XYZ import troubles

When trying to use the wonderful MarvinView Applet for a non-chemical archaeological project, it is unclear to me how to import data in the 3D Applet.


I understand that the parameter to be set should be something like:


<param name="molecule" value="potters.xyz">


The file potters.xyz looks like:


#Potters Test


4


Potter1 0.11 -0.15 -0.01


Potter2 -0.05 -1.16 -0.16


Potter3 -0.35 0.12 0.88


Potter4 -0.37 0.36 -0.78


However, this doesn't work. .mol or .pdb files do apparently not allow fir free atom/potter names.


Hence my 2 questions:


- Am I bound to use molecule names or can I use free labels, such as potters' names?


- Does anyone has an example up and running wich such a "free format" input file?





With many thanks in advance,





Allard Mees


RGZM Mainz

First of all, to load molecules into the viewer, use "mol" or "cell0" parameters.


Please see the following MarvinView examples: load a simple molecule and XYZ animation


I forward your questions about XYZ to the right person.

Dear Allard,





since it turned out that this question is related to MarvinSpace, we move this topic to the corresponding forum.





Can you please post the complementarity to your question you sent us in email here too? It helped us to better understand your needs.





Kind regards,


Judit

I'm briefly summarizing the question as I understood.





Allard would like to have MarvinSpace read 3D scatterplots visualized as dots or bubbles (without bonds). He tried to create PDB file from the XYZ file with leaving bond information, but the dots did not appear.





He'd like to have an example how to create a file that MarvinSpace can read and visualize from the free-format input file.

Hi,





as a quick workaround I suggest to use PDB, all points should be in a HETATM record and the residue type should be water, HOH.


Example:

Quote:

HETATM 1 O HOH 1 -3.425 -1.782 -0.553 1.00 0.00 NNN HETATM 2 O HOH 1 -3.169 -2.859 -0.643 1.00 0.00 NNN HETATM 3 O HOH 1 -3.627 -1.364 -1.561 1.00 0.00 NNN HETATM 4 O HOH 1 -4.344 -1.684 0.066 1.00 0.00 NNN HETATM 5 O HOH 1 -2.318 -1.045 0.097 1.00 0.00 NNN TER 27 NNN 1 END

Hope this helps.





BTW: there are others, who intend to use mspace for similar purpose as you, ie. visualize 3d scatter plots, so we may consider to support such usage.





Regards


Miklos