mr_rosetta: two proteins, one chain placed, build second chain
Dear phenixbb, I would like to use mr_rosetta to build a second protein chain. For the first protein, I have a search model with known structure. The search model can be placed with Phaser (TFZ 10). For the second protein, the structure of a homologue has been determined. The second protein accounts for about 2/3 of the residues in the ASU. I would like to fix the first protein chain and build the second protein chain with mr_rosetta. I have obtained fragment files for both proteins from robetta. What input parameters are required to tell mr_rosetta to build the second chain only? I have tried the fixed_ensemble_ID_list = ensemble1 option. Here is an excerpt of my parameter file with the input files: run a) search_models = "path/chainA.pdb" (from Phaser) search_models = "path/chainB.pdb" (homologue structure) fixed_ensembles { fixed_ensembleID_list = ensemble1 fixed_euler_list = 0.0 0.0 0.0 fixed_frac_list = 0.0 0.0 0.0 fixed_frac_list_is_fractional = True } alignment_files = "path/chainA.dat" alignment_files = "path/chainB.dat" with chainA.dat having twice the same sequence and chainB.dat with the target and template alignment. I have set fragment files with chain_list for both chains. I get this error when running phenix.mr_rosetta (running from command line with .eff file) "Sorry, the file /path/GROUP_OF_PLACE_MODEL_1/RUN_2/chainB_al_0.pdb representing group 0 has no atoms? This could indicate a problem with sequence alignment in rebuilding. It could be that there are near-duplicate sequences in your sequence file ...if this is the case then you may need to artificially rename your duplicated chains and renumber residues to make a single chain containing a duplication" This error also occurs run b) Without any alignment files run c) Without any alignment files and with just chainA.pdb as search model. An alignment of the sequences from chainA and chainB gives low identity (no duplicate regions), so I suspect the problem is located somewhere else? I have seen a post by Tom Terwilliger, explaining how to deal with two identical chains with different conformations where no alignment files are required. However, I would like to use the information from the homologue structure, that is why I specified the alignment file. By inputting chainB.pdb as search model, mr_rosetta also tries to use this model as a search model for molecular replacement, but I think this is not necessary (and gives a warning that the space group of the search model and the data file do not match). I just want to provide the structural information from structure chainB.pdb to mr_rosetta for building. ----- So in summary this is what I would like to do: chain A: keep fixed - use chainA.pdb as fixed model chain B: build - use information from homologue structure (chainB.pdb) and fragment files to build chain What is the best strategy to do this? What input parameters are required so that I do not get the error described above? ----- Thanks a lot in advance, Tobias.
Hi Tobias, If you download the new phenix version (available now) it should have the option of a fixed mode in mr_rosettal. I am hoping that this will do what you want; if it does not let me know and I'll try to help! All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Tobias Beck [[email protected]] Sent: Thursday, February 28, 2013 4:20 AM To: [email protected] Subject: [phenixbb] mr_rosetta: two proteins, one chain placed, build second chain Dear phenixbb, I would like to use mr_rosetta to build a second protein chain. For the first protein, I have a search model with known structure. The search model can be placed with Phaser (TFZ 10). For the second protein, the structure of a homologue has been determined. The second protein accounts for about 2/3 of the residues in the ASU. I would like to fix the first protein chain and build the second protein chain with mr_rosetta. I have obtained fragment files for both proteins from robetta. What input parameters are required to tell mr_rosetta to build the second chain only? I have tried the fixed_ensemble_ID_list = ensemble1 option. Here is an excerpt of my parameter file with the input files: run a) search_models = "path/chainA.pdb" (from Phaser) search_models = "path/chainB.pdb" (homologue structure) fixed_ensembles { fixed_ensembleID_list = ensemble1 fixed_euler_list = 0.0 0.0 0.0 fixed_frac_list = 0.0 0.0 0.0 fixed_frac_list_is_fractional = True } alignment_files = "path/chainA.dat" alignment_files = "path/chainB.dat" with chainA.dat having twice the same sequence and chainB.dat with the target and template alignment. I have set fragment files with chain_list for both chains. I get this error when running phenix.mr_rosetta (running from command line with .eff file) "Sorry, the file /path/GROUP_OF_PLACE_MODEL_1/RUN_2/chainB_al_0.pdb representing group 0 has no atoms? This could indicate a problem with sequence alignment in rebuilding. It could be that there are near-duplicate sequences in your sequence file ...if this is the case then you may need to artificially rename your duplicated chains and renumber residues to make a single chain containing a duplication" This error also occurs run b) Without any alignment files run c) Without any alignment files and with just chainA.pdb as search model. An alignment of the sequences from chainA and chainB gives low identity (no duplicate regions), so I suspect the problem is located somewhere else? I have seen a post by Tom Terwilliger, explaining how to deal with two identical chains with different conformations where no alignment files are required. However, I would like to use the information from the homologue structure, that is why I specified the alignment file. By inputting chainB.pdb as search model, mr_rosetta also tries to use this model as a search model for molecular replacement, but I think this is not necessary (and gives a warning that the space group of the search model and the data file do not match). I just want to provide the structural information from structure chainB.pdb to mr_rosetta for building. ----- So in summary this is what I would like to do: chain A: keep fixed - use chainA.pdb as fixed model chain B: build - use information from homologue structure (chainB.pdb) and fragment files to build chain What is the best strategy to do this? What input parameters are required so that I do not get the error described above? ----- Thanks a lot in advance, Tobias.
I have a feeling that it's some problem where the search model and the
sequence gets crossed over and since they don't align Sculptor ends up
discarding all the atoms in the search model.
I would try the new version with fixed mode and if that doesn't help I
would try it only with the model that covers 2/3rds of your complex. Your
solvent content will be wrong but I think you can get through a lot of
mr_rosetta before density modification comes into play.
Cheers,
Morten
On 28 February 2013 14:52, Terwilliger, Thomas C
Hi Tobias,
If you download the new phenix version (available now) it should have the option of a fixed mode in mr_rosettal. I am hoping that this will do what you want; if it does not let me know and I'll try to help!
All the best, Tom T
------------------------------ *From:* [email protected] [ [email protected]] on behalf of Tobias Beck [ [email protected]] *Sent:* Thursday, February 28, 2013 4:20 AM *To:* [email protected] *Subject:* [phenixbb] mr_rosetta: two proteins, one chain placed, build second chain
Dear phenixbb,
I would like to use mr_rosetta to build a second protein chain.
For the first protein, I have a search model with known structure. The search model can be placed with Phaser (TFZ 10). For the second protein, the structure of a homologue has been determined. The second protein accounts for about 2/3 of the residues in the ASU.
I would like to fix the first protein chain and build the second protein chain with mr_rosetta. I have obtained fragment files for both proteins from robetta.
What input parameters are required to tell mr_rosetta to build the second chain only? I have tried the fixed_ensemble_ID_list = ensemble1 option.
Here is an excerpt of my parameter file with the input files:
run a)
search_models = "path/chainA.pdb" (from Phaser) search_models = "path/chainB.pdb" (homologue structure)
fixed_ensembles { fixed_ensembleID_list = ensemble1 fixed_euler_list = 0.0 0.0 0.0 fixed_frac_list = 0.0 0.0 0.0 fixed_frac_list_is_fractional = True }
alignment_files = "path/chainA.dat" alignment_files = "path/chainB.dat"
with chainA.dat having twice the same sequence and chainB.dat with the target and template alignment.
I have set fragment files with chain_list for both chains.
I get this error when running phenix.mr_rosetta (running from command line with .eff file)
"Sorry, the file /path/GROUP_OF_PLACE_MODEL_1/RUN_2/chainB_al_0.pdb representing group 0 has no atoms? This could indicate a problem with sequence alignment in rebuilding. It could be that there are near-duplicate sequences in your sequence file ...if this is the case then you may need to artificially rename your duplicated chains and renumber residues to make a single chain containing a duplication"
This error also occurs
run b) Without any alignment files run c) Without any alignment files and with just chainA.pdb as search model.
An alignment of the sequences from chainA and chainB gives low identity (no duplicate regions), so I suspect the problem is located somewhere else?
I have seen a post by Tom Terwilliger, explaining how to deal with two identical chains with different conformations where no alignment files are required. However, I would like to use the information from the homologue structure, that is why I specified the alignment file.
By inputting chainB.pdb as search model, mr_rosetta also tries to use this model as a search model for molecular replacement, but I think this is not necessary (and gives a warning that the space group of the search model and the data file do not match). I just want to provide the structural information from structure chainB.pdb to mr_rosetta for building.
-----
So in summary this is what I would like to do:
chain A: keep fixed - use chainA.pdb as fixed model chain B: build - use information from homologue structure (chainB.pdb) and fragment files to build chain
What is the best strategy to do this? What input parameters are required so that I do not get the error described above?
-----
Thanks a lot in advance,
Tobias.
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-- Morten K Grøftehauge, PhD Pohl Group Durham University
participants (3)
-
Morten Groftehauge -
Terwilliger, Thomas C -
Tobias Beck