This sounds like a case for the Arcimboldo program developed by the Uson group (http://chango.ibmb.csic.es/ <http://chango.ibmb.csic.es/>), of which three versions are in CCP4 (Borges, Lite and Shredder). This will use short secondary structure elements in a mixed MR/ab initio approach. We almost never get it to work with our well-diffracting beta-structured proteins :-(, but for alpha-helical proteins it apparently has a really good success rate.
a recent paper on use of Arcimboldo for coiled coils is here: https://journals.iucr.org/d/issues/2018/03/00/cb5097/ <https://journals.iucr.org/d/issues/2018/03/00/cb5097/> Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 > On 10 Jul 2019, at 10:00, Shengyang Jin <jinshengy...@outlook.com> wrote: > > Dear all, > > We recently acquired a data set (2.0 A, P222) for a coiled coil protein > (according to Itasser, QUARK, Robetta, and Phaser). > Matthews coefficient indicates 1 copy of protein per ASU. Sequence of the > protein is quite novel with no apparent homolog in PDB. > We tried to to MR with various models (ab initio or homology based) but with > little success. > > We then tried to use AMPLE, but in ccp4 it always returned this error: > __main__.py: error: unrecognized arguments: -use_arpwarp True > (if we untick arpwarp and choose buccaneer instead, it returns -use_arpwarp > False) > > Could anyone help? > > Thank you very much. > > > Shengyang Jin > Nanyang Technological University > Singapore > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1><1.jpg> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
