build-example

There are 22 example systems; to run number four, for example:

$ pestifer build-example 4

Note

run-example is accepted as a synonym for build-example for backwards compatibility.

(Best to do that in a clean directory.)

You can use pestifer show-resources to list the examples:

$ pestifer show-resources examples

  Examples:

  Index        ID  Name                            Description
      1      6pti  bpti1                           Bovine Pancreatic Trypsin Inhibitor (BPTI)
      2      6pti  bpti2                           BPTI Excluding the Phosphate Ion
      3      6pti  bpti3                           BPTI with a Mutated-out Disulfide Bond
      4      6pti  bpti4                           BPTI with a Mutated-in Disulfide Bond
      5      1f7a  hiv-protease                    HIV Protease with Patches to Protonate Aspartates
      6      1fas  green-mamba-toxin               Green Mamba Toxin at pH 7.0
      7      4zmj  hiv-sosip-env-ectodomain1       Closed, Unliganded HIV-1 BG505 Env SOSIP.664 Trimer
      8      4tvp  hiv-sosip-env-ectodomain2       Closed, PGT122/35O22-Liganded HIV-1 BG505 Env SOSIP.664 Trimer (ligands removed)
      9      8fad  hiv-ad8-env-ectodomain          Cleaved, Asymmetric HIV-1 AD8 Env Ectodomain Trimer
     10      8fae  hiv-ae2-env-ectodomain          Cleaved, Asymmetric HIV-1 AE2 Env Ectodomain Trimer
     11      7txp  hiv-sosip-env-ectodomain3       Open, Symmetric D9/CD4-liganded HIV-1 SOSIP Env Ectodomain Trimer (ligands removed)
     12      5vn3  hiv-sosip-env-ectodomain4       Open, Symmetric 17b/CD4-liganded HIV-1 B41 SOSIP Env Ectodomain Trimer (ligands removed)
     13      2ins  insulin-hexamer                 DES-PHE B1 Bovine Insulin Hexamer
     14      4zxb  insulin-receptor-ectodomain     Human Insulin Receptor Ectodomain IRαβ
     15      7xix  sars-cov2-S-BA2                 Fully Glycosylated, Closed SARS-CoV-2 Omicron BA.2 Variant Spike
     16      6e8w  hiv-mpertm3-membrane1           HIV-1 Env MPER-TM Trimer in a DMPC/DHPC Symmetric Bilayer
     17      6e8w  hiv-mpertm3-membrane2           HIV-1 Env MPER-TM Trimer in an Asymmetric, Model Viral Bilayer
     18      5fkw  ecoli-polymerase                E. coli Replicative DNA Polymerase Complex Bound to DNA
     19      1mob  sperm-whale-myoglobin           Sperm whale myoglobin
     20    P22033  methylmalonyl-coa-mutase        Mitochondrial methylmalonyl-CoA mutase (Alphafold P22033)
     21      1aon  groel-groes-adp                 Asymmetric GroEL/GroES Chaperonin Complex
     22      2bgj  ferredoxin-fad                  Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus

fetch-example

This subcommand is like build-example, except it only copies the YAML input file needed to run the example to the CWD. It can be edited, if desired, and then run using the build subcommand.