Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

2019-03-25 Thread Wim Burmeister 

  
  
Hello,
I rather think the model has a problem. 
Are there large domains which are invisible in the structure ?
Is it possible that the data are twinned ?
Did you use TLS refinement to account for anisotropy ?
Just cutting the resolution will probably not help, unless there is
a serious problem in data quality.
Best
Wim

On 25/03/2019 13:31, Sharan Karade
  wrote:


  
As I understand helical assembly, the data some time is
  anisotropic (any one or two a*,b* or c* has more diffraction
  than other), which may be responsible for your high Rfactors.
  You can crop the data to the resolution using softwares.


Regards
Sharan
  
  
On Mon, Mar 25, 2019, 8:17
  AM Andreas Förster 
  wrote:


  
Yeah, good stuff:
  
  
  http://www.auspex.de/
  
  
  
  All best.
  
  
  
  
  Andreas
  
  
  
  

  
  
  
On Mon, Mar 25, 2019
  at 10:45 AM CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
  wrote:


  
Even if you can't see them, it may be
  worthwhile investigating with Auspex (Parkhurst,
  Thorn, Winter & Waterman - sorry, I can't
  remember the reference off-hand). There's an easy
  to use webserver somewhere that runs it...
  
  Harry
  --
  Dr
  Harry Powell


  On 25 Mar 2019, at 09:03, herman.schreu...@sanofi.com
  wrote:
  


  

  Dear
  ???,
  Do
  you have any ice rings (even hardly
  visible ones) in your diffraction data?
  Best,
  Herman

   
  Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
  Im Auftrag von StrBio
  Gesendet: Sonntag, 24. März 2019
  05:17
  An: CCP4BB@JISCMAIL.AC.UK
  Betreff: [EXTERNAL] [ccp4bb]
  Refinement
   
  

  ALL.


   


  I have data at 2.4 A
in P21 sp gr, helical protein. 


  Refined to Rwork 29
Rfree 34 with nice density map and all
nice statistics oither Rfactor (by
Phenix). Refmac quit same.
  


  Should I deposit it
or look better data?


  Any suggestion?


   


    

  
   
  

  
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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

2019-03-25 Thread Sharan Karade 
As I understand helical assembly, the data some time is anisotropic (any
one or two a*,b* or c* has more diffraction than other), which may be
responsible for your high Rfactors. You can crop the data to the resolution
using softwares.

Regards
Sharan

On Mon, Mar 25, 2019, 8:17 AM Andreas Förster  wrote:

> Yeah, good stuff:
>
> http://www.auspex.de/
>
> All best.
>
>
> Andreas
>
>
>
> On Mon, Mar 25, 2019 at 10:45 AM CCP4BB <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Even if you can't see them, it may be worthwhile investigating with
>> Auspex (Parkhurst, Thorn, Winter & Waterman - sorry, I can't remember the
>> reference off-hand). There's an easy to use webserver somewhere that runs
>> it...
>>
>> Harry
>> --
>> Dr Harry Powell
>>
>> On 25 Mar 2019, at 09:03, herman.schreu...@sanofi.com wrote:
>>
>> Dear ???,
>>
>> Do you have any ice rings (even hardly visible ones) in your diffraction
>> data?
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
>> ] *Im Auftrag von *StrBio
>> *Gesendet:* Sonntag, 24. März 2019 05:17
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] [ccp4bb] Refinement
>>
>>
>>
>> ALL.
>>
>>
>>
>> I have data at 2.4 A in P21 sp gr, helical protein.
>>
>> Refined to Rwork 29 Rfree 34 with nice density map and all nice
>> statistics oither Rfactor (by Phenix). Refmac quit same.
>>
>> Should I deposit it or look better data?
>>
>> Any suggestion?
>>
>>
>>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

2019-03-25 Thread Andreas Förster 
Yeah, good stuff:

http://www.auspex.de/

All best.


Andreas



On Mon, Mar 25, 2019 at 10:45 AM CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Even if you can't see them, it may be worthwhile investigating with Auspex
> (Parkhurst, Thorn, Winter & Waterman - sorry, I can't remember the
> reference off-hand). There's an easy to use webserver somewhere that runs
> it...
>
> Harry
> --
> Dr Harry Powell
>
> On 25 Mar 2019, at 09:03, herman.schreu...@sanofi.com wrote:
>
> Dear ???,
>
> Do you have any ice rings (even hardly visible ones) in your diffraction
> data?
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] *Im Auftrag von *StrBio
> *Gesendet:* Sonntag, 24. März 2019 05:17
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] Refinement
>
>
>
> ALL.
>
>
>
> I have data at 2.4 A in P21 sp gr, helical protein.
>
> Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics
> oither Rfactor (by Phenix). Refmac quit same.
>
> Should I deposit it or look better data?
>
> Any suggestion?
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

2019-03-25 Thread CCP4BB 
Even if you can't see them, it may be worthwhile investigating with Auspex 
(Parkhurst, Thorn, Winter & Waterman - sorry, I can't remember the reference 
off-hand). There's an easy to use webserver somewhere that runs it...

Harry
--
Dr Harry Powell

> On 25 Mar 2019, at 09:03, herman.schreu...@sanofi.com wrote:
> 
> Dear ???,
> Do you have any ice rings (even hardly visible ones) in your diffraction data?
> Best,
> Herman
>  
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von StrBio
> Gesendet: Sonntag, 24. März 2019 05:17
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] [ccp4bb] Refinement
>  
> ALL.
>  
> I have data at 2.4 A in P21 sp gr, helical protein.
> Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics 
> oither Rfactor (by Phenix). Refmac quit same.
> Should I deposit it or look better data?
> Any suggestion?
>  
>  
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

2019-03-25 Thread Herman . Schreuder 
Dear ???,
Do you have any ice rings (even hardly visible ones) in your diffraction data?
Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von StrBio
Gesendet: Sonntag, 24. März 2019 05:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Refinement

ALL.

I have data at 2.4 A in P21 sp gr, helical protein.
Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics 
oither Rfactor (by Phenix). Refmac quit same.
Should I deposit it or look better data?
Any suggestion?





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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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