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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