Dammin Dammif Dammaver CIF to PDB

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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jmarie
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Dammin Dammif Dammaver CIF to PDB

#1 Post by jmarie » 2022.06.16 08:40

Dear Software Developer

Since Atsas 3.1 Dammin, Dammif, Dammaver produce as output now cif file instead of certainly old but still convenient pdb.
Is there a way to either to choose a pdb as the output file or an easy way to convert the cif to pdb.

Thanks in advance

Jmarie

franke
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Re: Dammin Dammif Dammaver CIF to PDB

#2 Post by franke » 2022.06.20 09:35

In application where an output file name can be specified, just provide "something.pdb" and a PDB file will be created. In those, like dammif, where only a prefix can be supplied, .cif will be written. There is no option to change that. You can use

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$ cif2pdb dammif.cif -o dammif.pdb
to convert.

If you don't mind me asking: what would you need a dummy atom model PDB for? What kind of application can not yet read mmCIF, that is still useful?

jmarie
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Re: Dammin Dammif Dammaver CIF to PDB

#3 Post by jmarie » 2022.06.20 13:36

Hi
thank for the suggestion.
I indeed use pdbtools from haddock package.
Just as an example, I like to represent my bead shapes with situs and use colores to dock structure in it.
I don't think it can uses cif, yet.
But Cif is not as friendly as pdb for manipulating beads. And if you look to eom (I didn't use the last version). But it put the dummy atm at the end that confused software like pymol. So It happens that I renumber everything properly. Which is easy when it's a pdb less when it's a cif.
Again thank you
Cheers

franke
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Re: Dammin Dammif Dammaver CIF to PDB

#4 Post by franke » 2022.06.20 13:49

jmarie wrote: 2022.06.20 13:36 I indeed use pdbtools from haddock package.
Just as an example, I like to represent my bead shapes with situs and use colores to dock structure in it.
I don't think it can uses cif, yet.
Then (a) I would encourage you to contact the authors of these tools and request cif support, as this is the format that should be used in the future, i.e. now. And (b) I shall refrain from commenting on usage of bead models for docking. Sufficient to say that I would not recommend it.
jmarie wrote: 2022.06.20 13:36 But Cif is not as friendly as pdb for manipulating beads. And if you look to eom (I didn't use the last version). But it put the dummy atm at the end that confused software like pymol.
Not sure if I correctly read this, but if you are saying that previous ranch/eom had a broken PDB output, indeed. It did. This should now be fixed. Especially as the output now is also .cif :D

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