MediaWiki API result

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    "warnings": {
        "main": {
            "*": "Subscribe to the mediawiki-api-announce mailing list at <https://lists.wikimedia.org/postorius/lists/mediawiki-api-announce.lists.wikimedia.org/> for notice of API deprecations and breaking changes."
        },
        "revisions": {
            "*": "Because \"rvslots\" was not specified, a legacy format has been used for the output. This format is deprecated, and in the future the new format will always be used."
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        "pages": {
            "9": {
                "pageid": 9,
                "ns": 0,
                "title": "Rebuilding sequence databases",
                "revisions": [
                    {
                        "contentformat": "text/x-wiki",
                        "contentmodel": "wikitext",
                        "*": "__NOTOC__\n<!-- ## page was renamed from Rebuilding_sequence_databases -->\nOlder versions of the Modeller distribution contain a sequence database, in the files <code>modlib/CHAINS_*</code>. These files are\n* <code>CHAINS_all.seq</code> or <code>pdball.pir</code>: sequences for every chain in every structure in the PDB.\n* <code>CHAINS_3.0.95_XN.cod</code> or <code>pdb_95.cod</code>: all chains are clustered at 95% sequence identity, and for each cluster, the PDB code of the representative chain is listed in this file.\n* <code>CHAINS_3.0.95_XN.grp</code> or <code>pdb_95.grp</code>: for each representative, the other chains which are 95% sequence identical.\n* <code>CHAINS_3.0.40_XN.cod</code> and <code>CHAINS_3.0.40_XN.grp</code>: similar files, clustered at 40% sequence identity.\n\nThese files are obviously not updated whenever the PDB is, and are not included at all with newer versions of Modeller, but you can download updated copies from our [https://salilab.org/modeller/supplemental.html supplemental data file download page], or regenerate them yourself if you have a local copy of PDB. Firstly, to build <code>CHAINS_all.seq</code> or <code>pdball.pir</code>:\n\nFor each PDB file, run a script similar to that below. Set <code>code</code> to the PDB code and set <code>atom_files_directory</code> to the directory containing your local copy of PDB:\n  \n<syntaxhighlight lang=\"python\">\nfrom modeller import *\n\ne = Environ()\ne.io.atom_files_directory = ['/database/pdb/']\n\ncode = '1xyz'\nm = Model(e, file=code)\n\nm.make_chains(file=code, minimal_chain_length=30, minimal_stdres=30,\n              chop_nonstd_termini=True, max_nonstdres=10,\n              minimal_resolution=99.0, structure_types='structureN structureX')\n</syntaxhighlight>\n\n\nThis will produce a <code>.chn</code> file for every chain in PDB. Concatenate these together (e.g. with the Unix <code>cat</code> command) to make the new <code>CHAINS_all.seq</code> or <code>pdball.pir</code> file.\n\nNow you can build the <code>.cod</code> and <code>.grp</code> files for any sequence identity cutoff using the following script (adjust the <code>seqid_cut</code> variable accordingly):\n\n<syntaxhighlight lang=\"python\">\nfrom modeller import *\n\ne = Environ()\n\ns = SequenceDB(e, seq_database_file='CHAINS_all.seq', chains_list='all',\n               seq_database_format='PIR', minmax_db_seq_len=(30, 3000),\n               clean_sequences=True)\n\ns.filter(matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat',\n         gap_penalties_1d=(-500, -50), seqid_cut=40,\n         output_grp_file='CHAINS_3.0.40_XN.grp', output_cod_file='CHAINS_3.0.40_XN.cod')\n</syntaxhighlight>\n\n\nNote that this will take a long time to run. For high (>90%) sequence identity cutoffs, it is more efficient to use [http://weizhongli-lab.org/cd-hit/ CD-HIT] instead. A script that automates this is included as part of [https://salilab.org/modpipe/ ModPipe] (<code>python/ClusterPDB.py</code>).\n\n[[Category:Examples]]"
                    }
                ]
            },
            "38": {
                "pageid": 38,
                "ns": 0,
                "title": "Restraints on pseudo atoms",
                "revisions": [
                    {
                        "contentformat": "text/x-wiki",
                        "contentmodel": "wikitext",
                        "*": "__NOTOC__\n<!-- ## page was renamed from Restraints_on_pseudo_atoms -->\npseudo.py demonstrates the use of a restraint between a real atom and a pseudo atom. This input file should work with Modeller 10.0 or later. You will also need the [https://salilab.org/modeller/archive/pseudo-rsr-example/pseudo.atm pseudo.atm] input.\n\n\n<syntaxhighlight lang=\"python\">\nfrom modeller import *\nfrom modeller.optimizers import ConjugateGradients\n\ne = Environ()\ne.edat.dynamic_sphere = False\nlog.verbose()\n\n# Read in a dummy PDB, which defines five real atoms - four are positioned at\n# the corners of a square in the xy place, and the fifth is off in space\nm = Model(e, file='pseudo.atm')\n\n# Define a pseudo atom as the gravity center of the first 4 atoms, and add\n# it to the model's restraints\np = pseudo_atom.GravityCenter(m.atoms[0:5])\nm.restraints.pseudo_atoms.append(p)\n\n# Create a restraint on the distance between the real fifth atom and the newly\n# created pseudo atom, and add it to the model's restraints. Since the mean is\n# zero, this will force atom 5 to coexist with the gravity center.\nr = forms.Gaussian(group=physical.xy_distance,\n                   feature=features.Distance(m.atoms[4], p),\n                   mean=0.0, stdev=0.100)\nm.restraints.add(r)\n\n# Calculate the starting energy of all atoms in the system, then optimize\ns = Selection(m)\ns.energy()\ncg = ConjugateGradients()\ncg.optimize(s, max_iterations=200)\n\n# Write out the final coordinates\nm.write(file='pseudoout.atm')\n</syntaxhighlight>\n\n\nIt is straightforward to add restraints of this type to a comparative\nmodeling run - see for example, [https://salilab.org/modeller/10.0/manual/node28.html Adding additional restraints to the defaults].\n\n[[Category:Examples]]"
                    }
                ]
            }
        }
    }
}