[phenixbb] A question on MR_Rosetta

Terwilliger, Thomas Charles terwilliger at lanl.gov
Wed Mar 18 10:19:04 PDT 2015

Hi Fenyung,

1.  I'm not sure why the error message asking you to supply a sequence alignment didn't come up if you set ncs_copies=1; if you send me the input files I can check to see why not.  I suspect that supplying a sequence alignment is the right thing to do in any case.

2.  When you run Phaser with a given set of parameters you should expect to get the same answer each time.  However when you run mr_rosetta with "prerefine=true" you are generating starting models with Rosetta, which uses a random seed that changes every time.  Consequently it is not surprising that you would get different results. 

I hope that this helps!
All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Ni, Fengyun [fni at bcm.edu]
Sent: Wednesday, March 18, 2015 11:02 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] A question on MR_Rosetta

Hi All,

I am working on a dataset diffracted to ~2.8 A and the highest template identity is about 12%. I am trying MR_Rosetta following the online manual with the following command, hhr file and fragment files are prepared as online manual suggested.

phenix.mr_rosetta seq_file=../seq.dat data=../in.mtz hhr_files=../xxx-align.hhr read_hhpred.number_of_models=1 read_hhpred.number_of_models_to_skip=0  already_placed=False fragment_files=../aat000_03_05.200_v1_3 fragment_files=../aat000_09_05.200_v1_3 rescore_mr.relax=False ncs_copies=2 use_all_plausible_sg=True nproc=8  group_run_command=sh  resolution=4.5 place_model.mr_resolution=4.5 rosetta_modeling.map_resolution=4.5 run_prerefine=true number_of_prerefine_models=1000 >& log

this run ends up with the error message like this,

Trying to adjust the PDB sequence from alignment file:
to match the actual PDB sequence:
New alignment line 4 for PDB:
0 ---------------------------------------------------------------------------------KMNSKELSLKGLCLR--DDGPGIIIVVGNEKSCKFYENLVMK-------------------DMHNNSISKTWEGYLQDCKFKGWFMKVCNDQDSLLRTLGQ------------

Sorry: Sorry, please supply an alignment file for this job.
mr_rosetta cannot automatically generate alignments where there
are deletions required from the PDB file

This only happens when I set ncs_copies=2. If i change ncs_copies=1, no such error.
When I looked at the output file with ncs_copies=2, I find a MR solution with very high TFZ (~16) and high LLG (>500). So I re-run with ncs_copies=2 with the mr_rosetta_params.eff file in the first run, the program ends at the same point. But the MR solutions all have low TFZ (~5) and small LLG (<60).

Here are my two questions,
1) Why does the program stop if i set ncs_copies=2 but not ncs_copies=1?
2) Why the re-run on same data with same parameters give different result?

Thanks in advance for helping me on these problems.

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