Dear Mark and Shengyang, indeed, as Mark pointed out, we have a special mode in ARCIMBOLDO_LITE devised to tackle coiled-coil structures. Trough the ccp4i interface this will be available as an option you can tick when running an ARCIMBOLDO_LITE job. A tutorial is available on our website ( http://chango.ibmb.csic.es/tutorial_coiled) and you can also contact us directly if you have any questions regarding its use.
As for Mark's comment on beta structures, they are always more challenging for a number of reasons, but we have been successful in solving some of them using our libraries of general folds in ARCIMBOLDO_BORGES. There is also an example on our website (http://chango.ibmb.csic.es/tutorial) but if you have any particular question regarding parameterization or you need to generate a library of a fold that it is still not available trough CCP4 you can contact us and well be happy to help. Best wishes, Claudia ---------------------------------------------------------------------------------------- Claudia Millán (cmn...@ibmb.csic.es) Crystallographic Methods Group http://chango.ibmb.csic.es Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain LinkedIn: es.linkedin.com/in/claudiamillan/ <http://es.linkedin.com/pub/claudia-mill%C3%A1n/60/a76/821/> ResearchGate: https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf Twitter: https://twitter.com/cheshireminima El mié., 10 jul. 2019 a las 10:01, Mark J van Raaij (<mjvanra...@cnb.csic.es>) escribió: > This sounds like a case for the Arcimboldo program developed by the Uson > group (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/ > > 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 > <1.jpg> > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
