How to run partial_thread in RosettaCM when residure are more than 9999?

[Anonymous]

One step in RosettaCM is 

partial_thread.default.linuxgccrelease -in:file:fasta JN254802.fasta -in:file:alignment JN254802_5tx1.grishin -in:file:template_pdb 5tx1_clean.pdb

But there are more than 9999 residues in the JN254802.fasta. The output “5tx1_clean.pdb.pdb” writes residue number 10000, 10001, 10002, etc as 1000, because only four positions are allowed for residue numbering (see the example in the end of this post).

I am happy to renumber the output by a script. But how do I know when is the atom line for the next residue? Sometimes, there are two same residues consecutively occurring.

Also, can I confirm, does the residue numbering of the output of partial_thread MUST be from 1 to the end, throughout all the chains? Or can each chain be numbered from 1, so that it is worthwhile to renumber the output PDB by myself?

 

ATOM  15440 1HG2 VAL A9999      86.527 125.437 358.029  1.00  0.00           H  

ATOM  15441 2HG2 VAL A9999      85.053 124.741 357.313  1.00  0.00           H  

ATOM  15441 3HG2 VAL A9999      86.653 124.271 356.691  1.00  0.00           H  

ATOM  15441  N   ASN A1000      83.030 125.717 355.432  1.00  0.00           N  

ATOM  15441  CA  ASN A1000      81.771 125.126 355.834  1.00  0.00           C  

ATOM  15441  C   ASN A1000      80.989 124.419 354.760  1.00  0.00           C  

ATOM  15441  O   ASN A1000      79.890 123.938 355.002  1.00  0.00           O  

ATOM  15441  CB  ASN A1000      80.904 126.198 356.452  1.00  0.00           C  

ATOM  15441  CG  ASN A1000      80.557 125.883 357.866  1.00  0.00           C  

ATOM  15441  OD1 ASN A1000      80.120 126.753 358.615  1.00  0.00           O  

ATOM  15441  ND2 ASN A1000      80.745 124.619 358.253  1.00  0.00           N  

ATOM  15442  H   ASN A1000      83.103 126.722 355.367  1.00  0.00           H  

ATOM  15442  HA  ASN A1000      81.973 124.351 356.575  1.00  0.00           H  

ATOM  15442 1HB  ASN A1000      81.426 127.155 356.415  1.00  0.00           H  

ATOM  15442 2HB  ASN A1000      79.987 126.303 355.872  1.00  0.00           H  

ATOM  15442 1HD2 ASN A1000      80.530 124.346 359.191  1.00  0.00           H  

ATOM  15442 2HD2 ASN A1000      81.100 123.946 357.605  1.00  0.00           H  

ATOM  15442  N   MET A1000      81.548 124.357 353.568  1.00  0.00           N  

ATOM  15442  CA  MET A1000      80.859 123.696 352.488  1.00  0.00           C  

ATOM  15442  C   MET A1000      81.622 122.436 352.132  1.00  0.00           C  

ATOM  15442  O   MET A1000      81.037 121.377 351.924  1.00  0.00           O  

ATOM  15443  CB  MET A1000      80.790 124.618 351.279  1.00  0.00           C  

ATOM  15443  CG  MET A1000      79.833 124.149 350.198  1.00  0.00           C 

 

---

An update: I have written a script to renumber the residues from 1 for each chain for the output “5tx1_clean.pdb.pdb”, so that the maximum residue number does not exceed 9999. Then I run the next step: rosetta_scripts.mpi.linuxgccrelease @rosetta_cm.options, and I got the error:

protocols.hybridization.HybridizeProtocol: (0) [ ERROR ] Sequence mismatch between input fasta and template JN254802_on_5tx1.pdb at residue 1

protocols.hybridization.HybridizeProtocol: (0) [ ERROR ]    Expected: M   Saw: A

protocols.hybridization.HybridizeProtocol: (0) [ ERROR ] THE PDB INFO IS NOT IN SYNC WITH THE FASTA. ATTEMPTING TO RESOLVE THE ISSUE AUTOMATICALLY

This is because, in the second chain, the first two residues are “MA”, but “M” is not resolved in the structure, so only “A” exists in the PDB and was renumbered as 1.

So basically, it seems that the residues MUST be numbered from 1 to the very end, without considering the chains.

 

[Anonymous]

Hello,

What does the logs say after “ERROR” THE PDB INFO ….

 

it should try to correct it, and it should work with your renumbered, or the original un-renumbered pdb.

[Anonymous]

Hi Danpf,

After [ ERROR ] THE PDB INFO IS NOT IN SYNC WITH THE FASTA. ATTEMPTING TO RESOLVE THE ISSUE AUTOMATICALLY,

it is 

protocols.hybridization.HybridizeProtocol: (0) score: 1.58368e+06 identities: 13229/15862 gaps: 2633/15862

protocols.hybridization.HybridizeProtocol: (0)               target       1 MATPSMLPQWAYMHIAGQDASEYLSPGLVQ……………………..(omit very long sequence)

protocols.hybridization.HybridizeProtocol: (0)             pose_seq       1 MATPSMLPQWAYMHIAGQDASEYLSPGLVQ……………………..(omit very long sequence)

protocols.hybridization.HybridizeProtocol: (0) 

protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named “hybridize” of type Hybridize

protocols.rosetta_scripts.ParsedProtocol: (0) ParsedProtocol mover with the following movers and filters

protocols.rosetta_scripts.ParsedProtocol: (0) added mover “hybridize” with filter “true_filter”

protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN MOVER Hybridize – hybridize=======================

protocols.hybridization.HybridizeProtocol: (0) Found 12 domains using template JN254802_on_5tx1.pdb

protocols.hybridization.HybridizeProtocol: (0) domain 1: LOOP  begin  end  cut  skip_rate  extended

protocols.hybridization.HybridizeProtocol: (0) LOOP start: 1  stop: 992  cut: 0  size: 992  skip rate: 0  extended?: False

……(omit below)

 

In addition to the three error lines I posted, the following error lines are at the end of the log file. There are no other error lines.

protocols.rosetta_scripts.ParsedProtocol: (0) [ ERROR ] Exception while processing procotol: 

File: src/core/fragment/util.cc:178

[ ERROR ] UtilityExitException

ERROR: Assertion `tlen < slen` failed.

protocols.jd2.JobDistributor: (0) [ ERROR ] 

[ERROR] Exception caught by JobDistributor for job S_0001

File: src/core/fragment/util.cc:178

[ ERROR ] UtilityExitException

ERROR: Assertion `tlen < slen` failed.

protocols.jd2.JobDistributor: (0) [ ERROR ] 

protocols.jd2.JobDistributor: (0) [ WARNING ] S_0001 reported failure and will NOT retry

protocols.jd2.JobDistributor: (0) no more batches to process… 

protocols.jd2.JobDistributor: (0) 1 jobs considered, 1 jobs attempted in 4118 seconds

Error: (0) [ ERROR ] Exception caught by rosetta_scripts application:

File: src/protocols/jd2/JobDistributor.cc:328

1 jobs failed; check output for error messages

Error: (0) [ ERROR ] 

 

The log file is 121 MB, which can be downloaded at (only for 10 days) (I use EmEditor to open large txt file).

pick-up URL: https://wwwapps-live.ucl.ac.uk/cgi-bin/dropbox/dropbox-https.cgi?state=pickup_info&id=7b17c2a

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Pickup passcode is 65693efb.

 

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