Model building with ModelAngelo

Building an atomic model using ModelAngelo [JKZ+24] is done in the same way as in the SPA tutorial. First, download the protein sequence as a FASTA file from this link (Download Files -> FASTA Sequence).

Running the job

Select the ModelAngelo building job type and, on the I/O tab, set:

B-factor sharpened map::

PostProcess/job079/postprocess_masked.mrc

FASTA sequence for proteins::

rcsb_pdb_5L93.fasta

After inputing the path to the ModelAngelo executable and the GPUs to use and making sure that Perform HMMer search? is set to No on the Hmmer tab, we run the job.

Analysing the results

On our machine with 2 GPUs, this job took 3 minutes to run. The output is a coordinate file called ModelAngelo/job080/job080.cif that may be used in UCSF chimera together with the Postprocess/job079/postprocess.mrc map. Note that although ModelAngelo did a very good job on this relatively easy test case, you should always check its results carefully in a program like coot [ELSC10] . You will also need to perform a stereochemical refinement of the coordinates. For this, we like servalcat [YPBM21].