Building a super cell from .cif file

[Mohan maruthi sena]

Hi all,
          I recently started using vesta, I want to build a crystal structure from .cif file. I have used the option boundary conditions to build super cell. I want the order of atoms to be same as in .cif file , but vesta gives all first atoms at once  and then all second atoms at once , so on. Is there any option in vesta so that we can get the order of atoms same as in .cife file. Please find the attached .cif file and .pdb file for reference.

Thanks for reply in advance,

Mohan

[Philip Howie]

Hi Mohan,

I'm not exactly sure what you're asking.  If you're talking about the order in which the atoms appear in the 'Edit | Structure Parameters...' dialogue, then you can change the sort order by clicking on any column header.  In this way, you can sort by atom type, z coordinate, etc.  If the specific order in which the atoms appear in the .cif file is important, you can use the atom labels (_atom_site_label in the .cif file) to number the sites, then sort by this column.

If you're talking about the numbers for each individual atom which appear (as far as I can tell) only in the 'Edit | Vectors...' dialogue, then I believe these are sorted first by atom label and then by x, y and z coordinates in this order.  Perhaps KM can confirm this.

Hope that helps,

Philip

[Mohan maruthi sena]

 Thank you sir for a reply, I will try one of these things and let you know.

Regards,

Mohan

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[Mohan maruthi sena]

 Hello Sir,

                     Sorry for not being clear in my earlier mail,  Let me explain in this way, I have a acetoaminophen molecule. It contains 20 atoms  [ let say O1,H1 ,N1..  ],  When I build the the super cell using vesta it gives output pdb file as 01,O1,O1,O1 , then H1, H1, H1 ...., N1, N1,N1, but i want output in my pdb as O1, H1, N1  then for second molecule as O1, H1, N1.

How can i do this in vesta.

Thanks,

Mohan

[Philip Howie]

My apologies for misunderstanding your question.  I'm afraid I don't know how to do what you want; I suspect it isn't possible.  All I can suggest is that .pdb files are in a plain text format, and so it should be relatively straightforward to write some sort of script to reorder (and renumber) the lines in the way you want.

Philip

[a6r6n6i6e]

Dear Mohan,
how you build supercell from cif file in Vesta?

Thanks for reply in advance,

Ali

[Mohan maruthi sena]

Hi Ali,
          Sorry for late reply. Just replicate using boundary option in vesta.

Thanks,
Mohan

[ganta.pra...@gmail.com]

Hi Mohan  Maruthi,

Did you find any solution for it? I also have the same problem.

Regards,

Prasanth