[BiO BB] Advice on using Modeller

Boris Steipe boris.steipe at utoronto.ca
Mon Mar 6 09:05:39 EST 2006


Crystallographers have written many programs that will attempt to  
guess proton coordinates (eg. HGEN in the CCP4 suite). Web servers  
exist too, for example

http://swift.cmbi.kun.nl/WIWWWI/

However the combination of limited resolution and coordinate errors  
in the template, model coordinate uncertainty, and H placement  
uncertainty, will make the detailed interpretation of hydrogen atom  
geometries untenable.

HTH
B.


On 6 Mar 2006, at 08:35, Nagesh Chakka wrote:

> Hi Narcis,
> Thanks for the information. I should accept that I was not aware of  
> this
> (just re-read the documentation and found it). Is there any other  
> approach
> which addresses this issue.
> Thanks
> Nagesh
>
>> using modeller you only will get a model with all
>> non-hidrogen atoms.
>>
>> Yvan wrote:
>>> Hello Nagesh
>>> ,
>>> You should direct your modeller questions to this list:
>>>
>>> modeller_usage at salilab.org
>>>
>>> Cheers
>>>
>>> yvan
>>> _______________________________________________
>>> Bioinformatics.Org general forum  -
>>> BiO_Bulletin_Board at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>>
>>
>> --
>> Narcis Fernandez-Fuentes, phD
>> Seaver Center for Bioinformatics
>> Albert Einstein College of Medicine
>> 1300 Morris Park Ave, Bronx, NY 10461, USA
>> phone: (718)430-3233    fax: (718) 430-8565
>> mailto:narcis at fiserlab.org  (http://www.fiserlab.org)
>> _______________________________________________
>> Bioinformatics.Org general forum  -   
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>
>
> _______________________________________________
> Bioinformatics.Org general forum  -   
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board




More information about the BBB mailing list