[phenixbb] Tracing and refining b-strands at 3.3A resolution

[Gino Cingolani]

Sean,
thanks to you and to whoever else responded to my email.
Yes, I'd like to get your script.

Thanks in advance!
Gino

******************************************************************************
Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Office (215) 503 4573
Lab    (215) 503 4595
Fax    (215) 923 2117
E-mail:   gino.cingolani at jefferson.edu
******************************************************************************
"Nati non foste per viver come bruti, ma per seguir virtute e conoscenza"
("You were not born to live like brutes, but to follow virtue and knowledge")
Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120) 


---- Original message ----
>Date: Fri, 28 Aug 2009 08:35:08 +0100
>From: Wai-Ching Hon <hon at mrc-lmb.cam.ac.uk>  
>Subject: Re: [phenixbb] Tracing and refining b-strands at 3.3A resolution  
>To: PHENIX user mailing list <phenixbb at phenix-online.org>
>
>Dear Sean,
>
>That sounds wonderful. Can I have your scripts too?
>
>many thanks
>
>waiching.
>
>Sean Johnson wrote:
>> Gino,
>>
>> My lab recently refined a 3.4 A structure and dealt with similar 
>> problems. We found that using secondary structure restraints was the 
>> only effective way to maintain reasonable geometry during refinement. It 
>> is kind of a daunting task to input all of the definitions by hand, so 
>> we wrote a couple python scripts that are integrated with PyMol to write 
>> the appropriate restraint definition files. All you have to do is click 
>> on the atoms that you want restrained. You are welcome to the scripts if 
>> you like. Feel free to contact me if you are interested.
>>
>> Sean Johnson
>>
>>
>> Gino Cingolani wrote:
>>   
>>> Hi Phenix community, 
>>>
>>> I'm tracing a 3.3A averaged electron density map of 
>>> a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement?
>>>
>>> Thanks in advance for the feedback,
>>>
>>> Gino
>>>
>>>
>>>
>>>
>>> ******************************************************************************
>>> Gino Cingolani, Ph.D.
>>> Associate Professor
>>> Thomas Jefferson University
>>> Dept. of Biochemistry & Molecular Biology
>>> 233 South 10th Street - Room 826
>>> Philadelphia PA 19107
>>> Office (215) 503 4573
>>> Lab    (215) 503 4595
>>> Fax    (215) 923 2117
>>> E-mail:   gino.cingolani at jefferson.edu
>>> ******************************************************************************
>>> "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza"
>>> ("You were not born to live like brutes, but to follow virtue and knowledge")
>>> Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120) 
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>   
>>>     
>>
>>   
>________________
>hon.vcf (1k bytes)
>________________
>_______________________________________________
>phenixbb mailing list
>phenixbb at phenix-online.org
>http://www.phenix-online.org/mailman/listinfo/phenixbb