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    • C

      Statistic on current selection
      Feature requests • • Cyril

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      C

      It works great ! Thanks a lot !

    • A

      SAMSON SDK doesn't see any elements
      Getting started • • Andrii

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      A

      Thanks, SAMSON SDK 7 works properly, but v6 still not (I've checked all requirements and followed installation steps from the instruction). Still, I've got working version of SDK, so thank you again)

    • E

      Receiving signal when creating new Document
      Apps • • Elisa

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      E

      Thank you both, I will use the timer as a workaround for now.

      Seems 0.8.0 is going to have a lot of interesting changes :)

    • A

      Usage of existing elements created by someone else
      Simulation • • Andrii

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      DmitriyMarin

      @Andrii It can be done from the code. For now, we do not have docs/help web-pages for each of the SAMSON Elements, but it is in our plans to have them generated automatically for the exposed functionality.

      To get UUID and the class name of an Element from which you want to use functionality, you can open the Log (Edit menu -> Show log), then you can search for the Element and check its UUID and the class name:
      0_1541585623122_LogViewer-CheckUUIDAndNameOfSAMSONElement.png

      Now, in your code, you can do the following to print the exposed functionality of the Element:

      // Create a class proxy SBProxy* classProxy = SAMSON::getProxy("PDBDownload", SBUUID("6F5D45C5-E76E-CDC8-52D5-D2821C128BE8")); // Print class constructors classProxy->print(); // Prints the interface classProxy->getInterface()->print();

      It will print the exposed functionality (constructor factory, interface functions, attributes) in the terminal (std::cout stream), like this:

      Class proxy: Name :PDBDownload UUID :23E5619D-CF88-CD8D-C516-725286102AF8 Element :PDBDownload Type :10 Factory: PDBDownload() Interface: download(std::string, std::string) downloadPdb(std::string) downloadPdb1(std::string) Attributes:

      You might need to allow the terminal with "--logconsole" flag when running SAMSON.

      If you have some problems with std::cout not printing to your terminal, you might print it yourself into std::cerr:

      // Print interface std::cerr << "Interface:\n"; auto functionMap = classProxy->getInterface()->getFunctionMap(); for (auto i = functionMap.begin(); i != functionMap.end(); ++i) std::cerr << i->getKey() << "\n"; // Print attributes std::cerr << "Attributes:\n"; auto attributeMap = classProxy->getInterface()->getAttributeMap(); for (auto i = attributeMap.begin(); i != attributeMap.end(); ++i) std::cerr << i->getKey() << "\n";
    • K

      Bug in SBMInteractionModelParticleSystem?
      Simulation • • Khoa

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      Stephane

      ok great!

    • A

      DLL dependencies of an Element
      Apps • • Alain

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      K

      From here you can solve your issue related to the dll file, what you need to do is check missing Burutter.dll and copy the setting and save the dll file setting in your PC then you are able to replying of dll files.

    • K

      Conversion from radian to degree does not work
      Apps • • Khoa

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      K

      Thanks.
      It helps.

      SBQuantity::radian radianValue(1.5); SBQuantity::degree degreeValue = radianValue * SBConstant::RadToDeg;
    • H

      Solved Adding SBAtoms to SBGroupNode
      Modeling • • Haichao

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      H

      Thanks, this solves my problem!

    • J

      Using IM-UFF
      SAMSON • • Joseph 1

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      DmitriyMarin

      Currently, there is no public extension in SAMSON that can launch/use LAMMPS. But you can export your system into a LAMMPS Data format and load LAMMPS files (data and trajectories) back in SAMSON.

      We plan on adding the support for periodic boundary conditions in one of the future releases of SAMSON. For some systems, you can simulate without PBC or by freezing the boundary atoms to fix them.

      You can also combine simulations in SAMSON with e.g. ASE package using Python, see Python scripting: Combining SAMSON simulation with ASE calculators

    • S

      Autodock Vina PDBQT generation
      SAMSON Extensions • • Serena

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      DmitriyMarin

      Dear @Serena ,
      No, we do not use Open Babel or anything else for that. It is done by the AutoDock Vina Extended module.

    • A

      Not abe to install the application
      Getting started • • AntiDown

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      DmitriyMarin

      Dear @AntiDown ,

      Ok. I am glad it works for you now.
      Thank you for your reply!

    • A

      Could not load the Qt platform plugin "xcb" in "" even though it was found.
      Getting started • • Ahmet Can

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      DmitriyMarin

      Great! Thanks for letting us know.

    • 闽

      Installing samson in win11
      Getting started • • 闽乐

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      DmitriyMarin

      Dear @闽乐 ,

      In the new version, you can access the control parameters for the visual model via the Inspector. For that, simply select the Adenita visual model and open the Inspector - you can right-click on the Adenita visual model and choose Inspect in the context menu.

      See: User guide - Inspecting

    • E

      Animation - docking in Gaussian representation
      SAMSON Extensions • • Eva

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      DmitriyMarin

      Dear @Eva ,

      We have improved the performance of surface visual models (Gaussian, Solvent Accessible, and Solvent Excluded surfaces) in certain cases. For example, now animations with them should be much faster. The visual models should be automatically updated for you once you restart SAMSON.

    • A

      Export atom properties (charges, etc.) as a weight map
      Feature requests • • Afdeling

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      Admin

      Hi Luis, sorry for the delay! Could you please contact us at contact@samson-connect.net? It would be easier to chat / zoom about this so we can focus the development.
      Thanks!
      best,

      Stephane

    • L

      Van der Waals Tutorial - Casting Shadows
      Modeling • • Lauren

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      DmitriyMarin

      Dear @Lauren ,

      We have updated the Creating visualizations: Van der Waals visual model tutorial in our Developer Guide.

      You can also check out the code samples corresponding to this tutorial here: https://github.com/1A-OneAngstrom/SAMSON-Developer-Tutorials/tree/master/VanDerWaals. The code samples contain more optimized code and some additional functionality.

    • L

      Newly Generated Apps Not Appearing
      Apps • • Lauren

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      DmitriyMarin

      Great! Thanks for the reply.

      Please do not hesitate if you have more questions.

    • K

      Load and save camera settings
      SAMSON • • Khoa

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      K

      Thanks for the replies, Dmitriy and Stephane.

    • O

      Adenita not showing up
      SAMSON Extensions • • Olivia

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      DmitriyMarin

      Great! Thank you for your reply!

    • J

      Gromacs Wizard Membrane Protein
      SAMSON Extensions • • Jessica

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      Admin

      The error message ("atom N not found in buiding block 1ACE while combining tdb and rtp") suggests that, in your model, 1ACE contains a N that should not be there (according to GROMACS topologies). You might have to remove it, or move it to the next residue. You can reorganize atoms, residues, etc. easilyby just dragging nodes around in the Document View.