Phenix on Biowulf

Phenix logo

The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data.


Important Notes

This application requires an X-Windows connection. Further, there are combinations of X11 servers and drivers that cause Phenix to crash. It is known that XQuartz (v2.7.x) is incompatible with Phenix. Users are encouraged to use NX or FastX as their X11 servers.

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load Phenix
[user@cn3144 ~]$ phenix

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$


Phenix can launch graphical applications Coot and Pymol. Navigate to Preferences -> Graphics and insert this string into the text box for PyMOL path:

PyMOL path

Now when the PyMOL button is clicked, you should see this:

PyMOL window

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

module load Phenix
phenix.autobuild seq_file=p9.seq data=p9-solve.mtz \
  input_map_file=p9-resolve.mtz resolution=2.4  \
  ncs_copies=1 nproc=$SLURM_CPUS_ON_NODE \

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] --gres=lscratch:50
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. Phenix.swarm). For example:

phenix.elbow input_1.pdb
phenix.elbow input_2.pdb
phenix.elbow input_3.pdb
phenix.elbow input_4.pdb

Submit this job using the swarm command.

swarm -f Phenix.swarm [-g #] [-t #] --module Phenix
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module Phenix Loads the Phenix module for each subjob in the swarm
Using Rosetta within Phenix

Rosetta has been compiled specifically for Phenix, and is available via two environment variables PHENIX_ROSETTA_PATH and ROSETTA3_DB. Do NOT load the Rosetta modules built for Biowulf, as these are NOT compiled specifically for Phenix. Also note that structural models are limited to standard amino acids and other limitations.

Here is an example of structural refinement using Rosetta to generate structural models (this file is named

#SBATCH --cpus-per-task=4
#SBATCH --time=72:00:00
#SBATCH --mem=50g
#SBATCH --gres=lscratch:50
module load Phenix
phenix.rosetta_refine input.pdb input.mtz \
  temp_dir=/lscratch/$SLURM_JOB_ID \

Then submit to the cluster:

Using CryoFit within Phenix

The CryoFit protocol can be used to fit a fasta or pdb into a cryoEM map.

Both cryo_fit and cryo_fit2 can be run from the commandline. Here is how to run the tutorials:

cp $PHENIX_MODULES_DIR/cryo_fit/tutorial_input_files/*.{mrc,pdb} .
phenix.cryo_fit GTPase_activation_center_tutorial.pdb GTPase_activation_center_tutorial_gaussian_1p5.mrc
cp -R $PHENIX_MODULES_DIR/cryo_fit2/tutorial/input .
phenix.cryo_fit2 input/tutorial_cryo_fit2_model.pdb input/tutorial_cryo_fit2_map.ccp4 resolution=4