I'm new to Modeller. I have a protein segment I'm trying to model that
consists of 2 domains. This protein has 4 very similar domains; 2 have been
resolved and the other 2 have not (the ones I want to model). I go through
the motions of aligning the sequences and building the model; however, the 2
domains I modelled are basically entangled. Thus, my question is, how can I
keep this from happening (such as specifying a straight link between the
domains instead of the current one that loops back, if this is even
plausible)? Any suggestions are greatly appreciated.
[it appears that I accidentally sent this to the listowner rather than
the list. oops. sorry Ben]
This may seem like a rather strange question, but is it possible to get
Modeller to output a PDB structure based only on secondary structure
information and a few distance constraints (primarily dicystene
relationships). I realize that without an alignment to a known
structure, anything that is generated probably bears little resemblance
to reality, but I have a relatively short fragment that isn't
significantly related to anything in the PDB, and between the disulfide
linkages and a couple other known constraints, there aren't that many
ways that it could bend together. Basically, I'm trying to generate a
consistent structure that is in a possible conformation that doesn't
violate steric boundaries and such, without having to manually generate
the coordinates from the helix and sheet parameters. Can anyone make
I have a question of modelling the C-terminal region of my target. The protein matches with the crystal structure templates except the C-terminal region (named as C-tail here). I did BLAST search using this segment to against the proteins with known structures at Protein Data Band. It returns a match with a short region of an antibody at 56% sequence identity with the inclusion of 4 gaps. The function of my target protein has nothing to do with antibody. I am not sure if it is reasonable to use the BLAST match results as templates to model the conformation of the C-tail.
I have thought to model this C-tail region using the Loop Model in Modeller. There are some concerns here. First, the C-tail contains 24 amino acids. Will this be too long for the loop-model in Modeller? If the length is not the problem, how reliable are the conformations of the segment? Second, the segment is at the C-terminal of the protein. For my understanding, the Loop Model in Modeller requires the N and C terminus of the segment to be fixed. The position of the last residues of the segment will have significant influence on the Loop conformation. Which one is more reasonable, to model this segment based on the sequence homology, or use a loop modelling algorithm?
Your help and inputs will be much appreciated!
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I know this has been raised before but when looking through the archieves I could'nt find an answer to this problem, I've redone all the tutorials and out of ideas, so please can somebody help with this error message I'm getting?
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "modeller.top.py", line 18, in ?
a.make() # do the actual homology modeling
File "/home/fraizerangus/bin/modeller9v2/modlib/modeller/automodel/automodel.py", line 99, in make
File "/home/fraizerangus/bin/modeller9v2/modlib/modeller/automodel/automodel.py", line 399, in homcsr
aln = self.read_alignment()
File "/home/fraizerangus/bin/modeller9v2/modlib/modeller/automodel/automodel.py", line 389, in read_alignment
File "/home/fraizerangus/bin/modeller9v2/modlib/modeller/alignment.py", line 74, in append
_modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1CPG
I'm a new user of Modeller and I have a question about the model computing.
If I take one/or more models with a given alignment and I change just one or
more amino acids maintaning the same alignment, should I obtain a different
In other words, Can Modeller be used for calculating mutations?
Thank you so much,
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After loop refinement, we get files with .IL and .BL extensions. Which one should be used as the final model out of these? And after refinement through modeler there are some bad contacts and disallowed regions. How can we assess the models accuracy?
I have been modeling a homopentamer which should have a disulfide bond
in each subunit in the same position as the multiple templates that we
are using (the alignments have the cys residues of the target lined up
with the disulfide-forming cys in the templates). When I carry out the
alignment of the templates using salign, the XX_fit.pdb files for the
templates do not have the disulfides indicated using SSBOND, even though
the original pdb files (XX.pdb) do have the SSBOND lines in them.
I know that automodel will automatically include disulfide restraints
if the templates have them. However,the returned models, while
superimposing nicely on the template structure, do not have the
disulfides, even though the cysteines in the model are right where the
disulfide-forming cysteines are in the template. I assume that automodel
uses the XX_fit.pdb files for the fitting routines, and the fact that
the XX_fit.pdb files are missing the SSBOND lines is why the disulfides
are present in the model.
Is this correct? Can I just edit the XX_fit.pdb files to include the
SSBOND lines to force the model to have the disulfides?
Alternatively, I guess I could use model.patch as per node24 in the
online manual to force the disulfides to be where I want them to be, but
this just doesn't seem right if the templates all have the disulfide and
the alignments have the cysteines where they should be.
I have generated models for proteins but dont know how to optimize and refine those structures using modellar. I have tried using the optimize.py file to optimize with CG but i am not able to understand the script and where should I list the protein name to be optimized in that script file.