Re: [ccp4bb] NCS from electron density

[Francis E Reyes]

Each case is specific, but when I was learning, I found Phil's Notes on 
Averaging (http://xray0.princeton.edu/~phil/Facility/averaging.html) to be 
quite useful. 

F

On Dec 12, 2012, at 11:59 AM, Scott Thomas Walsh wrote:

> Hi Francis,
> 
> Do you have a specific "how to" on your experience with NCS (reference)?
> 
> Cheers,
> 
> Scott
> 
> 
> Scott T. R. Walsh, PhD
> Assistant Professor
> University of Maryland
> IBBR/CBMG
> 3127E CARB-2
> 9600 Gudelsky Drive
> Rockville, MD  20850  USA
> phone: (240) 314-6478
> fax: (240) 314-6225
> email: swals...@umd.edu
> 
> On Dec 12, 2012, at 2:55 PM, Francis E Reyes wrote:
> 
>> I've had good experience with GETAX if you have a self rotation peak. 
>> 
>> Be careful about moving the NCS operator from program to program. 
>> Phenix/DM/RAVE all have specific formats for how it should be presented. 
>> 
>> F
>> 
>> On Dec 12, 2012, at 10:01 AM, Nicolas Soler wrote:
>> 
>>> Dear all,
>>> 
>>> Is there a pipeline that will find NCS operators from a map, select the 
>>> relevant ones and apply them all in NCS averaging density modification? 
>>> Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup 
>>> so I wonder what happens with the origin when I pass the NCS operators from 
>>> one program to another).
>>> 
>>> Thanks for your help,
>>> 
>>> Nicolas
>> 
>> 
>> 
>> -
>> Francis E. Reyes PhD
>> 215 UCB
>> University of Colorado at Boulder
> 
> 
> 

Re: [ccp4bb] NCS from electron density

[Scott Thomas Walsh]

Hi Francis,

Do you have a specific "how to" on your experience with NCS (reference)?

Cheers,

Scott


Scott T. R. Walsh, PhD
Assistant Professor
University of Maryland
IBBR/CBMG
3127E CARB-2
9600 Gudelsky Drive
Rockville, MD  20850  USA
phone: (240) 314-6478
fax: (240) 314-6225
email: swals...@umd.edu

On Dec 12, 2012, at 2:55 PM, Francis E Reyes wrote:

I've had good experience with GETAX if you have a self rotation peak.

Be careful about moving the NCS operator from program to program. 
Phenix/DM/RAVE all have specific formats for how it should be presented.

F

On Dec 12, 2012, at 10:01 AM, Nicolas Soler wrote:

Dear all,

Is there a pipeline that will find NCS operators from a map, select the 
relevant ones and apply them all in NCS averaging density modification? 
Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup so 
I wonder what happens with the origin when I pass the NCS operators from one 
program to another).

Thanks for your help,

Nicolas



-
Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] NCS from electron density

[Francis E Reyes]

I've had good experience with GETAX if you have a self rotation peak. 

Be careful about moving the NCS operator from program to program. 
Phenix/DM/RAVE all have specific formats for how it should be presented. 

F

On Dec 12, 2012, at 10:01 AM, Nicolas Soler wrote:

> Dear all,
> 
> Is there a pipeline that will find NCS operators from a map, select the 
> relevant ones and apply them all in NCS averaging density modification? 
> Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup 
> so I wonder what happens with the origin when I pass the NCS operators from 
> one program to another).
> 
> Thanks for your help,
> 
> Nicolas



-
Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] NCS from electron density

[Randy Read]

Hi,

The only tool I'm aware of is Tom Terwiliger's phenix.find_ncs_from_density, 
the operators from which can be passed onto his phenix.ncs_average program.  
Most programs expect you to have heavy atom sites or protein models from which 
the NCS can be deduced.

Regards,

Randy

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

On 12 Dec 2012, at 18:01, Nicolas Soler wrote:

> Dear all,
> 
> Is there a pipeline that will find NCS operators from a map, select the 
> relevant ones and apply them all in NCS averaging density modification? 
> Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup 
> so I wonder what happens with the origin when I pass the NCS operators from 
> one program to another).
> 
> Thanks for your help,
> 
> Nicolas

[ccp4bb] NCS from electron density

[Nicolas Soler]

Dear all,

Is there a pipeline that will find NCS operators from a map, select the 
relevant ones and apply them all in NCS averaging density modification? 
Otherwise, what would be the best way to proceed ? (I have a P21 
spacegroup so I wonder what happens with the origin when I pass the NCS 
operators from one program to another).


Thanks for your help,

Nicolas