0.54  0.53
>  0.1997194  99.09   100.779.4  0.55  0.54 405   106.484.0
> 0.55  0.53
>  0.2147427  99.1887.670.9  0.53  0.52 40088.971.3
> 0.53  0.52
>  0.2297702  98.6877.361.2  0.52  0.52 39580.261.7
> 0.54  0.53
>  0.2447963  98.9265.652.3  0.48  0.48 42865.553.7
> 0.54  0.54
>  0.2588198  98.4856.844.6  0.46  0.46 43753.543.6
> 0.49  0.49
>  0.2738375  98.6647.737.5  0.43  0.43 42848.037.6
> 0.47  0.48
>  0.2888611  98.2440.932.1  0.42  0.42 45041.832.1
> 0.50  0.50
> $$
>
>
>
> On 7 December 2017 at 01:07, Bernhard Rupp 
> wrote:
>
>> You can find these numbers in the header of the output model coordinate
>> file.
>>
>>
>>
>> BR
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Xiao Lei
>> *Sent:* Wednesday, December 6, 2017 2:40 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] How to find the Rfree and R in the highest
>> resolution bin in Refmac 5?
>>
>>
>>
>> Dear All,
>>
>> I am asking how to find the Rfree and R in the highest resolution bin in
>> Refmac 5 output?
>>
>> I used Refmac5 in refinement of protein structure at 3A resolution.
>> Output of Refmac5 gives Rfee and R as:
>>
>>   InitialFinal
>>
>>R factor0.2900   0.2052
>>
>>  R free0.3015   0.2639
>>
>>
>> I'd also like to see the Rfree and R in the highest resolution bin. I
>> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
>> with columns of Rf_free and WR_free, I searched in internet and still could
>> not understand the Rf_free and WR_free label meaning.  I'd like to find
>> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
>> value in the parenthesis).
>>
>>
>>
>> thanks ahead.
>>
>>
>>
>>
>>
>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Xiao Lei]

This works. Thanks a lot Bernhard.

On Wed, Dec 6, 2017 at 5:07 PM, Bernhard Rupp 
wrote:

> You can find these numbers in the header of the output model coordinate
> file.
>
>
>
> BR
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao
> Lei
> *Sent:* Wednesday, December 6, 2017 2:40 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] How to find the Rfree and R in the highest resolution
> bin in Refmac 5?
>
>
>
> Dear All,
>
> I am asking how to find the Rfree and R in the highest resolution bin in
> Refmac 5 output?
>
> I used Refmac5 in refinement of protein structure at 3A resolution.
> Output of Refmac5 gives Rfee and R as:
>
>   InitialFinal
>
>R factor0.2900   0.2052
>
>  R free0.3015   0.2639
>
>
> I'd also like to see the Rfree and R in the highest resolution bin. I
> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
> with columns of Rf_free and WR_free, I searched in internet and still could
> not understand the Rf_free and WR_free label meaning.  I'd like to find
> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
> value in the parenthesis).
>
>
>
> thanks ahead.
>
>
>
>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Eleanor Dodson]

Dont you look at the graphs from the log file?

This table gives you all sorts of information including R and Rfree in
resolution shells..

Eleanor
Things for loggraph, R factor and
others


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2   539.4
0.59  0.62
 0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5   412.9
0.57  0.58
 0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6   431.4
0.57  0.57
 0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3   455.8
0.59  0.59
 0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2   354.8
0.55  0.54
 0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1   304.8
0.57  0.54
 0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5   229.6
0.60  0.58
 0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8   195.7
0.52  0.50
 0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4   170.1
0.59  0.56
 0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1   144.9
0.61  0.57
 0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1   115.1
0.57  0.53
 0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5   110.5
0.60  0.58
 0.1856963  99.12   116.693.8  0.55  0.53 390   113.496.3
0.54  0.53
 0.1997194  99.09   100.779.4  0.55  0.54 405   106.484.0
0.55  0.53
 0.2147427  99.1887.670.9  0.53  0.52 40088.971.3
0.53  0.52
 0.2297702  98.6877.361.2  0.52  0.52 39580.261.7
0.54  0.53
 0.2447963  98.9265.652.3  0.48  0.48 42865.553.7
0.54  0.54
 0.2588198  98.4856.844.6  0.46  0.46 43753.543.6
0.49  0.49
 0.2738375  98.6647.737.5  0.43  0.43 42848.037.6
0.47  0.48
 0.2888611  98.2440.932.1  0.42  0.42 45041.832.1
0.50  0.50
$$



On 7 December 2017 at 01:07, Bernhard Rupp  wrote:

> You can find these numbers in the header of the output model coordinate
> file.
>
>
>
> BR
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao
> Lei
> *Sent:* Wednesday, December 6, 2017 2:40 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] How to find the Rfree and R in the highest resolution
> bin in Refmac 5?
>
>
>
> Dear All,
>
> I am asking how to find the Rfree and R in the highest resolution bin in
> Refmac 5 output?
>
> I used Refmac5 in refinement of protein structure at 3A resolution.
> Output of Refmac5 gives Rfee and R as:
>
>   InitialFinal
>
>R factor0.2900   0.2052
>
>  R free0.3015   0.2639
>
>
> I'd also like to see the Rfree and R in the highest resolution bin. I
> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
> with columns of Rf_free and WR_free, I searched in internet and still could
> not understand the Rf_free and WR_free label meaning.  I'd like to find
> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
> value in the parenthesis).
>
>
>
> thanks ahead.
>
>
>
>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Bernhard Rupp]

You can find these numbers in the header of the output model coordinate file.

 

BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei
Sent: Wednesday, December 6, 2017 2:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to find the Rfree and R in the highest resolution bin in 
Refmac 5?

 

Dear All,
 
I am asking how to find the Rfree and R in the highest resolution bin in Refmac 
5 output?

I used Refmac5 in refinement of protein structure at 3A resolution.
Output of Refmac5 gives Rfee and R as:

  InitialFinal

   R factor0.2900   0.2052

 R free0.3015   0.2639


I'd also like to see the Rfree and R in the highest resolution bin. I checked 
log file in Refmac5 and found M(4SSQ/LL) resolution range table with columns of 
Rf_free and WR_free, I searched in internet and still could not understand the 
Rf_free and WR_free label meaning.  I'd like to find something like Rfree XXX 
(XXX);  R XXX (XXX)  (the highest resolution bin value in the parenthesis). 

 

thanks ahead.

 

 

[ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

[Xiao Lei]

Dear All,

I am asking how to find the Rfree and R in the highest resolution bin in
Refmac 5 output?

I used Refmac5 in refinement of protein structure at 3A resolution.
Output of Refmac5 gives Rfee and R as:

  InitialFinal

   R factor0.2900   0.2052

 R free0.3015   0.2639


I'd also like to see the Rfree and R in the highest resolution bin. I
checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
with columns of Rf_free and WR_free, I searched in internet and still could
not understand the Rf_free and WR_free label meaning.  I'd like to find
something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
value in the parenthesis).

thanks ahead.