Re: [ccp4bb] R/Rfree values

2016-12-15 Thread Pius Padayatti 
26 and 33 tells me you are over fitting your structure
the spread is more than 5%
If there is a ligand added and it really doesn't look like a good fit i
would try work on it
(remove it and look at alternatives)
When you refine you may use NCS if you have (NCS in your structure)

If there is a better resolution structure available or not run the lorestr
even your resolution is not a low resolution

Also i will look at the Ramachandran outliers, geometry validation, and
rotomer outlier checks
very thoroughly and will spend all the efforts to make the structure stick
to the conventions

Try Zanuda and see if your space group symmetry is right
and it will try higher symmetry or lower symmetry in your space group and
run refinement
and provide to if you are refining the structure in the correct space group
If you find higher or lower symmetry as judged by R and Rfree of its
refinements
i will go and refine it in all different space groups and see which give me
better R and R free spread

In any case i am 99% sure you are over fitting your density to what you
want to see and thus
being very biased which is very problematic

Best
Pius




On Wed, Dec 14, 2016 at 7:02 AM, rohit kumar  wrote:

> Dear All,
>
> I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
> values are 26/33, after many cycles of refinements (With or With out water)
> the R/Rfree values still same. Zanuda suggests that the space group seems
> to be correct and the model is looking fine in coot.
> Some one suggest what is the main problem.
> Should I again process my data? And what is the best way to fine right
> space group (If problem with space group).
> Please tell me if you need any information regarding may data.
>
> --
> WITH REGARDS
> Rohit Kumar Singh
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067
>



-- 
P

[ccp4bb] Antw: Re: [ccp4bb] R/Rfree values

2016-12-14 Thread Matthias Barone 
Dear Rohit
Additionally to the very good suggestions, I'd feed the structure into
the PDB_REDO server. Its a fast and easy way to detect if the refinement
strategy is correct. The server gives you a good feeling how tight the
x-ray weights need to be. 
If however PDB_REDO does not manage to decrease the Rfactor gap of 7%, I
would suggest to switch to Phenix and give it a try.
If this does bring the factors down and relax the structure, let
pointless have a look into the XDS_ASCII file. Pointless and Xtriage are
two fast programs to detect if you are correct with the choice of the
space group. They give you also a first hint about twinning and the
amount of twinning.
good luck,
matthias




>>> Prem Prakash <prem...@gmail.com> 14.12.16 19.20 Uhr >>>
Dear Rohit, I am totally agree with Mark, that just R free and R work
does not decide the structure solved, you have to see other parameters
as Mark already suggested. What is and redundancy and also what is the
mosaicity? please look at these parameters too. 

Best 
Prem 


On Wed, Dec 14, 2016 at 10:07 PM, Ashok Nayak <ashokgocrac...@gmail.com>
wrote:
Dear Rohit,
Look at what percentage of the reflections are in the Rfree set, if its
less say 5 %; and you have a good redundancy you can use 10 %. You might
like to use the other Rfree set[1 if you have already used the 0 set] or
consider using the whole set of reflections as a free set if need be if
you suspect a bias in your Rfree set.
As suggested earlier I would also look at how the Fobs and Fcalc
correlate as a function of resolution from the sigma A plot or CC*
values.

Sometimes overestimating the resolution would add up more noise and it
would give you bad R values.

and If the molecule is elongated you might have diffraction anisotropy
and in that case The R values don't come down.

I would also like to use Refmac along with Phenix; that helped in my
case.

So you would like to take them one by one and figure out carefully.

Best Wishes

Ashok Nayak
Post-Doctoral Fellow,
Department of Physiology and Biophysics
VCU Medical Centre,1101 E Marshall ST, 
Richmond,VA
USA


  


On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. <mcmor...@utmb.edu>
wrote:
  In addition to what others have mentioned, you might want to consider
the unpleasant possibility that part of your structure is simply built
incorrectly. Sometimes rebuilding a  short loop or even a few residues
in that loop can do the trick. Look carefully for regions of your map
with poor density and/or regions of your model with poor geometry, and
see if there might be an alternate way to build that region. There is
often a psychological  barrier to attempting these rebuilds, because
they are difficult (if they weren't we would have built correctly the
first time). However, once begun, it is often less painful than
expected. SA/composite omit maps can help.
   From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Eleanor Dodson [eleanor.dod...@york.ac.uk]
 Sent: Wednesday, December 14, 2016 9:49 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] R/Rfree values
 
 
 
 es - look carefully at your data quality indicators - batch scales,
Wilson plot - moments etc.. tHese can show up if there is a problem with
ice rings or crystal decay or whatever. 
 
 Then I always look at the REFMAC plot of  v  
 
 If they overlap well - good - but problems with scaling will show up
there.
 
 
 Eleanor
 
 
 On 14 December 2016 at 15:21, Mark J van Raaij 
<mjvanra...@cnb.csic.es> wrote:
  Dear Rohit,
 
 I wouldn’t judge a structure just by the Rwork and Rfree values, but
also by the validation and other statistics (bond lengths, angles,
Ramachandran plot, map quality, fit to map, average B values). If these
are all ok, you should be able to “get away with”  an Rfree of 33%.
 In your email you state that you have already made a significant effort
in different refinement strategies, so perhaps there is no improvement
to be made there.
 The reason for good, and reprocessing might help. Although the most likely 
outcome is
that you can’t significantly improve it, but at least trying will put
your mind more at ease.
 In the end, the only way to improve the structure, and R-factors, may
be to grow a better crystal, cryo-protect better and/or collect better
data - this particular crystal may just have some kind of disorder.
 
 Greetings,
 
 Mark J van Raaij
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 calle Darwin 3
 E-28049 Madrid, Spain
 tel.  (+34) 91 585 4616
 http://wwwuser.cnb.csic.es/~mjvanraaij
  
 


 
 
 
 > On 14 Dec 2016, at 16:02, rohit kumar <rohit...@gmail.com> wrote:
 >
 > Dear All,
 >
 > I am solving a data of 2.5 A (C121 space group). Right now the
R/Rfree values are 26/33, after many cycles of refinements (With or With
out water) the R/Rfree values still same. Zanuda suggests that the space
group seems to be correct and the model is looking  fine in

Re: [ccp4bb] R/Rfree values

2016-12-14 Thread Sudipta Bhattacharyya 
Hi Rohit,

Along with many excellent suggestions you already got...I want to add the
possibility of the presence of  twining (even a small but significant
percent) and/or the presence of t-NCS in the data.

Good luck!
Sudipta.

On Wed, Dec 14, 2016 at 12:19 PM, Prem Prakash <prem...@gmail.com> wrote:

> Dear Rohit,
> I am totally agree with Mark, that just R free and R work does not decide
> the structure solved, you have to see other parameters as Mark already
> suggested. What is and redundancy and also what is the mosaicity? please
> look at these parameters too.
>
> Best
> Prem
>
> On Wed, Dec 14, 2016 at 10:07 PM, Ashok Nayak <ashokgocrac...@gmail.com>
> wrote:
>
>> Dear Rohit,
>>
>> Look at what percentage of the reflections are in the Rfree set, if its
>> less say 5 %; and you have a good redundancy you can use 10 %. You might
>> like to use the other Rfree set[1 if you have already used the 0 set] or
>> consider using the whole set of reflections as a free set if need be if you
>> suspect a bias in your Rfree set.
>>
>> As suggested earlier I would also look at how the Fobs and Fcalc
>> correlate as a function of resolution from the sigma A plot or CC* values.
>>
>> Sometimes overestimating the resolution would add up more noise and it
>> would give you bad R values.
>>
>> and If the molecule is elongated you might have diffraction anisotropy
>> and in that case The R values don't come down.
>>
>> I would also like to use Refmac along with Phenix; that helped in my case.
>>
>> So you would like to take them one by one and figure out carefully.
>>
>> Best Wishes
>>
>> Ashok Nayak
>> Post-Doctoral Fellow,
>> Department of Physiology and Biophysics
>> VCU Medical Centre,1101 E Marshall ST,
>> Richmond,VA
>> USA
>>
>>
>>
>> On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. <mcmor...@utmb.edu>
>> wrote:
>>
>>> In addition to what others have mentioned, you might want to consider
>>> the unpleasant possibility that part of your structure is simply built
>>> incorrectly. Sometimes rebuilding a short loop or even a few residues in
>>> that loop can do the trick. Look carefully for regions of your map with
>>> poor density and/or regions of your model with poor geometry, and see if
>>> there might be an alternate way to build that region. There is often a
>>> psychological barrier to attempting these rebuilds, because they are
>>> difficult (if they weren't we would have built correctly the first time).
>>> However, once begun, it is often less painful than expected. SA/composite
>>> omit maps can help.
>>> --
>>> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
>>> Eleanor Dodson [eleanor.dod...@york.ac.uk]
>>> *Sent:* Wednesday, December 14, 2016 9:49 AM
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* Re: [ccp4bb] R/Rfree values
>>>
>>> es - look carefully at your data quality indicators - batch scales,
>>> Wilson plot - moments etc.. tHese can show up if there is a problem with
>>> ice rings or crystal decay or whatever.
>>> Then I always look at the REFMAC plot of  v 
>>> If they overlap well - good - but problems with scaling will show up
>>> there.
>>>
>>> Eleanor
>>>
>>> On 14 December 2016 at 15:21, Mark J van Raaij <mjvanra...@cnb.csic.es>
>>> wrote:
>>>
>>>> Dear Rohit,
>>>>
>>>> I wouldn’t judge a structure just by the Rwork and Rfree values, but
>>>> also by the validation and other statistics (bond lengths, angles,
>>>> Ramachandran plot, map quality, fit to map, average B values). If these are
>>>> all ok, you should be able to “get away with” an Rfree of 33%.
>>>> In your email you state that you have already made a significant effort
>>>> in different refinement strategies, so perhaps there is no improvement to
>>>> be made there.
>>>> The reason for the high-ish Rfree could be that the data is not so
>>>> good, and reprocessing might help. Although the most likely outcome is that
>>>> you can’t significantly improve it, but at least trying will put your mind
>>>> more at ease.
>>>> In the end, the only way to improve the structure, and R-factors, may
>>>> be to grow a better crystal, cryo-protect better and/or collect better data
>>>> - this particular crystal may just have some kind of disorder.
>>>>
>>>> Gre

Re: [ccp4bb] R/Rfree values

2016-12-14 Thread Prem Prakash 
Dear Rohit,
I am totally agree with Mark, that just R free and R work does not decide
the structure solved, you have to see other parameters as Mark already
suggested. What is and redundancy and also what is the mosaicity? please
look at these parameters too.

Best
Prem

On Wed, Dec 14, 2016 at 10:07 PM, Ashok Nayak <ashokgocrac...@gmail.com>
wrote:

> Dear Rohit,
>
> Look at what percentage of the reflections are in the Rfree set, if its
> less say 5 %; and you have a good redundancy you can use 10 %. You might
> like to use the other Rfree set[1 if you have already used the 0 set] or
> consider using the whole set of reflections as a free set if need be if you
> suspect a bias in your Rfree set.
>
> As suggested earlier I would also look at how the Fobs and Fcalc correlate
> as a function of resolution from the sigma A plot or CC* values.
>
> Sometimes overestimating the resolution would add up more noise and it
> would give you bad R values.
>
> and If the molecule is elongated you might have diffraction anisotropy and
> in that case The R values don't come down.
>
> I would also like to use Refmac along with Phenix; that helped in my case.
>
> So you would like to take them one by one and figure out carefully.
>
> Best Wishes
>
> Ashok Nayak
> Post-Doctoral Fellow,
> Department of Physiology and Biophysics
> VCU Medical Centre,1101 E Marshall ST,
> Richmond,VA
> USA
>
>
>
> On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. <mcmor...@utmb.edu>
> wrote:
>
>> In addition to what others have mentioned, you might want to consider the
>> unpleasant possibility that part of your structure is simply built
>> incorrectly. Sometimes rebuilding a short loop or even a few residues in
>> that loop can do the trick. Look carefully for regions of your map with
>> poor density and/or regions of your model with poor geometry, and see if
>> there might be an alternate way to build that region. There is often a
>> psychological barrier to attempting these rebuilds, because they are
>> difficult (if they weren't we would have built correctly the first time).
>> However, once begun, it is often less painful than expected. SA/composite
>> omit maps can help.
>> --
>> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor
>> Dodson [eleanor.dod...@york.ac.uk]
>> *Sent:* Wednesday, December 14, 2016 9:49 AM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] R/Rfree values
>>
>> es - look carefully at your data quality indicators - batch scales,
>> Wilson plot - moments etc.. tHese can show up if there is a problem with
>> ice rings or crystal decay or whatever.
>> Then I always look at the REFMAC plot of  v 
>> If they overlap well - good - but problems with scaling will show up
>> there.
>>
>> Eleanor
>>
>> On 14 December 2016 at 15:21, Mark J van Raaij <mjvanra...@cnb.csic.es>
>> wrote:
>>
>>> Dear Rohit,
>>>
>>> I wouldn’t judge a structure just by the Rwork and Rfree values, but
>>> also by the validation and other statistics (bond lengths, angles,
>>> Ramachandran plot, map quality, fit to map, average B values). If these are
>>> all ok, you should be able to “get away with” an Rfree of 33%.
>>> In your email you state that you have already made a significant effort
>>> in different refinement strategies, so perhaps there is no improvement to
>>> be made there.
>>> The reason for the high-ish Rfree could be that the data is not so good,
>>> and reprocessing might help. Although the most likely outcome is that you
>>> can’t significantly improve it, but at least trying will put your mind more
>>> at ease.
>>> In the end, the only way to improve the structure, and R-factors, may be
>>> to grow a better crystal, cryo-protect better and/or collect better data -
>>> this particular crystal may just have some kind of disorder.
>>>
>>> Greetings,
>>>
>>> Mark J van Raaij
>>> Dpto de Estructura de Macromoleculas
>>> Centro Nacional de Biotecnologia - CSIC
>>> calle Darwin 3
>>> E-28049 Madrid, Spain
>>> tel. (+34) 91 585 4616
>>> http://wwwuser.cnb.csic.es/~mjvanraaij
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> > On 14 Dec 2016, at 16:02, rohit kumar <rohit...@gmail.com> wrote:
>>> >
>>> > Dear All,
>>> >
>>> > I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
>>> values are 26/33, after many cycles of refinements (With or With out water)
>>> the R/Rfree values still same. Zanuda suggests that the space group seems
>>> to be correct and the model is looking fine in coot.
>>> > Some one suggest what is the main problem.
>>> > Should I again process my data? And what is the best way to fine right
>>> space group (If problem with space group).
>>> > Please tell me if you need any information regarding may data.
>>> >
>>> > --
>>> > WITH REGARDS
>>> > Rohit Kumar Singh
>>> > Lab. no. 430,
>>> > P.I. Dr. S. Gourinath,
>>> > School of Life Sciences,
>>> > Jawaharlal Nehru University
>>> > New Delhi -110067
>>>
>>
>>
>
>
> --
>
>

Re: [ccp4bb] R/Rfree values

2016-12-14 Thread Ashok Nayak 
Dear Rohit,

Look at what percentage of the reflections are in the Rfree set, if its
less say 5 %; and you have a good redundancy you can use 10 %. You might
like to use the other Rfree set[1 if you have already used the 0 set] or
consider using the whole set of reflections as a free set if need be if you
suspect a bias in your Rfree set.

As suggested earlier I would also look at how the Fobs and Fcalc correlate
as a function of resolution from the sigma A plot or CC* values.

Sometimes overestimating the resolution would add up more noise and it
would give you bad R values.

and If the molecule is elongated you might have diffraction anisotropy and
in that case The R values don't come down.

I would also like to use Refmac along with Phenix; that helped in my case.

So you would like to take them one by one and figure out carefully.

Best Wishes

Ashok Nayak
Post-Doctoral Fellow,
Department of Physiology and Biophysics
VCU Medical Centre,1101 E Marshall ST,
Richmond,VA
USA



On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. <mcmor...@utmb.edu> wrote:

> In addition to what others have mentioned, you might want to consider the
> unpleasant possibility that part of your structure is simply built
> incorrectly. Sometimes rebuilding a short loop or even a few residues in
> that loop can do the trick. Look carefully for regions of your map with
> poor density and/or regions of your model with poor geometry, and see if
> there might be an alternate way to build that region. There is often a
> psychological barrier to attempting these rebuilds, because they are
> difficult (if they weren't we would have built correctly the first time).
> However, once begun, it is often less painful than expected. SA/composite
> omit maps can help.
> --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor
> Dodson [eleanor.dod...@york.ac.uk]
> *Sent:* Wednesday, December 14, 2016 9:49 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] R/Rfree values
>
> es - look carefully at your data quality indicators - batch scales, Wilson
> plot - moments etc.. tHese can show up if there is a problem with ice rings
> or crystal decay or whatever.
> Then I always look at the REFMAC plot of  v 
> If they overlap well - good - but problems with scaling will show up there.
>
> Eleanor
>
> On 14 December 2016 at 15:21, Mark J van Raaij <mjvanra...@cnb.csic.es>
> wrote:
>
>> Dear Rohit,
>>
>> I wouldn’t judge a structure just by the Rwork and Rfree values, but also
>> by the validation and other statistics (bond lengths, angles, Ramachandran
>> plot, map quality, fit to map, average B values). If these are all ok, you
>> should be able to “get away with” an Rfree of 33%.
>> In your email you state that you have already made a significant effort
>> in different refinement strategies, so perhaps there is no improvement to
>> be made there.
>> The reason for the high-ish Rfree could be that the data is not so good,
>> and reprocessing might help. Although the most likely outcome is that you
>> can’t significantly improve it, but at least trying will put your mind more
>> at ease.
>> In the end, the only way to improve the structure, and R-factors, may be
>> to grow a better crystal, cryo-protect better and/or collect better data -
>> this particular crystal may just have some kind of disorder.
>>
>> Greetings,
>>
>> Mark J van Raaij
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616
>> http://wwwuser.cnb.csic.es/~mjvanraaij
>>
>>
>>
>>
>>
>>
>>
>> > On 14 Dec 2016, at 16:02, rohit kumar <rohit...@gmail.com> wrote:
>> >
>> > Dear All,
>> >
>> > I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
>> values are 26/33, after many cycles of refinements (With or With out water)
>> the R/Rfree values still same. Zanuda suggests that the space group seems
>> to be correct and the model is looking fine in coot.
>> > Some one suggest what is the main problem.
>> > Should I again process my data? And what is the best way to fine right
>> space group (If problem with space group).
>> > Please tell me if you need any information regarding may data.
>> >
>> > --
>> > WITH REGARDS
>> > Rohit Kumar Singh
>> > Lab. no. 430,
>> > P.I. Dr. S. Gourinath,
>> > School of Life Sciences,
>> > Jawaharlal Nehru University
>> > New Delhi -110067
>>
>
>


--

Re: [ccp4bb] R/Rfree values

2016-12-14 Thread Morais, Marc C. 
In addition to what others have mentioned, you might want to consider the 
unpleasant possibility that part of your structure is simply built incorrectly. 
Sometimes rebuilding a short loop or even a few residues in that loop can do 
the trick. Look carefully for regions of your map with poor density and/or 
regions of your model with poor geometry, and see if there might be an 
alternate way to build that region. There is often a psychological barrier to 
attempting these rebuilds, because they are difficult (if they weren't we would 
have built correctly the first time). However, once begun, it is often less 
painful than expected. SA/composite omit maps can help.

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[eleanor.dod...@york.ac.uk]
Sent: Wednesday, December 14, 2016 9:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] R/Rfree values

es - look carefully at your data quality indicators - batch scales, Wilson plot 
- moments etc.. tHese can show up if there is a problem with ice rings or 
crystal decay or whatever.
Then I always look at the REFMAC plot of  v 
If they overlap well - good - but problems with scaling will show up there.

Eleanor

On 14 December 2016 at 15:21, Mark J van Raaij 
<mjvanra...@cnb.csic.es<mailto:mjvanra...@cnb.csic.es>> wrote:
Dear Rohit,

I wouldn’t judge a structure just by the Rwork and Rfree values, but also by 
the validation and other statistics (bond lengths, angles, Ramachandran plot, 
map quality, fit to map, average B values). If these are all ok, you should be 
able to “get away with” an Rfree of 33%.
In your email you state that you have already made a significant effort in 
different refinement strategies, so perhaps there is no improvement to be made 
there.
The reason for the high-ish Rfree could be that the data is not so good, and 
reprocessing might help. Although the most likely outcome is that you can’t 
significantly improve it, but at least trying will put your mind more at ease.
In the end, the only way to improve the structure, and R-factors, may be to 
grow a better crystal, cryo-protect better and/or collect better data - this 
particular crystal may just have some kind of disorder.

Greetings,

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616<tel:%28%2B34%29%2091%20585%204616>
http://wwwuser.cnb.csic.es/~mjvanraaij







> On 14 Dec 2016, at 16:02, rohit kumar 
> <rohit...@gmail.com<mailto:rohit...@gmail.com>> wrote:
>
> Dear All,
>
> I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree values 
> are 26/33, after many cycles of refinements (With or With out water) the 
> R/Rfree values still same. Zanuda suggests that the space group seems to be 
> correct and the model is looking fine in coot.
> Some one suggest what is the main problem.
> Should I again process my data? And what is the best way to fine right space 
> group (If problem with space group).
> Please tell me if you need any information regarding may data.
>
> --
> WITH REGARDS
> Rohit Kumar Singh
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067

Re: [ccp4bb] R/Rfree values

2016-12-14 Thread Eleanor Dodson 
es - look carefully at your data quality indicators - batch scales, Wilson
plot - moments etc.. tHese can show up if there is a problem with ice rings
or crystal decay or whatever.
Then I always look at the REFMAC plot of  v 
If they overlap well - good - but problems with scaling will show up there.

Eleanor

On 14 December 2016 at 15:21, Mark J van Raaij 
wrote:

> Dear Rohit,
>
> I wouldn’t judge a structure just by the Rwork and Rfree values, but also
> by the validation and other statistics (bond lengths, angles, Ramachandran
> plot, map quality, fit to map, average B values). If these are all ok, you
> should be able to “get away with” an Rfree of 33%.
> In your email you state that you have already made a significant effort in
> different refinement strategies, so perhaps there is no improvement to be
> made there.
> The reason for the high-ish Rfree could be that the data is not so good,
> and reprocessing might help. Although the most likely outcome is that you
> can’t significantly improve it, but at least trying will put your mind more
> at ease.
> In the end, the only way to improve the structure, and R-factors, may be
> to grow a better crystal, cryo-protect better and/or collect better data -
> this particular crystal may just have some kind of disorder.
>
> Greetings,
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
>
>
>
>
>
>
>
> > On 14 Dec 2016, at 16:02, rohit kumar  wrote:
> >
> > Dear All,
> >
> > I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
> values are 26/33, after many cycles of refinements (With or With out water)
> the R/Rfree values still same. Zanuda suggests that the space group seems
> to be correct and the model is looking fine in coot.
> > Some one suggest what is the main problem.
> > Should I again process my data? And what is the best way to fine right
> space group (If problem with space group).
> > Please tell me if you need any information regarding may data.
> >
> > --
> > WITH REGARDS
> > Rohit Kumar Singh
> > Lab. no. 430,
> > P.I. Dr. S. Gourinath,
> > School of Life Sciences,
> > Jawaharlal Nehru University
> > New Delhi -110067
>

Re: [ccp4bb] R/Rfree values

2016-12-14 Thread Mark J van Raaij 
Dear Rohit,

I wouldn’t judge a structure just by the Rwork and Rfree values, but also by 
the validation and other statistics (bond lengths, angles, Ramachandran plot, 
map quality, fit to map, average B values). If these are all ok, you should be 
able to “get away with” an Rfree of 33%.
In your email you state that you have already made a significant effort in 
different refinement strategies, so perhaps there is no improvement to be made 
there.
The reason for the high-ish Rfree could be that the data is not so good, and 
reprocessing might help. Although the most likely outcome is that you can’t 
significantly improve it, but at least trying will put your mind more at ease.
In the end, the only way to improve the structure, and R-factors, may be to 
grow a better crystal, cryo-protect better and/or collect better data - this 
particular crystal may just have some kind of disorder.

Greetings,

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij







> On 14 Dec 2016, at 16:02, rohit kumar  wrote:
> 
> Dear All,
> 
> I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree values 
> are 26/33, after many cycles of refinements (With or With out water) the 
> R/Rfree values still same. Zanuda suggests that the space group seems to be 
> correct and the model is looking fine in coot. 
> Some one suggest what is the main problem.
> Should I again process my data? And what is the best way to fine right space 
> group (If problem with space group).
> Please tell me if you need any information regarding may data.  
> 
> -- 
> WITH REGARDS
> Rohit Kumar Singh
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067

Re: [ccp4bb] R/Rfree values

2016-12-14 Thread Rajesh Kumar 
Dear Rohit,

Try to run sfcheck or XTRIAGE and check, if your data is fine. Check for
twinning or pseudo-translation. You can send your processed mtz to me and I
would be more than happy to help you.

You can look into cumulative intensity distribution (if you processed with
XDS, it will be in CORRECT.LP file) and it will give you indication of
twinning.


Thank you
Rajesh

 ---x
With regards
Rajesh K. Harijan, Ph.D.
Albert Einstein College of Medicine
1300 Morris Park Ave., Bronx, NY 10461
Tel: 718.430.2777  |  Fax: 718.430.8565



On Wed, Dec 14, 2016 at 10:02 AM, rohit kumar  wrote:

> Dear All,
>
> I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
> values are 26/33, after many cycles of refinements (With or With out water)
> the R/Rfree values still same. Zanuda suggests that the space group seems
> to be correct and the model is looking fine in coot.
> Some one suggest what is the main problem.
> Should I again process my data? And what is the best way to fine right
> space group (If problem with space group).
> Please tell me if you need any information regarding may data.
>
> --
> WITH REGARDS
> Rohit Kumar Singh
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067
>