[phenixbb] Autobuild error (ligands)

Thomas C. Terwilliger terwilliger at lanl.gov
Thu May 21 06:17:40 PDT 2009

Hi Katya,

I'm sorry for the problem. It could be the ligand as you are guessing, but
it also might be something else in the model that is confusing autobuild. 
In any case this is a bug because autobuild should give you a nice error
message, not stop like that.

Here are some things that should help figure out what is going on:

1. run again, and add the keyword:


This will send output to the terminal and give you a more complete error
message at the end. You can send that error message to me as it has the
line numbers in autobuild where the error occurs.

2. run again, but leave your ligands out of the PDB file, and see if it
still happens.

I'll be very happy to fix the error,
All the best,
Tom T

...>> Hi,
>> I'm using autobuild in phenix-1.4-59 to rebuild the structure.
>> Autobuild throws the error:
>> ****************************************
>> AutoBuild Input failed
>> Sorry, the generation of cif files from
>> AutoBuild_run_2_/TEMP0/LIGANDS.pdb did not work. Error message was:
>> 'NoneType' object has no attribute 'id'
>> ****************************************
>> I think this may have to do with carbohydrates that I have in the
>> structure. I provided the .eff and the .cif files for the carbohydrates
>> but something must be going wrong. Could you, please, let me know how
>> to troubleshoot this error?
>> Katya
>> --
>> Ekaterina Heldwein, Ph.D.
>> Assistant Professor
>> Department of Molecular Biology and Microbiology
>> Tufts University 136 Harrison Ave
>> Boston, MA 02111
>> phone: 617-636-0858
>> fax: 617-636-0337
>> e-mail: katya.heldwein at tufts.edu
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list