Building in missing residues from a known structure
I've looked through the mailing list archives and online documentation, but I'm having some trouble wrapping my head around the proper way to accomplish the following. I have two PDB files of a protein in different conformations, where in one of the two PDBs, a short stretch of residues are missing, but in the other the complete coordinates in that region are known. Both PDBs have different missing residues throughout their chain, but I'm only interested at this time in modeling that small section that's present in one and not in the other.
My alignment file looks something like:
>P1;A structureX:A: 1 :A:149 :A:::-1.00:-1.00 ---------FIRIMVFAIYVALPIGV--------------------AGKSLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRSNKKLLTILAVFWISLYIFVNLTSVLYL*
>P1;B structureX:B:1 :A:149 :A:::-1.00:-1.00 --------SFIRIMVFAIYVALPIGVGLWV-------------------SLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRS----LTILAVFWISLYIFVNLTSVLYL*
In B the sequence `NKKL` is missing. Because they are in different conformations, I want to use the PDB for B as an initial model. In each of the PDB files, the residues follow the number in the above sequence alignment, and only contain coordinates for the residues that are not marked with a `-`.
My script looks like: ----------------------------------------------------- ----------------------------------------------------- # Modeling using a provided initial structure file (inifile) from modeller import * from modeller.automodel import * # Load the automodel class
log.verbose() env = environ()
# directories for input atom files env.io.atom_files_directory = ['.', '../structures']
class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('123', '126'))
a = MyModel(env, alnfile='../sequences/alignments.ali', # alignment filename knowns='A', # codes of the templates sequence='B', # code of the target inifile='B.pdb') # use 'my' initial structure a.starting_model = 1 # index of the first model a.ending_model = 1 # index of the last model a.make() # do homology modeling ----------------------------------------------------- -----------------------------------------------------
If in my alignment file, I specify that each structure starts at residue 1, I get an error:
> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 1", chain " A"; atom file name: ../structures/A.pdb
However if I change the starting residue to 10 in A and 9 in B, Modeller runs, but it builds a different set of residues than I intended, because I think it is numbering the residues in sequential order as they are read in from the PDBs, ignoring the missing residues (determined by running the small script in FAQ #17).
I've seen advice on renumbering residues on the mailing list, but I'm not sure if I'm missing something more basic.
Any suggestions or pointers would be most appreciate.
Josh
On 09/12/2012 01:13 PM, Joshua Adelman wrote: > I've looked through the mailing list archives and online documentation, > but I'm having some trouble wrapping my head around the proper way to > accomplish the following. I have two PDB files of a protein in different > conformations, where in one of the two PDBs, a short stretch of residues > are missing, but in the other the complete coordinates in that region > are known. Both PDBs have different missing residues throughout their > chain, but I'm only interested at this time in modeling that small > section that's present in one and not in the other.
This is a very simple case of multiple template modeling, very similar to question 1 in the FAQ: http://salilab.org/modeller/9.11/FAQ.html#1
Simply add a third sequence 'C' to your alignment (the sequence you want to model) and align it with both A and B, then use regular automodel with knowns=('A', 'B') and sequence='C'.
Ben Webb, Modeller Caretaker
Hi Ben,
On Sep 12, 2012, at 5:28 PM, Modeller Caretaker wrote:
> On 09/12/2012 01:13 PM, Joshua Adelman wrote: >> I've looked through the mailing list archives and online documentation, >> but I'm having some trouble wrapping my head around the proper way to >> accomplish the following. I have two PDB files of a protein in different >> conformations, where in one of the two PDBs, a short stretch of residues >> are missing, but in the other the complete coordinates in that region >> are known. Both PDBs have different missing residues throughout their >> chain, but I'm only interested at this time in modeling that small >> section that's present in one and not in the other. > > This is a very simple case of multiple template modeling, very similar to question 1 in the FAQ: > http://salilab.org/modeller/9.11/FAQ.html#1 > > Simply add a third sequence 'C' to your alignment (the sequence you want to model) and align it with both A and B, then use regular automodel with knowns=('A', 'B') and sequence='C'. >
There are a couple of things that I'm still missing: 1. I still want to use B.pdb as my initial model and only change those residues in my selected residue_range. When I specify B.pdb as my inifile, Modeller kicks out an error: _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " ", chain " "; atom file name: B.pdb
I'm not sure where I'm suppose to be specifying the starting position. If I remove the inifile argument to the model instantiation, then everything runs fine, but it builds the model for all of 'C', rather than just 'B' plus the four missing residues of interest (see #2).
2. If 'C' is the complete sequence that fills in all of the gaps in 'A' and 'B', how do I stop Modeller from building in residues outside of my selected residue_range, ensuring that my output model is just B.pdb unchanged, except for the 4 residues that are built from A.pdb? Should I be changing the aligned sequence for A to be all dashes, except for the 4 residues that are missing in B? In this case what should the start and ending residues be in the alignment file in the fields after structureX? Should C by identical to B, except the 4 residues marked with dashes should be filled in?
So basically if A and B are:
>P1;A structureX:A: 1 :A:149 :A:::-1.00:-1.00 ---------FIRIMVFAIYVALPIGV--------------------AGKSLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRSNKKLLTILAVFWISLYIFVNLTSVLYL*
>P1;B structureX:B:1 :A:149 :A:::-1.00:-1.00 --------SFIRIMVFAIYVALPIGVGLWV-------------------SLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRS----LTILAVFWISLYIFVNLTSVLYL*
should C be: >P1;C structureX:A: 1 :A:149 :A:::-1.00:-1.00 AAAAAAAAAFIRIMVFAIYVALPIGVAAAAAAAAAAAAAAAAAAAAAGKSLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRSNKKLLTILAVFWISLYIFVNLTSVLYL*
or
>P1;C structureX:B:1 :A:149 :A:::-1.00:-1.00 --------SFIRIMVFAIYVALPIGVGLWV-------------------SLPWYAVGASLIAANISAEQFIGGMS SAYSIGLAIASYRWMSALTLIIVGKYFLPIFIEKGIYTIPEFVRKRSNKKLLTILAVFWISLYIFVNLTSVLYL*
Also should A alternatively be: >P1;A structureX:A: 1 :A:149 :A:::-1.00:-1.00 --------------------------------------------------------------------------- -----------------------------------------------NKKL-----------------------*
(or maybe with a few extra surrounding residues?). If A is the latter should the start and end residues in the header fields just encompass the `NKKL` (123-126 in the entire sequence)?
I've played around with some of these combinations, but when I actually get things to run, it's building residues 123-126 not in terms of the the absolute position in the sequence, but the relative position in terms of how many residues are present in the PDB. Should my sequences include the chain break character (/) somewhere?
Thanks in advance for helping to clarify these issues.
Josh
> Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage
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Joshua Adelman -
Modeller Caretaker