[phenixbb] Re: ReadySet and cif

Hi Nigel, In fact ReadySet, in my case reads cif files. I tried with 7k00.cif (ribosome) from the PDB and other cif files. Then, ReadySet provides a pdb for the entire system with hydrogens as an output. It would be nice to also have a cif file for a ribosome with generated hydrogens. Then you are right, although ReadySet can swallow cif files it can only provide a PDB file as does the original reduce program. However, reduce does a better job for modified nucleotides since all of them are correctly hydrogenated. Then reduce does the same as ReadySet for some modified amino acids as detailed in a companion post. Thus for now, using coot and editing the files for modified residues and adding manually hydrogens where needed and deleting inappropriate ones seems a good option. Coot, although not perfect, does a better job and is to be recommended for such systems as it can generate cif files. As a side note, in the ReadySet GUI, what is the meaning of “Output file base” ? Pascal

Le 2 avr. 2026 à 17:00, Nigel Moriarty a écrit :

Hi Pascal

When you say you want a "cif file" do you want the output model from ReadySet! to be in mmCIF or do you want restraints in CIF format?

ReadySet! will do the latter for unknown ligands but will not read model mmCIF or write it.

Cheers

Nigel

--- Nigel W. Moriarty Building 92-4-431M1, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected] Web : CCI.LBL.gov http://cci.lbl.gov/ ORCID : orcid.org/0000-0001-8857-9464 https://orcid.org/0000-0001-8857-9464

On Wed, Apr 1, 2026 at 10:28 AM Pavel Afonine mailto:[email protected]> wrote:

...

Hi Pascal,

Okay, I gave it a try. I don't even see an option in ReadySet!'s GUI to output a model in mmCIF.

So my next instinct was to supply a model in mmCIF and expect it to take that as a signal to output it as mmCIF. Nope, it still outputs PDB.

We must be missing something. Let's see what Nigel says. Enabling it to output mmCIF (if not there yet!) is no more than a 10-minute exercise (including adding tests).

Now I wonder what happens if input mmCIF has long residue names..

Pavel

On 4/1/26 09:37, [email protected] mailto:[email protected] wrote:

...

Hi,

Is it possible to get a cif file as an output when using the ReadySet gui ? What is "Output file base" ? If I precise "output.cif" the program seems not to be happy !

Thanks,

Pascal _______________________________________________ phenixbb mailing list -- [email protected] mailto:[email protected] To unsubscribe send an email to [email protected] mailto:[email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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