Xray crystal structures

User 870ab5b546

24-03-2006 21:19:43

Hello,





I would like to see MarvinSpace be able to load SHELX files and display thermal ellipsoids.





-- Bob

ChemAxon efa1591b5a

27-03-2006 08:45:42

Hi Bob,





perhaps, yes. It depends on how complex this task is, which I cannot estimate yet, I need more info.





Do you mean the .ins or the .hkl file (or both?)


Could you provide us a link to the appropriate file format definitions?


Also, some sample pictures would be helpful, is there any web page to look at that you can recommend?





Cheers,


Miklos

User 870ab5b546

27-03-2006 12:18:34

I mean the .res or .cif file. I am attaching examples of .res and .cif files and a .pdf image of the asymmetric unit that I produced from the .res file with the CAChe software. (But of course I would rather use MarvinSpace.)





(Your forum would not let me post the .res and .cif files as such, so I had to add the .txt extension.)





You might want to use an open source converter such as Open Babel. The SHELX home page is here. The CIF specification is here.

ChemAxon efa1591b5a

27-03-2006 12:26:15

Thanks for the links and refs, Bob.


CIF format has already been on our todo list, tough the task was not yet scheduled.


We'll look through the documentation you referred to and i'll let you know what we can do and when.





Thanks


Miklos

ChemAxon efa1591b5a

28-03-2006 10:09:19

We tried OpenBabel, it recognized the .res file, but not .cif, and produced a PDB that MSpace could read. ANISOU records were not generated, though the information was present in the .res file.





The .cif file format is rather horrible, we can probably process .res with less pain. Though bond information is not present in that file, which is sad.





Summarizing, what we can do:


- read .res file


- process ANISOU record if present in the PDB


- draw the thermal ellipsoids (only one draw type in the beginning)


- selection mechanism will not be implemented for the ellipsoids





Is that o.k. for you?


Do you need this new feature urgently, or it falls in the 'would be nice' category?





Miklos

User 870ab5b546

28-03-2006 12:06:41

mvargyas wrote:
Summarizing, what we can do:


- read .res file


- process ANISOU record if present in the PDB


- draw the thermal ellipsoids (only one draw type in the beginning)


- selection mechanism will not be implemented for the ellipsoids





Is that o.k. for you?


Do you need this new feature urgently, or it falls in the 'would be nice' category?
The latter. As I said, I already own software that produces the picture I attached, but I would rather use MarvinSpace.





You should definitely try to overcome your .cif problems, though, because this is the format that journals archive.

ChemAxon efa1591b5a

30-03-2006 12:21:33

Right, then .cif support will be implemented (along with ANISOU record in PDB), probably after the UGM.


Miklos

User 870ab5b546

21-11-2006 15:06:42

Hi Miklos,





Has either .res or .cif support been implemented yet?





I went to MarvinSpace 1.3.1 Help and clicked on Loading Molecules into MarvinSpace, then supported formats, and got this error:





Cannot load page jar:file:/Applications/ChemAxon/MarvinBeans/lib/MarvinBeans.jar!/doc/dev/formats.html





-- Bob

ChemAxon efa1591b5a

23-11-2006 10:52:45

Hi Bob,





1, .res .cif: no, and none is planned in the short term.





2, Thanks for the bug report, we will fix that. In the meantime you may wish to use this link http://www.chemaxon.com/marvin/doc/dev/formats.html to get the information needed.





Regards,


Miklos