Category Archives: Pymol

Pymol 1.8.x now fetches mmCIF files by default and shows missing residues in Sequence View

Long time Pymol users will be familiar with the fetch command by which it retrieved the selected file from the Protein Data Bank (PDB). Up until version 1.8, Pymol fetched the PDB version of the file by default over the … Continue reading

Posted in Chem, mmCIF, mmCIF files, modeling, Pymol, software | Leave a comment

When in Pymol, don’t call your model “model”

Sometimes it pays to read the blurb that loads in a textport when software loads. Folks, there is an inherent problems when viewing your Swissmodel results in Pymol. Like many people I usually look away from the screen when I boot a … Continue reading

Posted in Chem, Chem_Comp, modeling, Pymol, software | Leave a comment

Pymol and very large PDB files. The Zika Cryo-EM structure as a case study

One of my major research interests is the Flavivirus group of viruses. In our work at the University of Queensland we’ve been involved in developing inhibitors of viral proteins associate with Dengue and West Nile viruses. Particularly inhibitors of the … Continue reading

Posted in Chem, Chem_Comp, mac, Pymol, Uncategorized | Tagged , , | 2 Comments