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== Attendees & Time==
== Attendees & Time==


Date: April 2nd, 2010. 105 pm.
Sarah, Michael M, Ryan, Magdalena, Peter, Kong, Jens, Dahlia, John
 
Date: April 2nd, 2010. 1:05 pm.


== Slides ==
== Slides ==


#Philosophy
1. '''[http://www.urbandictionary.com/define.php?term=philosophy Philosophy]'''
**deleted unused things
*deleted unused things
**cleaned up code
*cleaned up code
**streamlined call graph
*streamlined call graph
***single mode gone (use version 3.5.54.70)
*single mode gone (use version 3.5.54.70)
***contact scoring gone
*contact scoring gone
***precalculate various grid terms
*precalculate various grid terms
 
2. '''[[DOCK 3.5.54]].72 improvements'''
*chem.bmp bumping instead of distmap contact bumping
*new hierarchy code (should eliminate some broken)
*no more out of bounds molecules
*no more clashing molecules
*deprecated unused keywords (more later)
*vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
*64bit/32bit builds (use dock.csh instead of calling directly)
*speedups (3-5x)
 
3. '''Deprecated keywords'''
*write_coordinates
*standard_pdb
*focus_ratio
*normalize_save
*restart_interval
*mirror_ligands
*scoring_option
*mode
*ligand_type
*restart
*output_hydrogens
*recombine_fragments
*interpolate
*ligand_sphere_file


#DOCK 3.5.54.72 improvements
4. '''New keywords'''
**chem.bmp bumping instead of distmap contact bumping
*keyword                            default  suggested
**new hierarchy code (should eliminate some broken)
*remove_positive_solvation no         YES
**no more out of bounds molecules
*check_clashes                    yes        YES
**no more clashing molecules
**deprecated unused keywords (more later)
**vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
**64bit/32bit builds (dock.csh instead of calling directly)
**speedups (3-5x)


#Deprecated keywords
5. '''[[Main_Page|DISI]]'''
**write_coordinates
*it is great
**standard_pdb
**focus_ratio
**normalize_save
**restart_interval
**mirror_ligands
**scoring_option
**mode
**ligand_type
**restart
**output_hydrogens
**recombine_fragments
**interpolate
**ligand_sphere_file
**write_coordinates
**standard_pdb
**focus_ratio


#New keywords
**keyword                            default  suggested
**remove_positive_solvation no          YES
**check_clashes                    yes        YES


#DISI
'''All of this is live since Mar 18 2010 in dock72!'''
**it is great


== Hardware updates==
== Hardware updates==
Line 57: Line 59:
== Requests/Improvements ==
== Requests/Improvements ==


Sarah raised the issue of the flexible protein code of Niu Huang:
* Is it compatible with the current improvements? <math>\rightarrow</math> probably not.
* Is anybody using it?
* Would it be worth it to update and include it?
* Can it be used in an automatic fashion, e.g. for [[DOCK Blaster]]?
* How can we predict water positions and usefulness (maybe initial water placement with [[PLOP]])?
<math>\Rightarrow</math> who will be doing all of this?


== Database updates ==
== Database updates ==

Latest revision as of 20:11, 8 October 2012

Attendees & Time

Sarah, Michael M, Ryan, Magdalena, Peter, Kong, Jens, Dahlia, John

Date: April 2nd, 2010. 1:05 pm.

Slides

1. Philosophy

  • deleted unused things
  • cleaned up code
  • streamlined call graph
  • single mode gone (use version 3.5.54.70)
  • contact scoring gone
  • precalculate various grid terms

2. DOCK 3.5.54.72 improvements

  • chem.bmp bumping instead of distmap contact bumping
  • new hierarchy code (should eliminate some broken)
  • no more out of bounds molecules
  • no more clashing molecules
  • deprecated unused keywords (more later)
  • vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
  • 64bit/32bit builds (use dock.csh instead of calling directly)
  • speedups (3-5x)

3. Deprecated keywords

  • write_coordinates
  • standard_pdb
  • focus_ratio
  • normalize_save
  • restart_interval
  • mirror_ligands
  • scoring_option
  • mode
  • ligand_type
  • restart
  • output_hydrogens
  • recombine_fragments
  • interpolate
  • ligand_sphere_file

4. New keywords

  • keyword default suggested
  • remove_positive_solvation no YES
  • check_clashes yes YES

5. DISI

  • it is great


All of this is live since Mar 18 2010 in dock72!

Hardware updates

Software updates

Requests/Improvements

Sarah raised the issue of the flexible protein code of Niu Huang:

  • Is it compatible with the current improvements? <math>\rightarrow</math> probably not.
  • Is anybody using it?
  • Would it be worth it to update and include it?
  • Can it be used in an automatic fashion, e.g. for DOCK Blaster?
  • How can we predict water positions and usefulness (maybe initial water placement with PLOP)?


<math>\Rightarrow</math> who will be doing all of this?

Database updates

Varia

Errata

Action Items

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