[phenixbb] Autobuild with "build semet residues"

Wed Dec 10 15:06:33 PST 2014

Hi Todd,

I'm sorry for the problem!  This sounds like a bug; I haven't seen this happen before.  I just did a little test run with an MSE model with rebuild_in_place=True as you did and it seems to run fine in my demo case.   In your log file (or the sub_log files RUN_FILE_xxx.log ) it is supposed to say "model has selenomethionine as MSE" just before refinement, then it should refine with MSE and not complain.  Does it have that line?  I'm guessing something unusual happened in model-building late in the rebuilding cycles but it is hard to tell what.

Can you possibly send me all the input files and the full log file and I'll have a look?

All the best,
Tom T

On Dec 10, 2014, at 3:55 PM, Todd Jason Green wrote:

Hello all-

I have been trying to use autobuild with a semet dataset. I have checked the "build semet residues" option in the autobuild gui. At some point after the composite build, the error below is generated and the final model has been stripped of all semethionines. I am using phenix version 1.8.4-1496 on a macbook. I have now downloaded the new version. But can someone expand on my problem. My input sequence and model pdb contain Methionine but I expected the rebuild process to alter them. Should I change the one letter code for semet from m to something else.

-Todd

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Final composite model # 1 :  AutoBuild_run_11_/MULTIPLE_MODELS/model.pdb_1
Final composite mtz # 1 :  AutoBuild_run_11_/MULTIPLE_MODELS/resolve_composite_map.mtz_1

AutoBuild_combine_iter  AutoBuild  Run 11 Wed Dec 10 14:51:18 2014

AutoBuild_combine  AutoBuild  Run 11 Wed Dec 10 14:51:18 2014

 Done with combine

finished  AutoBuild  Run 11 Wed Dec 10 14:51:18 2014

Finishing  AutoBuild Run 11
Facts written to AutoBuild_run_11_/AutoBuild_Facts.dat

Warnings:
Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_:
NOTE: The following residues (and similar residues) from
AutoBuild_run_5_/overall_ortho_best_bchain_molrep1_refmac1_semettomet_ed.pdb are not PROTEIN or do not
match the sequence  and will not be part of the building process :
MSE B33, MSE B45, MSE B59, MSE B63, MSE B68, MSE B194, MSE B201, MSE B210, MSE B216, MSE B256, MSE B266, MSE B308, MSE A33, MSE A45, MSE A59, MSE A63, MSE A68, MSE A194, MSE A201, MSE A210, MSE A216, MSE A256, MSE A266, MSE A308, MSE C33, MSE C45, MSE C59, MSE C63, MSE C68, MSE C194, MSE C201, MSE C210, MSE C216, MSE C256, MSE C266, MSE C308, MSE D33, MSE D45, MSE D59, MSE D63, MSE D68, MSE D194, MSE D201, MSE D210, MSE D216, MSE D256, MSE D266, MSE D308,

Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_:

Warning: some residues not rebuilt successfully on cycle 2:
Chain 'A':   32,   44,  200,  217- 221,  280- 299,  314- 323,
Chain 'C':   22-  32,   39-  44,  148- 152,  163- 167,  188- 193,  211- 215,  217- 221,  334- 336,
Chain 'B':   32,   44,  118- 122,  193,  227- 231,  309- 318,
Chain 'D':   12-  32,   34-  44,   46-  50,  143- 147,  158- 162,  188- 193,  334- 336

Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_:

Warning: some residues not rebuilt successfully on cycle 3:
Chain 'A':   32,   39-  44,  193,  217- 226,  280- 294,
Chain 'C':   22-  32,   34-  44,   46-  55,  153- 162,  193,  200,  211- 215,  217- 221,  242- 246,  324- 336,
Chain 'B':   32,   44,  118- 122,  193,  262- 265,  319- 323,
Chain 'D':   17-  32,   34-  44,   46-  50,  143- 162,  188- 193,  200,  334- 336

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