hello Guillermo,
I want these domains move (as rigid body)randomly and freely to sample all
possible conformations of the RNA.
Yikan
Ph. D candidate
TsingHua University
School of life Sciences
Beijing, China
tel:010-62773783
> 在 2017年12月11日，下午11:27，Bermejo, Guillermo (NIH/CIT) [E]
> <[email protected]> 写道：
>
> Hi Yikan,
>
> Can you tell me what you are trying to do?
>
> Best,
>
> Guillermo
>
>
> From: ZhangYikan <[email protected]>
> Sent: Friday, December 8, 2017 6:56 PM
> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
> Subject: Re: [Xplor-nih] Wrong topology structures in conformational sampling
>
> hi Guillermo,
> yes, i have received your last mails. And the attachment is my scripts.
>
>
> Yikan
> Ph. D candidate
> TsingHua University
> School of life Sciences
> Beijing, China
> tel:010-62773783 <tel:010-62773783>
>
>
>
>> 在 2017年12月9日，上午12:43，Bermejo, Guillermo (NIH/CIT) [E]
>> <[email protected] <mailto:[email protected]>> 写道：
>>
>> Hi Yikan,
>>
>> I realized that my original response was only sent to you and not included
>> in the mailing list. Here it is.
>>
>> One possibility is that there's something wrong with your script(s).
>>
>> I recommend basing your calculations on the scripts found in eginput/rna
>> directory (within your Xplor-NIH directory). There you'll find:
>>
>> * fold.py, for initial calculations starting from an extended conformation.
>> * refine.py, for subsequent refinement.
>>
>> In addition, you'll find all the restraints for an example system, in case
>> you want to play with the scripts before venturing into your data. The
>> scripts are highly commented, which should help in customizing them for your
>> needs. There's also a paper describing them [Bermejo et al., 2016,
>> Structure 24, 806-815].
>>
>> Best,
>>
>> Guillermo
>>
>>
>>
>>
>>
>> From: [email protected]
>> <mailto:[email protected]>
>> <[email protected]
>> <mailto:[email protected]>> on behalf of ZhangYikan
>> <[email protected] <mailto:[email protected]>>
>> Sent: Friday, December 8, 2017 6:53 AM
>> To: [email protected] <mailto:[email protected]>
>> Subject: [Xplor-nih] Wrong topology structures in conformational sampling
>>
>>
>>
>> hello all,
>>
>> Recently, I am doing conformational sampling with Xplor-NIH. And I got many
>> pdbs, but when I check them I found that some pdbs have wrong topology
>> structures like the attachments(in the pink cycle ): The RNA linker did not
>> run with the right way and It went through the helix. I have tried to pick
>> the structures by the “total energy” or “repel” terms, but it make no sense.
>> Are there someone know how to kick out these wrong structures or to void
>> these errors in the sampling process? Thank you!
>> Yikan
>> Ph. D candidate
>> TsingHua University
>> School of life Sciences
>> Beijing, China
>> tel:010-62773783 <tel:010-62773783>
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