OneAngstrom

Dear @Tanish ,

Adenita is a third-party extension developed by external developers. Since it is open-source, we started porting it ourselves to the latest SAMSON. The latest SAMSON compared to the versions of SAMSON which support Adenita has a lot of major changes meaning that the porting process will take quite some time especially together with fixing some issues in Adenita. Currently, we cannot give a time estimate since we work on it occasionally in our free time, but we hope it will be ready in the upcoming months.

We are sorry about the inconvenience.

Dear @Matthew-1 ,

Currently, for the Solvent Accessible Surface visual model, it is not possible to access the list of nodes (molecules, atoms, etc) to which it is applied to. We can expose this in the next version along with increasing the maximum value of the probe radius.

If you want to compute the Solvent Accessible Surface Area (SASA) of a molecule, then you can use the Protein-Ligand Interaction Analyzer: just set the molecule as a receptor, do not set any ligand, specify the probe radius for SASA computations (you can set up to 30A) and click Analyze - it will compute SASA for the receptor along with some other properties. Please note, that setting a large value for the probe radius will lead to more computations due to the used algorithm.

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.

For now, you can check the updated code in our GitHub repository: SAMSON-Developer-Tutorials.

In the Developer Guide, this tutorial's code and some of its descriptions are for its previous version and will be updated soon.

Dear @Lauren ,

We are sorry, the tutorial might be slightly outdated in that it was done with the previous version of SAMSON SDK. It should rather be a single display function that gets SBNode::RenderingPass:

class SEVanDerWaalsVisualModel: public SBMVisualModel {

	SB_CLASS

public :

	// ...

	virtual void			display(SBNode::RenderingPass renderingPass);			///< Displays the visual model

	// ...

}

I will update the tutorial shortly and will let you know. Thank you for reporting this issue.

Great! Thanks for the reply.

Please do not hesitate if you have more questions.

Dear @Lauren ,

Could you please verify if you followed all the instructions as written in the Documentation: Building on Mac OS X.

Does the ALL_BUILD target build successfully? Did you build the install target afterward? Do both build and run steps have the same Debug/Release configuration?

Once loaded, you should see a Path node in the Document view. You can double-click on it to start/stop the trajectory.

To play the trajectory frame-by-frame or go to a specific frame, you can use the Inspector - right-click on the Path node in the document and click on "Inspect" - this should open the Inspector for this node. Please note, that some functionality of the Inspector is disabled in the Starter plan version, you can try the Standard or Professional plans for a free 30-day trial period.

If you don't have access to the Inspector, then you can create Conformations out of the Path. For that, right-click on the Path in the document and click on "Create conformations from paths" - this will create conformations in the document for each frame of the Path. Then you can simply double-click on a conformation in the document to restore it.

Dear @luis ,

To load an XYZ file with a trajectory it needs to be in a special format. For example, a trajectory of 3 hydrogens:

3
 STEP:           1
 H      0.967485      6.687080      5.821420
 H      2.507099      7.320300      6.535832
 H      2.819131      8.163311      3.557150
 3
 STEP:         2
 H      0.987382      6.755653      5.887846
 H      2.528730      7.288068      6.545012
 H      2.899837      8.187620      3.675997
 

The first number is the number of atoms, the following comment line should contain the word 'Step' (or 'step' or 'STEP'), and the atoms in each step should be in the same order.

Dear @Oisin ,

Covalent bonds are created based on the interatomic distances. Maybe the atoms are placed too far from each other? Could you please check the distance between atoms in your system - you can do it using the Measure editor by clicking on two atoms consecutively. Could you please attach a .cif file in which you experience the problem such that we could check it.

By the way, are you referring to .cif for biomolecules (mmcif/PDBx format) or .cif for crystals?