Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Camelid antibody (VHH) modelling
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Anonymous.
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April 5, 2017 at 5:52 am #2629
Anonymous
Im modelling a camelid antibody (vhh) amino acid sequence using Rosetta (rosetta_src_2016.32.58837_bundle). I cannot generate these input files : “FR02_H.pdb”, “FR02.cst”, “FR02.cst_fa”. Please tell me which ‘bin’ sould I use to get this inputs for “camelid antibody graffeting”. Thanks.
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April 5, 2017 at 2:01 pm #12262
I think there have been some issues with camelid antibodies; you might need to try a more recent release. I’ve pinged the antibody group for more details.
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April 5, 2017 at 2:01 pm #12783
I think there have been some issues with camelid antibodies; you might need to try a more recent release. I’ve pinged the antibody group for more details.
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April 5, 2017 at 2:01 pm #13304
I think there have been some issues with camelid antibodies; you might need to try a more recent release. I’ve pinged the antibody group for more details.
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April 5, 2017 at 5:14 pm #12263
Yes, there has been a few issues within the past year. First, please try a recent weekly release. If you still have trouble, please post your full command line and log output so that we may debug the issue. Thanks.
-Jared
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April 5, 2017 at 5:14 pm #12784
Yes, there has been a few issues within the past year. First, please try a recent weekly release. If you still have trouble, please post your full command line and log output so that we may debug the issue. Thanks.
-Jared
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April 5, 2017 at 5:14 pm #13305
Yes, there has been a few issues within the past year. First, please try a recent weekly release. If you still have trouble, please post your full command line and log output so that we may debug the issue. Thanks.
-Jared
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April 7, 2017 at 1:59 pm #12264
Thank you for this instructions, I tired the last weekly release “rosetta_src_2017.08.59291_bundle”, same thing, I still not able to generate the inputs data (which is necessary to run the command) for the bin: “antibody_graft.default.linuxgccrelease”
– Inputs data : …/Rosetta/rosetta_src_2017.08.59291_bundle/main/tests/integration/tests/antibody_H3_camelid/inputs
“aaFR02_03_05.200_v1_3” “aaFR02_09_05.200_v1_3” “FR02.cst” “FR02.cst_fa” “FR02_H.pdb”
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April 7, 2017 at 1:59 pm #12785
Thank you for this instructions, I tired the last weekly release “rosetta_src_2017.08.59291_bundle”, same thing, I still not able to generate the inputs data (which is necessary to run the command) for the bin: “antibody_graft.default.linuxgccrelease”
– Inputs data : …/Rosetta/rosetta_src_2017.08.59291_bundle/main/tests/integration/tests/antibody_H3_camelid/inputs
“aaFR02_03_05.200_v1_3” “aaFR02_09_05.200_v1_3” “FR02.cst” “FR02.cst_fa” “FR02_H.pdb”
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April 7, 2017 at 1:59 pm #13306
Thank you for this instructions, I tired the last weekly release “rosetta_src_2017.08.59291_bundle”, same thing, I still not able to generate the inputs data (which is necessary to run the command) for the bin: “antibody_graft.default.linuxgccrelease”
– Inputs data : …/Rosetta/rosetta_src_2017.08.59291_bundle/main/tests/integration/tests/antibody_H3_camelid/inputs
“aaFR02_03_05.200_v1_3” “aaFR02_09_05.200_v1_3” “FR02.cst” “FR02.cst_fa” “FR02_H.pdb”
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April 7, 2017 at 3:29 pm #12265
So by “not able to generate the inputs data” – you mean you don’t have a problem running Rosetta, but instead you don’t know what the inputs are supposed to be?
Have you read the documentation?
The “aa…..” files are 3mer and 9mer fragments. The .cst and .cst_fa files are constraints. The last input is a PDB – I don’t know the protocol specifically, but if you are grafting, I assume it is a skeleton to graft into.
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April 7, 2017 at 3:29 pm #12786
So by “not able to generate the inputs data” – you mean you don’t have a problem running Rosetta, but instead you don’t know what the inputs are supposed to be?
Have you read the documentation?
The “aa…..” files are 3mer and 9mer fragments. The .cst and .cst_fa files are constraints. The last input is a PDB – I don’t know the protocol specifically, but if you are grafting, I assume it is a skeleton to graft into.
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April 7, 2017 at 3:29 pm #13307
So by “not able to generate the inputs data” – you mean you don’t have a problem running Rosetta, but instead you don’t know what the inputs are supposed to be?
Have you read the documentation?
The “aa…..” files are 3mer and 9mer fragments. The .cst and .cst_fa files are constraints. The last input is a PDB – I don’t know the protocol specifically, but if you are grafting, I assume it is a skeleton to graft into.
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April 7, 2017 at 4:13 pm #12266
I think it’s not a matter of reading doumentation.
In the documentation a “ram_build_loop_wrapper.pl” file is required to generate all this files ( “aaFR02_03_05.200_v1_3” “aaFR02_09_05.200_v1_3” “FR02.cst” “FR02.cst_fa” “FR02_H.pdb”), the problem is that in the last version of Rosetta (3.7 & 3.
this script file does not even exist.Thank you.
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April 7, 2017 at 4:13 pm #12787
I think it’s not a matter of reading doumentation.
In the documentation a “ram_build_loop_wrapper.pl” file is required to generate all this files ( “aaFR02_03_05.200_v1_3” “aaFR02_09_05.200_v1_3” “FR02.cst” “FR02.cst_fa” “FR02_H.pdb”), the problem is that in the last version of Rosetta (3.7 & 3.
this script file does not even exist.Thank you.
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April 7, 2017 at 4:13 pm #13308
I think it’s not a matter of reading doumentation.
In the documentation a “ram_build_loop_wrapper.pl” file is required to generate all this files ( “aaFR02_03_05.200_v1_3” “aaFR02_09_05.200_v1_3” “FR02.cst” “FR02.cst_fa” “FR02_H.pdb”), the problem is that in the last version of Rosetta (3.7 & 3.
this script file does not even exist.Thank you.
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April 7, 2017 at 4:50 pm #12267
ram_build_loop_wrapper.pl – great, that’s a specific problem, I’ve farmed it out to the antibody group. (Your original question was too vague for us to know how to help.)
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April 7, 2017 at 4:50 pm #12788
ram_build_loop_wrapper.pl – great, that’s a specific problem, I’ve farmed it out to the antibody group. (Your original question was too vague for us to know how to help.)
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April 7, 2017 at 4:50 pm #13309
ram_build_loop_wrapper.pl – great, that’s a specific problem, I’ve farmed it out to the antibody group. (Your original question was too vague for us to know how to help.)
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April 8, 2017 at 12:56 pm #12269
Ok Thank you smlewis and jadolfbr
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April 8, 2017 at 12:56 pm #12790
Ok Thank you smlewis and jadolfbr
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April 8, 2017 at 12:56 pm #13311
Ok Thank you smlewis and jadolfbr
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April 14, 2017 at 11:00 am #12273
Please I’m still waiting for the intervention of the “Rosetta antibody group”;
…/rosetta_src_2017.08.59291_bundle/main/tests/integration/tests/antibody_H3_camelid/inputs
Please how can I generate this inputs (see path) ??
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April 14, 2017 at 11:00 am #12794
Please I’m still waiting for the intervention of the “Rosetta antibody group”;
…/rosetta_src_2017.08.59291_bundle/main/tests/integration/tests/antibody_H3_camelid/inputs
Please how can I generate this inputs (see path) ??
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April 14, 2017 at 11:00 am #13315
Please I’m still waiting for the intervention of the “Rosetta antibody group”;
…/rosetta_src_2017.08.59291_bundle/main/tests/integration/tests/antibody_H3_camelid/inputs
Please how can I generate this inputs (see path) ??
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April 17, 2017 at 2:50 pm #12286
Dear Jared
I tried to run the protocol described in this paper: http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html, the problem is that the antibody.cc application is dedicated specially for classical antibodies (antibody with heavy and light chain), In my case Im working only with heavy chain antibodies (lacking light chain “VHH” or “Nanobodies”), so when I run the antibody.cc application, I have this error ;
ERROR: Error can’t find section ‘light’ in fasta file /home/ksouri/antibody_example/antibody.fasta!
Thank you
Ayoub
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April 17, 2017 at 2:50 pm #12807
Dear Jared
I tried to run the protocol described in this paper: http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html, the problem is that the antibody.cc application is dedicated specially for classical antibodies (antibody with heavy and light chain), In my case Im working only with heavy chain antibodies (lacking light chain “VHH” or “Nanobodies”), so when I run the antibody.cc application, I have this error ;
ERROR: Error can’t find section ‘light’ in fasta file /home/ksouri/antibody_example/antibody.fasta!
Thank you
Ayoub
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April 17, 2017 at 2:50 pm #13328
Dear Jared
I tried to run the protocol described in this paper: http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html, the problem is that the antibody.cc application is dedicated specially for classical antibodies (antibody with heavy and light chain), In my case Im working only with heavy chain antibodies (lacking light chain “VHH” or “Nanobodies”), so when I run the antibody.cc application, I have this error ;
ERROR: Error can’t find section ‘light’ in fasta file /home/ksouri/antibody_example/antibody.fasta!
Thank you
Ayoub
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April 17, 2017 at 6:17 pm #12287
Sounds good. I’ll forward this to Sergey. In the meantime, try passing an arbitrary fasta for the light chain, and then removing it from the PDB after antibody.cc. The core modeling is done afterward, so this will work fine. Both antibody_H3 and snugdock should run with the camelid antibodies, as I had made them work with camelids at some point over the past few years…
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April 17, 2017 at 6:17 pm #12808
Sounds good. I’ll forward this to Sergey. In the meantime, try passing an arbitrary fasta for the light chain, and then removing it from the PDB after antibody.cc. The core modeling is done afterward, so this will work fine. Both antibody_H3 and snugdock should run with the camelid antibodies, as I had made them work with camelids at some point over the past few years…
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April 17, 2017 at 6:17 pm #13329
Sounds good. I’ll forward this to Sergey. In the meantime, try passing an arbitrary fasta for the light chain, and then removing it from the PDB after antibody.cc. The core modeling is done afterward, so this will work fine. Both antibody_H3 and snugdock should run with the camelid antibodies, as I had made them work with camelids at some point over the past few years…
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April 19, 2017 at 10:16 pm #12296
Dear jadolfbr, thank you for your help, I tried an arbitrary fasta for the light chain with my ‘VHH’ heavy chain, I’ve got this outputs :
– debug-model-A-*.pdb (from 0 to 9)
– debug-model-B-*.pdb (from 0 to 9)
– frh-*.pdb (from 0 to 9)
– frl-*.pdb (from 0 to 9)
– frh_after_seqeunce_adjustment-*.pdb (from 0 to 9)
– frh_frl_oriented-*.pdb (from 0 to 9)
– model-*.relaxed.pdb (from 0 to 9)
– orientation-*.pdb (from 0 to 9)
I think that the best way is to use “frh.pdb” or “frh_after_seqeunce_adjustment.pdb” as inputs for antibody_H3 application. But what about removing the light chain from the “model-*.relaxed.pdb ” as you mentioned above.
Thank you
Ayoub
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April 19, 2017 at 10:16 pm #12817
Dear jadolfbr, thank you for your help, I tried an arbitrary fasta for the light chain with my ‘VHH’ heavy chain, I’ve got this outputs :
– debug-model-A-*.pdb (from 0 to 9)
– debug-model-B-*.pdb (from 0 to 9)
– frh-*.pdb (from 0 to 9)
– frl-*.pdb (from 0 to 9)
– frh_after_seqeunce_adjustment-*.pdb (from 0 to 9)
– frh_frl_oriented-*.pdb (from 0 to 9)
– model-*.relaxed.pdb (from 0 to 9)
– orientation-*.pdb (from 0 to 9)
I think that the best way is to use “frh.pdb” or “frh_after_seqeunce_adjustment.pdb” as inputs for antibody_H3 application. But what about removing the light chain from the “model-*.relaxed.pdb ” as you mentioned above.
Thank you
Ayoub
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April 19, 2017 at 10:16 pm #13338
Dear jadolfbr, thank you for your help, I tried an arbitrary fasta for the light chain with my ‘VHH’ heavy chain, I’ve got this outputs :
– debug-model-A-*.pdb (from 0 to 9)
– debug-model-B-*.pdb (from 0 to 9)
– frh-*.pdb (from 0 to 9)
– frl-*.pdb (from 0 to 9)
– frh_after_seqeunce_adjustment-*.pdb (from 0 to 9)
– frh_frl_oriented-*.pdb (from 0 to 9)
– model-*.relaxed.pdb (from 0 to 9)
– orientation-*.pdb (from 0 to 9)
I think that the best way is to use “frh.pdb” or “frh_after_seqeunce_adjustment.pdb” as inputs for antibody_H3 application. But what about removing the light chain from the “model-*.relaxed.pdb ” as you mentioned above.
Thank you
Ayoub
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April 7, 2017 at 5:48 pm #12268
I have never heard of that script. Can you give a link to where it is mentioned? For the most recent documentation (which does NOT include the antibody_graft application), please see this paper: http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html
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April 7, 2017 at 5:48 pm #12789
I have never heard of that script. Can you give a link to where it is mentioned? For the most recent documentation (which does NOT include the antibody_graft application), please see this paper: http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html
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April 7, 2017 at 5:48 pm #13310
I have never heard of that script. Can you give a link to where it is mentioned? For the most recent documentation (which does NOT include the antibody_graft application), please see this paper: http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html
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April 14, 2017 at 6:52 pm #12280
Hi Ayoub. I am a part of the antibody modeling team and was on that paper I pointed to you eariler. The code you are referring to is deprecated and unsupported. Please use the antibody.cc application that is in the paper. If you have issues with this, we will be happy to help and fix whatever needs to be fixed.
-Jared
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April 14, 2017 at 6:52 pm #12801
Hi Ayoub. I am a part of the antibody modeling team and was on that paper I pointed to you eariler. The code you are referring to is deprecated and unsupported. Please use the antibody.cc application that is in the paper. If you have issues with this, we will be happy to help and fix whatever needs to be fixed.
-Jared
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April 14, 2017 at 6:52 pm #13322
Hi Ayoub. I am a part of the antibody modeling team and was on that paper I pointed to you eariler. The code you are referring to is deprecated and unsupported. Please use the antibody.cc application that is in the paper. If you have issues with this, we will be happy to help and fix whatever needs to be fixed.
-Jared
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