Dear Shengyuang,
Some further suggestions. To create a model towards MR searches, you could try our server for modelling coiled coils: https://pharm.kuleuven.be/apps/biocryst/ccfold.php It takes a few seconds to run. The reference is here: https://www.ncbi.nlm.nih.gov/pubmed/28968723 I recommend trying a full-length model but also truncated versions (e.g. 1/2 of the total length; those may be more accurate locally). Another thought, if you happen to have data for several crystal forms do try them all towards MR. The success of MR with coiled coils is highly dependent on the packing/space group. Some discussion on the matter can be found here: https://www.ncbi.nlm.nih.gov/pubmed/28101862 HTH, Sergei Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of Pharmaceutical Sciences, KU Leuven O&N2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab pages: http://pharm.kuleuven.be/Biocrystallography<http://pharm.kuleuven.be/anafar> ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Shengyang Jin <jinshengy...@outlook.com> Sent: Wednesday, July 10, 2019 10:00 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] MR for coiled coil structure 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
