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You can also do this with pdb-tools: pdb_selchain -A prot.pdb > prot_A.pdb

The comment by Devon Ryan is correct - looks like your blastpgp command is not working properly. For a protein of that length it's more likely to be a problem with the BLAST executable running on your …

The target variable, which is set to the first part of the sequence file name, should be sequence according to your given command line. However the error message thinks it is c600m2-tail-before-lysin- …

DMPfold tends to produce low-variability models - it produces a small number of distinct conformations, and either the right one is in there or it isn't. This arises from the way the models are genera …

From the docs: The final model is final_1.pdb and other structures may or may not be generated as final_2.pdb to final_5.pdb if they are significantly different. Many other files are generated tot …

The sequence_n.pdb files are temporary and are combined into an ensemble.i.pdb file after each iteration i. That file has many structures in. After the run is complete there will be a final_1.pdb file …

For DMPfold you might like to look at Figure 5B of the paper, which implies that performance starts to drop off after ~600 residues. Only proteins up to 500 residues were used in the training set, for …

RMSD is a measure of similarity between two structures. The relevant RMSD in protein structure prediction is between a model and the native structure. If you don't have a native structure you cannot h …

This is described briefly in the paper. The four quantities are inputs to the estimator of model accuracy: nres is the sequence length. neff is an effective sequence count, or how deep the alignment …

Searching "misfolded" on the RCSB PDB turns up 64 hits. Most of these won't be relevant, but there are some interesting entries on tumor associated EGFR and misolded RNA. In order to experimentally o …

Distance between C-alphas can also be found using the BioStructures.jl package in Julia: using BioStructures struc = read("1AKE.pdb", PDB) calphas = collectatoms(struc['A'], calphaselector) dm = Dist …

A contact map predictor will usually output the probability of a contact for every residue pair in a protein, often ommitting very close pairs (e.g. less than 6 residue separation). To calculate the L …

Converting a PDB file to some version of an mmCIF file is always possible provided the PDB file doesn't have any "problems". However grouping identical molecules into the same entity is non-trivial so …

Protein sequences from the same family form a sequence alignment. Some positions in the alignment will be conserved, i.e. the same in all sequences. These are often associated with function, e.g. a ca …

As others have said, there is no short cut and you will need to spend some time with a good book. I would say there are 3 broad areas of understanding you have to have as a structural bioinformaticia …