Re: [ccp4bb] "Core dumped" problem when running autoSHARP

[Thanh Nguyen]

Thank you all for information and suggestion. I have tried with stand-alone SHARP (meant with command line) but it yielded the same problem. For running on the SHARP server, I couldn´t get it work as it required the .htgroup file in the sushi configuration folder. Indeed, it worked with my boss computer. So, there must be something wrong with my programs. But in this case, the dataset is not obviously good either to solve it straight away (dataset is good at 3.0A and CCanom overall is at about 0.2). That could be the reason why it generated the error when auto building struggled to build the model. ‎ ‎I will try with other suggestions such as Phenix (usually takes quite a long time to finish) and Solve/Resolve (not free license for non-US academic version). Thanks you very much, Thanh Nguyen On Wed, Sep 28, 2016 at 1:25 AM, abhimanyu singh <abhisingh....@gmail.com> wrote: Hi Thanh, A floating point exception is raised when an invalid or erroneous operation is executed by the program routine. In absence of any subroutine to handle this signal, the core is dumped and program terminates. Your log file shows that in the last internal autobuilding cycle 22 residues were sequenced after pruning while 23 were uniquely allocated which, most likely is the problem. The reason is unclear to me and the code developers should be able to shed more light on it. Meanwhile you may try a different version of the program. Greetings, Abhi Abhimanyu Kumar Singh, Ph.D. School of Biosciences University of Kent Canterbury, UK. On 27 Sep 2016 22:39, "Thanh Nguyen" <hongthanh1...@gmail.com> wrote: Dear All, I got the problem when running autoSHARP for automated phasing one of my Hg derivative dataset (good at 3.0 Angstrom). Program started okay and kept running until the density modification step. In the first round of automatic model building by buccaneer, it stopped with an error message: "Floating point exception (core dumped)" (log file attached). I tried with different computers (but the same version of CCP4i and autoSHARP) and got the same problem. I have looked up it on the Internet but did not find any useful information. Does someone have idea about the source of the problem and the solution to fix it? Thank you very much, Thanh Nguyen -- ============================ Nguyen Hong Thanh, Ph.D. student Lab 20B. Macromolecular Structures Department Centro Nacional de Biotecnologia, CSIC C/ Darwin 3, Campus de Cantoblanco 28049, Madrid, Spain -- ============================ Nguyen Hong Thanh, Ph.D. student Lab 20B. Macromolecular Structures Department Centro Nacional de Biotecnologia, CSIC C/ Darwin 3, Campus de Cantoblanco 28049, Madrid, Spain ============================ Genetic Engineering Laboratory Institute of BioTechnology Viet Nam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam