Hi Yikan,
I think using Monte Carlo (in the torsion angle randomization) is appropriate. Good luck, Guillermo ________________________________ From: ZhangYikan <[email protected]> Sent: Monday, December 11, 2017 6:36 PM To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected] Subject: Re: [Xplor-nih] Wrong topology structures in conformational sampling hell Guillermo, By the way, although I have known that the comformational sampling problem has been an untrival problem util now; how can I make sure that I have sampled almost all possible conformations of this RNA? Yikan Ph. D candidate TsingHua University School of life Sciences Beijing, China tel:010-62773783 > 在 2017年12月12日，上午7:25，ZhangYikan <[email protected]> 写道： > > 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 >> >> >> >>> 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 >>> >>> >>> >>>> 在 2017年12月9日，上午12:43，Bermejo, Guillermo (NIH/CIT) [E] >>>> <[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] >>>> <[email protected]> on behalf of ZhangYikan >>>> <[email protected]> >>>> Sent: Friday, December 8, 2017 6:53 AM >>>> To: [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 >> >> <fold.py> > > _______________________________________________ > Xplor-nih mailing list > [email protected] > https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih Xplor-nih Info Page<https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih> dcb.cit.nih.gov To see the collection of prior postings to the list, visit the Xplor-nih Archives. Using Xplor-nih: To post a message to all the list members ...
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