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
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