@emmanuel
For now, you can just reapply the Hydrophobicity color scheme (Biology menu > Colorize > Hydrophobicity).

Dear @Oliver ,

We expect it to be fixed in a few weeks.

Dear Sebastian,

one possibility might be to ask the Vina extension to compute many modes (e.g. 1000) and then use a script to filter out the conformations that do not satisfy the distance constraint. Another possibility might be to directly modify the source code of Vina to add a term to the scoring function that would penalize one or more unsatisfied constraint(s) (similar to a NMR energy function). We're going to look into this. Thanks for the suggestion.

Best,

Stephane

@shozeb Here is the process to uninstall SAMSON :

delete : rm -rf ~/.local/share/OneAngstrom/
delete : rm -rf ~/OneAngstrom/
delete : rm -rf ~/Documents/OneAngstrom/
delete : rm -rf ~/.config/OneAngstrom/
delete : rm -rf ~/.config/NANO-D (if exists)

After that you may try to reinstall SAMSON as described in the documentation.

Don't hesitate to contact us again if the issue is not solved. Users are our priority.

Jocelyn

Ah ok good. Yes SAMSON determines which importer to use based on the file extension.

It is saying it as a problem. Backing up of file is working anymore. Rest of the log is normal but it got stuck at this point and then nothing works.

Thanks!! Solved!

Dear @Tom-1 ,

We have added an example of how to build molecules using Python Scripting in SAMSON, please see SAMSON-Python-Samples > building.

Please let us know if you have any questions or feedback.

Hi Stephane,

thanks for your answer, I'll do that then.

Best

Laëtitia

Dear Stephane,

Thanks for the quick reply. I will add the position in three attributes for now. Looking forward to 0.8.0!

It seems it works. Thanks.

Perfect thanks.

Dear Camps,

I thought I'd clarify what's going on with Brenner and ASED-MO. While SAMSON and numerous SAMSON Elements are and will remain free forever, both for academia and industry, some SAMSON Elements will now have a commercial license (for industry and / or academia).

In effect, SAMSON Connect is becoming a marketplace for molecular modeling, where developers have the possibility to integrate and commercialize their tools (think App store for molecular modeling, except everything is integrated into a single, universal platform which makes it possible to combine modules together and gives new possibilities). Our goal is to contribute to the development of an integrated ecosystem for molecular modeling, where users can install tools in a few clicks, have them all integrated in the same platform, are able to combine them, pipeline them, etc. Since SAMSON has an open architecture, and the SAMSON API makes it possible for anyone to integrate existing tools, create new ones from scratch, develop new force fields, create new visualizations, etc., you can imagine the huge possibilities the SAMSON model gives.

As with other marketplaces (iOS, Android, etc.), many SAMSON Elements are and will continue to be free, and new free SAMSON Elements will continue to be published. However, our goal with this hybrid economic model is to reach the best of both worlds: serve the molecular modeling community while supporting the development of the best possible platform.

At the moment, anyone can get a free month of some commercial SAMSON Elements (including Brenner) by answering the short survey at https://forms.office.com/Pages/ResponsePage.aspx?id=Cg7MSY8KzkinPF492orBMZM0kpSnVmtKp3madpYYjexUQ0c5V1Q3VUEwVEtHQlhSWVVJRUFGN1lVQy4u.

At the end of the survey, they can choose which SAMSON Element they want among:

Brenner interaction model (interactive simulation for carbon nanotubes, graphene, etc.) Crystal creator (build complex crystals structures) Normal modes advanced (non-linear normal modes analysis for proteins binding sites)

and we'll add it to their account (registering is and will always be free, and SAMSON itself will always be free).

Best,

Stephane

Sorry for the issue!

I created a ticket.
thanks for your answer!

Thank you!
I will try it with this.

Yes, I meant SBStructuralGroup :)

Thank you! Using the GetClass and GetElementUUID methods is enough for my purposes :)

Thanks Ibrahima! Let us know if we can help in any way.

Another possibility could be to start from a selenium crystal and "sculpt it".

Get a CIF file for a crystal you like at http://rruff.geo.arizona.edu/AMS/minerals/Selenium. You will need the CIF importer in the Crystal Creator SAMSON Element (https://samson-connect.net/app/main?key=element&uuid=58a75a78-abbc-2c60-6214-e668b5c45a0d). In this example, I'm using this CIF file: http://rruff.geo.arizona.edu/AMS/download.php?id=10390.cif&down=cif. When you import the CIF file, use a big enough number of cells, for example 10 in each direction:
0_1528385266091_08798f27-b8d7-4139-8e87-97f67c07b32f-image.png
This will create 32000 atoms:
0_1528385319471_d2cb857d-3ff4-4d2f-ba1b-9f52e0170c30-image.png Select one atom around the center of the crystal, with the selection editor 0_1528385357394_dd40b047-a00b-4346-8801-e0193268107e-image.png:
0_1528385397414_315ea865-a94f-4f62-a4be-8348071ee4e0-image.png
(look around to make sure the selected atom is approximately in the center) Open the Find window (CTRL / CMD + F or Selection / Find...):
0_1528385478242_d43a3244-962b-4bcd-94f1-4ea3c052fe58-image.png Enter the following search string: n.t a w 20A of n.s in the box named "Selection string" and press the OK button. This is the short form of "node.type atom within 20 Angstrom of node.selected", i.e. all atoms within 20A of the current selection. This selects atoms in a 20A radius sphere:
0_1528385607949_e9280e37-b54c-4560-9e6a-133282b1f0bc-image.png Open the Find window again, to invert the selection with the following NSL expression: n.t a and !n.s (in the box named "Selection string", then press OK). This means "all nodes that are atoms and that are not selected". This selects everything outside the nanoparticle:
0_1528385806987_1.png Press the "delete" key to erase the selected atoms, or click on the "Current selection" widget and select "Erase selection":
0_1528385902405_a3c8d30d-c47e-41ed-a5da-5d9a307eb47c-image.png
This leaves the particle alone:
0_1528385954376_7e5484ab-1bb4-44b0-8d96-f6534eb60b9d-image.png In the Document view, select the Property model called "Selenium crystal" and delete it, i.e. go from
0_1528386023100_d66cd933-e574-4c80-bbc9-35c1820851ee-image.png
to
0_1528386038473_4a83e287-d616-4cbb-ad50-695cc3fd846d-image.png You now have a spherical selenium nanoparticle with a 20A radius. Save it to a SAMSON file format or export it to a PDB file. Here is the SAMSON version: 0_1528386144295_Selenium nanoparticle.sam

Hope this helps,

Stephane

First of all I have to thank you for the quick response. Funnily, I thought of using const_cast on the matrix pointer beforehand but considered it as too "hacky".
There should be several possibilites how one could introduce this into the API:

Each camera gets a state that determines whether it implements a symmetric or asymmetric projection including two methods that query and set the state. Then, an additonal method (possibly like SetPlanesAsymmetric(float left, float right, float top, float bottom)) could be used to transfer the wanted plane values to SAMSON. This approach would leave the old API intact, if the symmetric projection is the standard state. Derive a class like SBDAsymmetricDocumentCamera from the currently available SBDDocumentCamera, overriding all methods concerning the projection matrix. This is probably the least favourable alternative, although the old API would still be valid. The camera gets two additional methods SetValuesSymmetric(float aspect, float fovy, float zNear, float zFar) and SetValuesAsymmetric(float left, float right, float top, float bottom, float zNear, float zFar). Then, the GetProjectionMatrix() and GetProjectionMatrixTranspose() methods would have to be changed to take an additional boolean input parameter determining which kind of matrix is wanted. This would break the old API and I am not sure how this would propagate to the convenience display methods like SAMSON::displayCylinders(...).

Unfortunately I do not know which of these possibilities (and I probably missed some additional ones) would fit best into your way of writing SAMSON.

Best,
Karsten