FAQ_Denfert Help

List FAQs

Questions

  1. Who can I contact for a question ?
  2. What output files does Denfert produce at the end of each simulated annealing session?
  3. What to do if the final obtained model is not fully covered by hydration beads?
  4. Why don't I receive the e-mail with the download link ?
  5. Which version of Mac OS has Denfert been tested with?
  6. Is the Denfert executable for Windows 32-bit or 64-bit?
  7. Which versions of Linux has Denfert been tested with?

Answers

Q: Who can I contact for a question ?
A: 

Please upload your question in the "Add Suggestion" item. If you already have the answer to your question, you may help other users by uploading it as well.

Q: What output files does Denfert produce at the end of each simulated annealing session?
A: 

At the end of each session the following files are written on disk.

- 3 pdb files (_model, _hydration_layer, _solvent) that correspond to protein/nucleic acid, hydration layer and solvent respectively.

- an ascii file (_raw.fit) containing the final fit of the experimental curve

- an ascii .log file containing information about the annealing procedure

Q: What to do if the final obtained model is not fully covered by hydration beads?
A: 

Most probably the used bead packing radius is quite high. Try a new run with smaller bead packing radius.

Q: Why don't I receive the e-mail with the download link ?
A: 

The e-mail sender is "noreply". It might be filtered out by the spam catcher server of your institution. Try with another address.

Q: Which version of Mac OS has Denfert been tested with?
A: 

OSX version 10.9

Q: Is the Denfert executable for Windows 32-bit or 64-bit?
A: 

It is a 32-bit application.

Q: Which versions of Linux has Denfert been tested with?
A: 

Successfully tested on Ubuntu Linux.