3.2 Example Executions

This section has a series of example flynn command-line executions. Each example is followed by a brief description of its behavior.

prompt> flynn -in 1nhu.ism -map 1nhu-sigma.mtz -prot pdb1nhu-nolig.ent
              -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.

prompt> flynn -in 1nhu.ism -map 1nhu-sigma.mtz -prot pdb1nhu-nolig.ent
              -out 1nhu-poses.pdb

Use the ligand specified by 1nhu.ism and fit it against the density in the mtz file 1nhu-sigma.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 pdb1nhu-nolig.ent will be used to mask the density before the map is searched for appropriately sized ligand volumes.

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

prompt> flynn -in 1nhu.ism -map 1nhu-sigma.mtz -prot pdb1nhu-nolig.ent
              -out 1nhu-poses.pdb -residues 528B,477B

prompt> flynn -in 1nhu.ism -map 1nhu_sigma.mtz -prot pdb1nhu_nolig.ent
              -out 1nhu_poses.pdb -box 1nhu.pdb -boxpad 2.0 -boxThenBlobs

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 angstroms. Furthermore, if a suitable blob is not found, then the pruned density will be used as is.

prompt> flynn -in 1nhu.ism -map 1nhu_sigma.mtz -prot pdb1nhu_nolig.ent
              -out 1nhu_poses.pdb -box 1nhu.pdb -boxpad 2.0
              -boxThenBlobs -autoMTZ false -Fobs Frefined1 -Fc FC
              -Phic PHIC -mtype Fo-Fc -autoMTZ false

This is the same as above except that the map is generated using Frefined1 as the observed amplitude column, FC as the calculated amplitude column and PHIC as the calcualted phase column. Furthermore, the difference map Fo-Fc is used.

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				FLYNN