hello Guillermo,
Thank you for your scripts, I have tried it. I found that there are still some 
wrong topology structures and clahes(some overlaps):1) I will try to fix the 
repel parameter and rerun the script;
2) in the outputs of the previous zp_0-3.py, I found the terms of “impr” seems 
unusual(in the .viols), did you have some tools to analysis this energy term ?

Thank you!
Best,

Yikan
Ph. D candidate
TsingHua University
School of life Sciences 
Beijing, China
tel:010-62773783



> 在 2017年12月12日,上午2:00,Bermejo, Guillermo (NIH/CIT) [E] 
> <[email protected]> 写道:
> 
> Hi Yikan,
> 
> I notice that your script seems to be more complicated than it has to be.  
> I'm not sure this will solve your problem, but I'm attaching a simpler script 
> based on eginput/rna/fold.py.   It's basically the script used to fold an RNA 
> molecule from an extended conformation (described in the paper I mentioned 
> before).  I modified it so that you load your input pdb structure and define 
> the different rigid bodies (look for the lines with an inline comment "# 
> COMPLETE !", where you must enter the right information).  Then, it does 
> torsion angle dynamics using the remaining torsional degrees of freedom 
> (i.e., at the linker(s)).
> 
> I commented all the experimental restraints.  If you want to have the radius 
> of gyration term (which appears in your script), you can introduce it 
> yourself.  Also, you might want to use it as a starting point for more 
> complicated stuff, like "breaking" the linkers and randomizing the position 
> of the domains.
> 
> A suggestion to try to avoid (and detect) knotted structures is to increase 
> the atomic radii (see the 'repel' argument in initRepel).  
> 
> Best,
> 
> Guillermo
> 
> From: ZhangYikan <[email protected]>
> Sent: Monday, December 11, 2017 10:43 AM
> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
> Subject: Re: [Xplor-nih] Wrong topology structures in conformational sampling
>  
> 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 <tel:010-62773783>
> 
> 
> 
>> 在 2017年12月11日,下午11:27,Bermejo, Guillermo (NIH/CIT) [E] 
>> <[email protected] <mailto:[email protected]>> 写道:
>> 
>> Hi Yikan,
>> 
>> Can you tell me what you are trying to do?
>> 
>> Best,
>> 
>> Guillermo
>> 
>> 
>> From: ZhangYikan <[email protected] <mailto:[email protected]>>
>> Sent: Friday, December 8, 2017 6:56 PM
>> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected] 
>> <mailto:[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>
> <fold.py>

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