How to get multiple chains in PDB from Fold and Dock

[Anonymous]

I have attempted to run fold and dock on a protein (see an alternate post on this board for details) with C4 symmetry defined but but when I run:

/home/chxcja/rosetta3.3_bundles/rosetta_source/bin/score.linuxgccrelease -database ~/rosetta3.3_bundles/rosetta_database/ -in:file:silent default-c4membrane.out -in::file::fullatom -out:output

to get a pdb file of the models the pdbs only contain 1 chain.

Does anyone have any ideas how I can get the pdb of the complex (in this case a C4 symmetric structure).

Thanks for your help

Chris

[Anonymous]

Which silent file type is it? (open the file in a text editor, paste a hundred lines or so into a .txt file, and attach it to a post if you aren’t sure). I can’t tell if it’s a problem in fold-and-dock or extraction.

[Anonymous]

Steven,

Thanks for your reply. I think the output is a binary silentfile (attached). I have pasted a chunk below the *** just in case I’m wrong.

Thanks for trying to help

Chris

*************************************************
SEQUENCE: MCAQNDETITASSSIIPSKTAMITRDAALSPTPSNTPEIYLSKLDDSDNNGLDDHHDRNLVMTPITAVKYTYSLALLAFSIILIVSVIFNQGTKLSTVNPWLALCVMVGTIVWLGMMEGQQGALVGLTGVVDHLVYKESHSLAFRNTQLAYRGDNLDRYVTGRQFMVLMCVFVINLCGSPLPGMSESSLNLPQIIEEIFLKTGIAMILMTAMISQLPPQVNASHCMIDFINNYFALFTLYTALIIEFSGVMHASYLIQNIISLISGKPVKTREEPRTRLQASFFWLRVLMSLSTLCFSMAVTVVALFQGKTTMWQGVPEWVSLVLFFVLLTIVGMLEGMQIAFLATSKMRREQRGTSFFGKKTVEVISKKNGQNLPAFFIGRQLMVVGCFFILARVTTPDVEVGTGNNIFGVSDGAQAFLNTGLHAALLMTILASNTWKLAASTFPVAFVNLPFTYILLWCGLILEATGICSGAWVLARILKRVTKLKYDEEYVGTPERPTLSQDYLDAQMPESLVGQSQDVLDEKPGEDREGAKPPESKVPSTDALDEQAQSQGELDVESGLAKSRGPFEGKPIPNPLLGLDSTRT
SCORE: score vdw Mpair rama Menv Mcbeta Menv_non_helix Menv_termini Menv_tm_proj Mlipo hs_pair ss_pair rsigma sheet co clashes_total clashes_bb time description
SCORE: 135.589 14.494 -1.051 -8.508 -7.440 82.097 40.380 0.000 0.000 -24.008 4.414 0.000 0.000 35.211 17.922 0.000 0.000 28379.000 S_00000001
REMARK BINARY SILENTFILE
ANNOTATED_SEQUENCE: M[MET_p:NtermProteinFull]CAQNDETITASSSIIPSKTAMITRDAALSPTPSNTPEIYLSKLDDSDNNGLDDHHDRNLVMTPITAVKYTYSLALLAFSIILIVSVIFNQGTKLSTVNPWLALCVMVGTIVWLGMMEGQQGALVGLTGVVDHLVYKESHSLAFRNTQLAYRGDNLDRYVTGRQFMVLMCVFVINLCGSPLPGMSESSLNLPQIIEEIFLKTGIAMILMTAMISQLPPQVNASHCMIDFINNYFALFTLYTALIIEFSGVMHASYLIQNIISLISGKPVKTREEPRTRLQASFFWLRVLMSLSTLCFSMAVTVVALFQGKTTMWQGVPEWVSLVLFFVLLTIVGMLEGMQIAFLATSKMRREQRGTSFFGKKTVEVISKKNGQNLPAFFIGRQLMVVGCFFILARVTTPDVEVGTGNNIFGVSDGAQAFLNTGLHAALLMTILASNTWKLAASTFPVAFVNLPFTYILLWCGLILEATGICSGAWVLARILKRVTKLKYDEEYVGTPERPTLSQDYLDAQMPESLVGQSQDVLDEKPGEDREGAKPPESKVPSTDALDEQAQSQGELDVESGLAKSRGPFEGKPIPNPLLGLDSTRT[THR_p:CtermProteinFull] S_00000001
LAAAAAAAAAAAAAAAAH/pu/AAAAAAAAAAA1DJAAlBy1+DAAAAApVVQAF/Ea/DvXQyPmqi//cKgF9rxfq5v8hyMAxrbQAczVV9vAAAA/e9sd7LAAA0v S_00000001
L5Kyq/gn1TAUWCkzv4Cr4/8NrsBUygN1vXnEF/YWlUCU15g2vRoXe+uSYRCETai+vtR7IAJxZtB047iAwl5EZANm/yBkTPMBwK9QA/kiGBAUMPt5v S_00000001
LPz+++8I9xCUrfsUPvegH/KRLQD0J3ndPVktR/eG8nDETjt5vqpdV+kLqzDUtV1+vTyf1+29ovDUAUA6PFDi1+SjovDUqx/5PP3zm/ImYzC0/0F0P S_00000001
LWVYAATp9uDEfv78vITCFAP/9BEEa2iDwJb+ZAzGZOEUlYRDwyETkA30fIEUTdUAwcVIGAT9/iD0cPCIwZvIw/G1dMDUb9sKwd1oMAr6hlDEVdO4v S_00000001
LkwUbAjpnfEUFhXGwImPnAzi6sEk54eGw+xtoADYY3EUm89Jw2+7gA3D27EEQwXLw8k/mA7i09EEFHICwCBopAXun/EUSPV8vVCwOAL5mjE0+bWIw S_00000001
LuPvyA3vQ7EUzTtKw26P1AvzNFF0cPRNwDEh/ATdRSFU3gGNw3tWDB7RMNF0W3iLw2oO2A3JP0EE+jdPwYn1xAjvctE09geQwOhx4ADjN3EknsdJw S_00000001
Lo1EABjxHjFkiutOwxbxEBbn8wFEsFwOwSMnFBjCy6FEaOwQwAZyBBDLb+F0tpfRwcRQEB3ySBGkkQpMwZfuFBHYOGGUUdjJww395Af+bmF0Xl8Pw S_00000001
Lx+oKB3PD/FEn2FRwcf/LBbRPEGkBbYSweMBRBbOFLGEpMSSwu7iUBnH9IGE/6dRw5/0MBjUM3FkwXdTwwKEMBXl/vFk93xTwTjmNB7br7FEDBcQw S_00000001
LpqURB3qTTGEe1HTwl76VBr3eaG0ReITwQw3WBziFfGUfchUwvvHTBXcfgGEBQTVwioNVB/9ujG0laISwCYuVBHfNmGkxAGRwVnSOB36nUGECPxTw S_00000001
L8J6bBfJbhGENE1UwmJXdBjI4lGEiHIWwHzIhBPBCtGE+KBWwaG3iBrvUrGE5lKVwcYdeBDyAdGU4QKXwngydBHeSZGUDLeXwBmzeB/OFgGEaUJUw S_00000001
HuVShB7LD1Gkry4Ww+JijB/6e8GEdA5WwpgKmBPtq2GkY7IXw3JIoBP/W4GkdWbWwDuGjBjVLFH0Ry7XwdzGjBf9KFH0Qw7XwbCnfBbUB2GkeCkXw S_00000001
HzOMmBznzvG087EYwXqkoBfpopGk4qPYwY/hpBzFFjG0GGTXwK31rBPB6jGkts4Ww5yAoB/vZiGE1k1YwZddnB7fxfG0MRAZwzLhkBj31uG0HpWYw S_00000001
HDgvnBDGkcG0A7vWwO8ZoBnY0VGUG0mVwyrZpBTHfcGEesbUws6crBP5+ZG0X90TwEg/lBrqPPG0AlMVwzy8kBXUOOG0N3GVwQ/3lBnsRcGkldIXw S_00000001
HuA8nB7L/kGUFZHUwcNroBTnDsGkZBBTw3RfrBvFfwGkf8MTwyY5sB3sqyGEvtOSw7+qmBrNH1G0jc5SwJa9lBbgK4GE1RDTw6WRmBfAmmGEqlpUw S_00000001
HxCTsB3GzxGE0QdUwrN7uBzXL2GU7fxUwaAIxBvHBuGUPkgUwFwezB3/zwGkKdbUwutFvBDV35G0uXPWwV/suBTfcAHkDe7Wwg2DrBHYtvGkziNVw S_00000001
LF9VwBbq6jGkE6XUwmHQyBHjTbGEouIUwIqVzB/msbGUIttSwQs3xB/c7ZG0IEwRwNM/wBDXQQGkOyYUw6AiwBvqOKG0vEJVwBCYuBDIKiG0b8bUw S_00000001
L8061BLiBeGEorlSwVaN3B/2neGk+ISRwaaJ3Bfg1TGE30kQwWnD3BvjcLGEy+NRwWDF6BnxQiG0IVmRw5q+4BrClhG0f3STw S_00000001
LziM3BH9GUGEjqfOwyNO3BLGWKGEpk5MwN8i5BHzHDGko9rNwgCO5B3k2yFkzC+NwdiX3Bj7ENGUOt8JwcDp3Bb7NPGEOrCJwGzN3BD5QbGk0njNw S_00000001
L7K57Bbr5HGUkfCOw/yS+Bzb3BG06HuOw+bf+BrcCAGEXP3QwoOVACb7b8FkWWZRwAWZACzDqHGk6etNwEP9BCTHxIGEyh3KwzJB8BLA7PGEHD1Nw S_00000001
LndN8BbJiAGEbsiRwWnG8BHG48FEKb+Sw7UN8Brl9kF0o7QTwtlb6BPQ8YFUNO3Sw8xj5B/mKDGU+FnTwkK34B/oxGGU0RvTwjbg6BDPaCG04XDRw S_00000001
E2RT+BngJeFUlr9Twkbq+BjVmHFEGmSUwoXn+BTXBEFk/AzVwbWm/BbEQRFEHKkWwbcoAC7jS/E0NesTwiZoACToS/E0rhsTwjVr/B/c3oFUfuRUw S_00000001
EKwd9BbuDyEkfuNWwse09BrOMqEkY1kXwEjd/BraqVEUPFmXw3sg+B/RuEEUxzLXwqmG7BPBfmEU4fHYw/I94BvegwE0WHvYwmJU8BDtopEUNokVw S_00000001
ES09ACX0RXEkhYCYwby9BCzhtGEEd01XwAiDCCfo1uDUYwgYwgSTCCDdO8DkM9EZw8wWDCLRaQEEc3kXwPPBECnLAXEk9L0WwTAOBCvcUkEEzqTYw S_00000001
EBq2BCTisFD0GLYYwe3tBCHG+lCkWG6Ywz9pCCDjQACE69yYwKg/CC/xSrBk2lOYw9WRACD/SVCU3Y9Yw6fZ/BfdAYC0JFAZwF3yBCfxJ8CELtyXw S_00000001
Lg3EDC/eNYB095VZwBTyDCn91GA00hTZwQT0CCjfmu9zgzUZwcFKDCfA534Lh2HZwtx2ECL929/j161ZwNZEHC/5NDAU/tZawej5CCTnnyB062yZw S_00000001
LL8mBCDZpX+zvfkZw8OiACHCBN5zpeiZwXRt/B/aob5Dh42YwlGFAC/stO+z+AdYwM2A/BjRlp7Dv0Fawruh+B/LcJ4TLwjawsbbBCT3PFAEILyZw S_00000001
L1YC+BTk4J9b06uYwprh8Bjpnd974FHYwhgX6BvMhU5TMSFYw/qg4BLV+X5TtJfYw9GT7BXa6PAMZ5BYwOGT7Br61PAcR5BYwQwz9BnEHC/rmBFZw S_00000001
LK0n6BXxEP+zPKNXwqMq4BHviLA02bBXwQa31Br+EO/TqA0WwURf1BHjos8jPQCWwKqc5BfSdEB0ni2Vw3jc5BP/aEB05k2VwO3N8BfVRJ+jNllWw S_00000001

[Anonymous]

I think the problem lies with my calculation. Changing my settings now gives me a silent file (attached) with the correct number of sequences in the annotated sequence….

ANNOTATED_SEQUENCE: M[MET_p:NtermProteinFull]CAQNDETITASSSIIPSKTAMITRDAALSPTPSNTPEIYLSKLDDSDNNGLDDHHDRNLVMTPITAVKYTYSLALLAFSIILIVSVIFNQGTKLSTVNPWLALCVMVGTIVWLGMMEGQQGALVGLTGVVDHLVYKESHSLAFRNTQLAYRGDNLDRYVTGRQFMVLMCVFVINLCGSPLPGMSESSLNLPQIIEEIFLKTGIAMILMTAMISQLPPQVNASHCMIDFINNYFALFTLYTALIIEFSGVMH[HIS_D]ASYLIQNIISLISGKPVKTREEPRTRLQASFFWLRVLMSLSTLCFSMAVTVVALFQGKTTMWQGVPEWVSLVLFFVLLTIVGMLEGMQIAFLATSKMRREQRGTSFFGKKTVEVISKKNGQNLPAFFIGRQLMVVGCFFILARVTTPDVEVGTGNNIFGVSDGAQAFLNTGLHAALLMTILASNTWKLAASTFPVAFVNLPFTYILLWCGLILEATGICSGAWVLARILKRVTKLKYDEEYVGTPERPTLSQDYLDAQMPESLVGQSQDVLDEKPGEDREGAKPPESKVPSTDALDEQAQSQGELDVESGLAKSRGPFEGKPIPNPLLGLDSTRT[THR_p:CtermProteinFull]M[MET_p:NtermProteinFull]CAQNDETITASSSIIPSKTAMITRDAALSPTPSNTPEIYLSKLDDSDNNGLDDHHDRNLVMTPITAVKYTYSLALLAFSIILIVSVIFNQGTKLSTVNPWLALCVMVGTIVWLGMMEGQQGALVGLTGVVDHLVYKESHSLAFRNTQLAYRGDNLDRYVTGRQFMVLMCVFVINLCGSPLPGMSESSLNLPQIIEEIFLKTGIAMILMTAMISQLPPQVNASHCMIDFINNYFALFTLYTALIIEFSGVMH[HIS_D]ASYLIQNIISLISGKPVKTREEPRTRLQASFFWLRVLMSLSTLCFSMAVTVVALFQGKTTMWQGVPEWVSLVLFFVLLTIVGMLEGMQIAFLATSKMRREQRGTSFFGKKTVEVISKKNGQNLPAFFIGRQLMVVGCFFILARVTTPDVEVGTGNNIFGVSDGAQAFLNTGLHAALLMTILASNTWKLAASTFPVAFVNLPFTYILLWCGLILEATGICSGAWVLARILKRVTKLKYDEEYVGTPERPTLSQDYLDAQMPESLVGQSQDVLDEKPGEDREGAKPPESKVPSTDALDEQAQSQGELDVESGLAKSRGPFEGKPIPNPLLGLDSTRT[THR_p:CtermProteinFull]M[MET_p:NtermProteinFull]CAQNDETITASSSIIPSKTAMITRDAALSPTPSNTPEIYLSKLDDSDNNGLDDHHDRNLVMTPITAVKYTYSLALLAFSIILIVSVIFNQGTKLSTVNPWLALCVMVGTIVWLGMMEGQQGALVGLTGVVDHLVYKESHSLAFRNTQLAYRGDNLDRYVTGRQFMVLMCVFVINLCGSPLPGMSESSLNLPQIIEEIFLKTGIAMILMTAMISQLPPQVNASHCMIDFINNYFALFTLYTALIIEFSGVMH[HIS_D]ASYLIQNIISLISGKPVKTREEPRTRLQASFFWLRVLMSLSTLCFSMAVTVVALFQGKTTMWQGVPEWVSLVLFFVLLTIVGMLEGMQIAFLATSKMRREQRGTSFFGKKTVEVISKKNGQNLPAFFIGRQLMVVGCFFILARVTTPDVEVGTGNNIFGVSDGAQAFLNTGLHAALLMTILASNTWKLAASTFPVAFVNLPFTYILLWCGLILEATGICSGAWVLARILKRVTKLKYDEEYVGTPERPTLSQDYLDAQMPESLVGQSQDVLDEKPGEDREGAKPPESKVPSTDALDEQAQSQGELDVESGLAKSRGPFEGKPIPNPLLGLDSTRT[THR_p:CtermProteinFull]M[MET_p:NtermProteinFull]CAQNDETITASSSIIPSKTAMITRDAALSPTPSNTPEIYLSKLDDSDNNGLDDHHDRNLVMTPITAVKYTYSLALLAFSIILIVSVIFNQGTKLSTVNPWLALCVMVGTIVWLGMMEGQQGALVGLTGVVDHLVYKESHSLAFRNTQLAYRGDNLDRYVTGRQFMVLMCVFVINLCGSPLPGMSESSLNLPQIIEEIFLKTGIAMILMTAMISQLPPQVNASHCMIDFINNYFALFTLYTALIIEFSGVMH[HIS_D]ASYLIQNIISLISGKPVKTREEPRTRLQASFFWLRVLMSLSTLCFSMAVTVVALFQGKTTMWQGVPEWVSLVLFFVLLTIVGMLEGMQIAFLATSKMRREQRGTSFFGKKTVEVISKKNGQNLPAFFIGRQLMVVGCFFILARVTTPDVEVGTGNNIFGVSDGAQAFLNTGLHAALLMTILASNTWKLAASTFPVAFVNLPFTYILLWCGLILEATGICSGAWVLARILKRVTKLKYDEEYVGTPERPTLSQDYLDAQMPESLVGQSQDVLDEKPGEDREGAKPPESKVPSTDALDEQAQSQGELDVESGLAKSRGPFEGKPIPNPLLGLDSTRT[THR_p:CtermProteinFull]XXXX S_0001

Unfortunately although I use the -out:pdb flag no pdb’s are automatically generated. And when I run …

score.linuxgccrelease -database ~/rosetta3.3_bundles/rosetta_database/ -in:file:silent default.out -in::file::fullatom -out:output

to try to generate my pdb’s manually I get the following error.

*******************
Starting work on structure: S_0001_0001 <--- S_0001
USERTAGS:
protocols.jobdist.main: Working on: S_0001

ERROR: !core::pose::symmetry::is_symmetric( pose )
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 577

*******************

So clearly re-scoring to get a pdb is choking on the symmetry of the system (C4).

Does anyone have any ideas how I can get my structures out?

Thanks

Chris

[Anonymous]

I tried adding the -rescore:output_only flag (mentioned in http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d2/da0/score_commands.html) to see if I can by pass it and I get an error…

score.linuxgccrelease -database ~/rosetta3.3_bundles/rosetta_database/ -in:file:silent default.out -in::file::fullatom -out:output -rescore:output_only
ERROR: Option matching -rescore:output_only not found in command line top-level context

[Anonymous]

Try score_jd2.linuxgccrelease -database $$ -in:file:silent default.out -in:file:silent_struct_type binary -out:pdb -in:file:tags S_0001

Add as many tags as you need; I like to put them in a flat file and pass “-in:file:tags `cat tags`” (note the backticks)

[Anonymous]

Hi Steven

Thanks for the quick response. I had ago with your recommendation
/home/chxcja/rosetta3.3_bundles/rosetta_source/bin/score_jd2.linuxgccrelease -database ~/rosetta3.3_bundles/rosetta_database/ -in:file:silent output-firstrun.txt -in:file:silent_struct_type binary -out:pdb -in:file:tags S_0001

But unfortunately I still get the same error message:
ERROR: !core::pose::symmetry::is_symmetric( pose )
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 577

Chris

[Anonymous]

There is apparently a trick to extracting symmetric poses: you need to provide a symmetry definition file (-symmdef_file, or -symmetry_definition, or something like that).

The contents of the flag get ignored, but its presence triggers a symmetry mode that you need, so it can be an empty file (or just use the real file you had earlier).

(I haven’t tried this – this is from a lab coworker)

[Anonymous]

Fantastic, adding -symmetry_definition and a link to my symmetry definition file spat out the symmetric model

The full command I used

/home/chxcja/rosetta3.3_bundles/rosetta_source/bin/score_jd2.linuxgccrelease -database ~/rosetta3.3_bundles/rosetta_database/ -in:file:silent output-firstrun.txt -in:file:silent_struct_type binary -out:pdb -in:file:tags S_0001 -symmetry_definition input/elizC4.symm

That’s brilliant, thanks very much for your help.

Chris

[Anonymous]

That’s definitely a binary silent file, and the file itself is set up for a single, nonrepeated chain (the annotated sequence contains only one N and C terminus and no repeats). This means it’s a problem in fold-and-dock, not extraction; I’ve forwarded this along.

[Author]

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