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Dear Randy, Thank you for your reply! Yes, I was in a rush to generate the log file and made a mistake to have accidentally switched the coordinates for ensemble 1 and 2. But it is good to know that this error code means nothing but phaser encountered something fatal so that it had to terminate. However, I tried it again with the correct setting and it stopped again somewhere much later. I am looking forward to ccp4 updates so that I could see explicitly what the error is. Thanks a lot, Chen On Thu, May 5, 2016 at 12:36 PM, Randy Read <[log in to unmask]> wrote: > Dear Chen, > > I'm copying this response to the BB in case someone else runs into a > similar issue. It turns out that Phaser generated a fatal runtime error > because of a problem with the input, but we'll have to work out how to make > the ccp4i GUI deal with this in a way that makes the problem more obvious > to the user! > > The problem was that your second model is large enough to account for > nearly 90% of what you have specified as the composition. Because you are > telling Phaser to look for 4 copies, it tries to adjust the composition to > make this possible, but then it turns out that the revised composition > could not possibly fit in the asymmetric unit of your crystal! This causes > the fatal error. > > I suspect that you were intending to give Phaser a smaller part of > whatever is in the PDB file for the second model. Perhaps there are > multiple chains in that file and you only wanted to use one as a model? > > Best wishes, > > Randy Read > > On 5 May 2016, at 17:25, Chen Zhao <[log in to unmask]> wrote: > > Dear Randy, > > I appreciate it! Here is the logfile for my most recent run, which did not > go a long way. It ran longer before, but with the same error. However > unfortunately I already deleted those log files... > > Best, > Chen > > On Thu, May 5, 2016 at 12:15 PM, Randy Read <[log in to unmask]> wrote: > >> Dear Chen, >> >> Could you provide a bit more information? Did Phaser run for a while >> before this error message was triggered. If so, could you send me the >> logfile that was produced before it crashed (preferably offline)? >> >> Thanks for reporting the problem! >> >> Best wishes, >> >> Randy Read >> >> On 5 May 2016, at 17:06, Chen Zhao <[log in to unmask]> wrote: >> >> Dear all, >> >> I encountered a fairly common error from phaser (2.6.1) but I do not know >> how to fix it. The error message is: >> >> >> *************************************************************************** >> >> The program run with command: /usr/local/src/ccp4-7.0/bin/phaser >> >> has failed with error message >> >> child killed: segmentation violation >> >> *************************************************************************** >> >> >> I was trying to search for 1 copy of ensemble1 and 4 copies of ensemble2. Alternatively, I also tried search 1 copy of ensemble1 and 4 times 1 copy of ensemble2. And both way yielded this error. >> >> I appreciate your input! >> >> Best, >> >> Chen >> >> >> >> ------ >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: + 44 1223 336500 >> Wellcome Trust/MRC Building Fax: + 44 1223 336827 >> Hills Road E-mail: [log in to unmask] >> Cambridge CB2 0XY, U.K. >> www-structmed.cimr.cam.ac.uk >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www-2Dstructmed.cimr.cam.ac.uk&d=AwMFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=les-enJtWoqo28f8H2sFJttFWw9HMDi0esN1muOvhuE&s=N4oP_sQShupNTM5F9TrVuglMKdUdK_AraUBshZIpsh0&e=> >> >> > <29_phaser_MR.log> > > > ------ > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > Hills Road E-mail: [log in to unmask] > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www-2Dstructmed.cimr.cam.ac.uk&d=AwMFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=UPPCJPPMss8pAGYIAqj35OZFOduwUrC_cm8AgJRlDlI&s=wxTIQnasigGW420JaYYU_R8yL1P9tjs7D2z-Dc9Q7Vo&e=> > >