Dear Chen,
No, it’s definitely not a waste of our time to report bugs! The GUI shouldn’t report such a misleading, generic message when a failure was detected by Phaser itself.
Could you send me the new logfile (offline) so we can make sure that whatever fix we implement will work with this case as well!
Thanks,
Randy Read
-----
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
> On 5 May 2016, at 22:26, Chen Zhao <[log in to unmask]> wrote:
>
> Yes, that was a stupid mistake where a molecule clashes with a symmetry mate. Thank you so much for your help and sorry for wasting your time!
>
> Best,
> Chen
>
> On Thu, May 5, 2016 at 2:47 PM, Randy Read <[log in to unmask]> wrote:
> If it's like the last one there's probably an indication in the log file. You could send that to me as well, but you might now be able to see yourself what has gone wrong!
>
> Randy
>
> ----
> Randy J. Read
>
> On 5 May 2016, at 17:56, Chen Zhao <[log in to unmask]> wrote:
>
>> 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
>>>
>>>
>>> <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
>>
>>
>
|