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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Sam, I think Kevin Cowtan's work http://dx.doi.org/10.1107/S2052252514019290 has been implemented in Coot? In Section 4.1: "The software is available as a part of the Coot model-building package from version 0.7 using the scripting command find_nucleic_acids_local(6) or by a right mouse click on the top tool bar to add the `NA build' button. From build 5199 it is also available through the `Other Modelling Tools' menu. A slower implementation which includes model refinement is available in the CCP4 software suite from version 6.3.0 under the name Nautilus." Best, Tim On Saturday, April 23, 2016 08:48:01 PM Sam Tang wrote: > Hello Tim and Robert, > > Thanks for the suggestions. I will definitely give a try on both. > > Meanwhile, do you have any suggestions for an alternative to RCrane? We do > not work on RNA very often but would for sure like to know more on that. > > Thanks a lot! > > Sam > > Biochemistry Programme, School of Life Sciences, CUHK > > On 23 April 2016 at 03:35, Tim Gruene <[log in to unmask]> wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > Dear Sam, > > > > as far as I know, RCrane has not been developed for 4 years or more. Kevin > > Keating had already taken up a new position when I worked on the knuspr > > GUI > > interface to RCrane back in 2012. > > > > I guess there are naming discrepancies between the RCrane code and the PDB > > standards used by Refmac5. > > > > You might get away with fixing the RCrane code for the atom names or RNA > > residue names without breaking it. Make sure you have a backup, though. > > > > Best regards, > > Tim > > > > On Friday, April 22, 2016 02:16:03 PM Sam Tang wrote: > > > Hi again > > > > > > I am wondering if anyone has the experience using a plugin in Coot > > > called > > > RCrane to build RNA and then refine with Refmac. It happens that refmac > > > cannot recognize my di-/tri-nucleotide and complains of missing atoms. > > > No > > > problem for single nucleotides built from the Coot library. > > > > > > Would be glad if anyone with similar experience could share further on > > > this. > > > > > > Thanks in advance. > > > > > > Kind regards > > > > > > Sam > > > > > > Biochemistry Programme, School of Life Sciences, CUHK > > > > - -- > > - -- > > Paul Scherrer Institut > > Tim Gruene > > - - persoenlich - > > OFLC/102 > > CH-5232 Villigen PSI > > phone: +41 (0)56 310 5297 > > > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v2 > > > > iD8DBQFXGnz4UxlJ7aRr7hoRAoGtAJ4xt+GPojZIviBdaMMOQsuuIo/cIQCggfAm > > GLr2Z5CCs+fxMm5m34gfO7c= > > =upQ2 > > -----END PGP SIGNATURE----- - -- - -- Paul Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iD8DBQFXHzAqUxlJ7aRr7hoRAliQAJ9PfVp0OFm+4P5rB3WelWxiO+qtXQCguAG+ I2lGXyS25vRbmMF8ONxZQLc= =vAZC -----END PGP SIGNATURE-----