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Anonymous.
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December 16, 2011 at 10:45 pm #1121
Anonymous
I would like to substitute one of the serines (S43) in my sequence to be phosphorylated. How would I do that?
I tried substituting [SER_p] in the fasta sequence and -residues:patch_selectors phosphorylation but that did not work. Any suggestions?
Thanks!
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December 19, 2011 at 12:00 am #6439
Anonymous
I think you read SER_p from annotated sequence files that look like [SER_p:Cterminusful] or something like that. The problem is that the p does not stand for phosphate, it stands for patch, indicating it is a patched residue.
I don’t know what the annotation code for phosphoserine is. I think it will be [SER_p:phosphorylated], assuming it’s otherwise a normal (not terminus, etc) residue. That’s from its patch file at rosetta_database/chemical/residue_type_sets/fa_standard/patches.
To get it for sure, find (any) phosphoserine PDB. Get Rosetta to read it in correctly with score_jd2, using the -out:pdb flag, and make sure the output PDB still has phosphoserine. If that works, then use -out:file:silent result.out -out:file:silent_struct_type binary on the same file; the result silent file will have an annotated sequence line. You can copy the phosphoserine residue name from that. Let me repeat: this doesn’t have to be your protein, just any P-ser to copy from.
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December 20, 2011 at 12:46 am #6450
Anonymous
I think I might know what the problem is. The centroid folding aspect of ab initio didn’t recognize the Ser_p:phosphorylated patch. I tried -ignore_unrecognized_res but it didn’t work, so I added a ser_phosphorylated.txt (similar to tyr_sulphated patch) modified centroid/patches.txt to include the same.
Now I have a different problem:
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===================================================================
Finished Abinitio
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can not find a residue type that matches the residue SER_p:phosphorylatedat position 43ERROR: core::util::switch_to_residue_type_set fails
ERROR:: Exit from: src/core/util/SwitchResidueTypeSet.cc line: 135
Any suggestions?
To answer your previous question the patches.txt (../fa_standard/) file does contain the uncommented path to the ser_phosphorylated.txt and -run:level 500 doesn’t work. -
December 21, 2011 at 2:25 am #6456
Anonymous
The [SER_p:phosphorylated] patch works separately but it doesn’t work in conjugation with another patch. i.e. can’t use two patches together. The centroid fix works well for ab initio folding.
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March 19, 2012 at 8:47 pm #6828
Anonymous
I know this is an old thread, but I have the exact same problem. My patch file appears to have worked for ab-initio, but not in conjunction with another patch. Any advice?
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March 19, 2012 at 8:53 pm #6829
Anonymous
Can you be more specific? Does it not work because the double-patched residue type is not created, or because the double-patched residue type is dysfunctional? You can check what gets created with -out:level 500, which will produce *gobs* of output on which residue types exist.
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March 19, 2012 at 9:27 pm #6830
Anonymous
My specific error is:
can not find a residue type that matches the residue ASN_p:glyat position 70
ERROR: core::util::switch_to_residue_type_set fails
ERROR:: Exit from: src/core/util/SwitchResidueTypeSet.cc line: 135Applying -out:levels does give a ton of information. What am I looking for in it though?
The score application reads the fullatom patch just fine.
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March 20, 2012 at 2:52 pm #6832
Anonymous
Looks like that was it. I needed to include the patch file in the centroid directory as well. Thanks everybody.
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December 19, 2011 at 10:51 pm #6448
Anonymous
I tried [SER_p:phosphorylated] (and also confirmed the usage using score_jd2 with a phosphoserine pdb) and still obtained the error:
ERROR: unrecognized residue name ‘SER_p:phosphorylated’
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.hh line: 151Is there anything else I can try?
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December 19, 2011 at 11:53 pm #6449
Anonymous
Er, I should have checked this first – is it available as a residue type? Try checking patches.txt (the full path to approximately there was in my earlier post) to see that it’s not commented out (no # in front of it). Also try running Rosetta in super-verbose mode (I think it’s -run:level 500; I know there’s a thread about it on the board somewhere). It will output a huge list of all the residue types that exist, look for your phosphoserine there to confirm Rosetta is creating it properly.
I can find that flag for you later if you can’t find it.
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March 20, 2012 at 12:22 am #6831
Anonymous
That error message looks to me like you’re having a centroid/fullatom issue. You probably should check that the residue patches you’re trying to use exist both in the centroid parameter set and the full atom parameter set. (Also, you’re not using the -correct flag, by any chance, are you?)
Regarding the output, usually the relevant lines are the ones at the very end – the ones which are output just before the program terminates. – But Steven is also referring to early on in the log where you’ll see a large number of lines like
core.chemical: successfully patched: SER_p:NtermProteinFull to: SER_p:NtermProteinFull_p:phosphorylated
You can check those lines to see if your desired patched residue was actually created.
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