Example Commands

The example commands in this section can be run with files found in the data/1nhu directory under the top-level installation directory.

Basic Usage

> flynn -in 1nhu.ism -map 1nhu_prot.mtz -prot 1nhu_prot.pdb \
           -out 1nhu-poses.pdb

Use the ligand specified by 1nhu.ism and fit it against the density in the mtz file 1nhu_prot.mtz. Since this is an mtz file and -autoMTZ is defaulting to true, the Fdelwt map will automatically be generated and used as the density target. The protein atoms specified in 1nhu_prot.pdb will be used to mask the density before the map is searched for appropriately sized ligand volumes.

Generating Reports

> flynn -in 1nhu.ism -map 1nhu_prot.mtz -prot 1nhu_prot.pdb \
           -out 1nhu-poses.pdb -precheck -reporthtml 1nhu.html

Performs a preliminary check of the data, ensuring that the ligand can be processed and that the mtz file can be opened. An html file is generated 1nhu.html with a corresponding image file 1nhu.html.gif. The html file can be opened with a web browser to view the ligand being fit and any corresponding issues.

The output will be written to 1nhu-poses.pdb in pdb format.

Choosing box regions of density

> flynn -in 1nhu.ism -map 1nhu_sigma.mtz -prot 1nhu_prot.ent \
           -out 1nhu_poses.pdb -box 1nhu.pdb -boxpad 2.0

This is the same as above except that the density is pruned down to the bounding box specified by 1nhu.pdb padded by 2.0 Ångströms. Furthermore, if a suitable blob is not found, then the pruned density will be used as is. This is quite effective for regions of density with a high degrees of disorder. It is also useful to select this option when using the supplied interface to coot.

Choosing density close to residues

Use the -residues and -distance flags to indicate residues close near the desired density. Only blobs that are found within -distance to the selected residues will be selected. Residues are specified by <residuenumber><chain> separated by commas.

> flynn -in 1nhu.ism -map 1nhu_prot.mtz -prot 1nhu_prot.pdb \
           -out 1nhu-poses.pdb -residues 528B,477B

Choosing MTZ columns

> flynn -in 1nhu.ism -map 1nhu_sigma.mtz -prot 1nhu_prot.ent \
           -out 1nhu_poses.pdb -box 1nhu.pdb -boxpad 2.0 \
           -boxThenBlobs -autoMTZ false -Fobs Frefined1 -Fc FC \
           -Phic PHIC -mtype 2Fo-Fc -autoMTZ false

This example shows how to choose a non-standard column from the MTZ file. the map is generated using Frefined1 as the observed amplitude column, FC as the calculated amplitude column and PHIC as the calculated phase column. Furthermore, the regular map 2Fo-Fc is used. Note that -autoMTZ must be set to false for these settings to take effect.

Fragment usage

The -fragment flag may be included with any of the above commands. There are three main differences when running in fragment mode:

  1. Multiple ligands are fit simultaneously.
  2. If the blobs detected for difference ligands overlap, the ligands are assigned to the same blob. (This is for reporting purposes)
  3. Ligands are sorted according to the Real Space Correlated Coefficient.
> flynn -fragment -in 1nhu.ism -map 1nhu_prot.mtz -prot 1nhu_prot.pdb \
           -out 1nhu-poses.sdf

When in fragment mode, it is better to output to a format that supports SD style data (.sdf, .oeb). This makes it much easier to analyze the results in a molecular viewer that supports a sortable spreadsheet. (VIDA, MOE and so on)

To sort the results using another scoring function, use the -sortBy flag.

> flynn -sortBy chemscore -in 1nhu.smi ...