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There were 14 questions found in this category:
  1. questionHowTo: Start FlexX standalone with FlexV
    Release 3:Start FlexX/-SIS in commandline mode(flexx --commandline); The location for FlexV is specified using File | Global Preferences. Then proceed as described below ignoring the bit about config.dat.Release 2 and older:This description assumes you already have a FlexX installation, perhaps ...

  2. questionHowTo: Installation for Beginners (Windows)
    Release 3 and newer:Double click the installer executable. The rest is self-explanatory.If you stumble, please write to us (support AT biosolveit . de )Release 2 and older:In these versions, FlexX is a command-line tool only which is connected to a graphical viewer. That means, (once it's runni ...

  3. questionHow to get a co-crystallized ligand into ReCore within LeadIT's Receptor Preparation Wizard?
    The quick information: Use the ligand’s context menu (right mouse click) in the ProjectTree. We aim to improve support of this workflow. Background Information: PDB typically lacks information such as bond orders, atom type etc. We try to augment the existing information as good as ...

  4. questionHow to run FlexX on Windows Vista (compatibility)...
    FlexX/SIS pre-3.1.2 versions can be made to run under Windows Vista.You need to enable the executable to run in XP compatibilitiy mode.To do so:. please do a right-click on the executable's icon in Explorer- open the properties widget;on the second tab (Compatibility), you can select Windows XP ...

  5. questionHowTo: Add a metal ion to the RDF
    Release 3.1 (pre) and newer:Metals and respecting their coordination chemistry are supported in the GUI intuitively during the receptor preparation. RDF handling is obsolete.Release 2, 3.0 and older:In order to add metal ions to the Receptor Description File (RDF) you have to add two lines to t ...

  6. questionHowTo: Covalent Docking
    Release 3:Start FlexX/-SIS in commandline mode(flexx --commandline); then proceed as described below.Release 2 and older:Many people don't even know that FlexX can dock covalently bound ligands. Therefore, we found it all the more important to bring this topic to our readers' attention. In the ...

  7. questionHowTo: Determine the processor ID
    There are several ways to determine the BIOSOLVE processor ID of a computer (this is not the CPU-ID you can determine with other tools). Download the tool "FlexIDgen" from http://www.biosolveit.de/download unzip the file and run the included executable "flexidgen" (or flexidgen.exe on Windo ...

  8. questionHowTo: Escape to the Operating System - Shell Escape
    FlexX/S and FTrees allow you to temporarily escape to your operating system. This can be convenient, for example, to zip or unzip input or output files. Also your custom analysis program or more complicated scripted tasks can be executed from within Flex*/FTrees. The shell escape is invoked wit ...

  9. questionHowto: Large Scale Virtual Screening with FlexX or FlexSIS (Howto).
    Large Scale Screening with FlexX/-SIS   This applies to FlexX and FlexSIS Release 3 and newer.There are three stages we will explain below.   Part 1: Receptor Preparation Part 2: Screening Part 3: Parallel Processing (requires more than 1 license and Linux/Unix)   General Approach: Use the grap ...

  10. questionHowTo: Rescoring with FlexX
    Release 3:Start FlexX/-SIS in commandline mode(flexx --commandline); then proceed as described below.Release 2 and older:It is of course possible to calculate a rescoring for a given complex. You can use the command SCORE that can be found in the menu DOCKING/ANALYZE. In this submenu you will a ...

  11. questionHowTo: Running a FlexLM License Server
    The regularly licensed versions of most of our tools allow that license requests for all installations in a network are managed by a single, so-called  'license server'. This is not a machine but a piece of software running on a computer. Such a server may manage the license requests for hundre ...

  12. questionHowTo: Set up FlexX for parallel mode
    Release 3:Parallel processing is adjusted in File | Global Preferences. The respective settings will be written to your home directory and must therefore be available to the parallel compute nodes.Release 2 and older: 1. Create a link to FlexX in ~pvm3/bin/<$PVM_ARCH>/<executable> T ...

  13. questionHowTo: The Protonation of protein amino acids
    Release 3 and newer: The GUI's wizard (Receptor | Define) will guide you through the necessary steps. Release 2 and older: Using the RDF file On the receptor side, the protonation is controlled by the RDF-file which contains information about the protein and the residues that define the binding ...

  14. questionHowTo: Use a Gaussian Filter
    Release 3:* Use the access_scaling dialog in DOCKING | DEFINE | SCORING.* For more advanced configuration, start FlexX/-SIS using the commandline (flexx --cli), then proceed as below. Release 2: Preconception: FlexX placements are sometimes found at the rim of the binding site. True — b ...

Last modified Wednesday, 08. Sep 2010 15:45 CEST by WebMaster