Hi, I have an optimized structure of some peptides and I would like to represent it as a secondary structure - cartoon. Ok, so server apps ask for pdb file (like Stride).
I tried in different ways to change the format from xyz to pdb using openbabel, vmd etc and always get error when reading.
I tried using vmd and which invoke stride behind the scenes but getting error as well.
Someone had a similarly unpleasant experience and had found a workaround ??
Thx
Hi Kamil Makowski ,
It's very strange that the file can't be read by VMD. Have you tried using PyMOL?
It's possible that the XYZ file is in a different format than expected by the programs you've tried. The wikipedia article on XYZ does mention that there is no defined format for XYZ really.
Perhaps post a sample XYZ file here (and tag me so I see it), and I'll be able to see what the issue is. At worst, it will require a quick custom Python script to convert it to something more readable by VMD etc.
Best regards from a fellow Poznaniak,
Patrick
Many thanks Patrick Timmons Co u Ciebie? I have no problem opening the xyz files (VMD, PyMol, avogadro). The problem is the assignment of secondary structure to the optimized peptide. I would like to se cartoon representation of it. Thanks for looking into it. Do uslyszenia!
Kamil
Wszystko spoko, zostalo tylko pare miesiecy wna doktoracie, a u ciebie?
Ok, I've taken a look at the XYZ file you sent. Because there's pretty much no information in it, other than element names and coordinates, there's only the hard way of fixing this.
What I would do is generate a generic pdb structure file for your peptide. Try using PDB-Builder (article attached, you can download it for Python). You can also try some other methods, the coordinates don't have to be correct, you just want the format and atom names for your primary sequence. Then go through each atom in VMD, identify which atom it is and to which residue it belongs, and copy and paste the coordinates into your generic pdb file, replacing the dummy coordinates. It's a manual conversion, and a real pain, but it's the only way I can think of getting out of xyz. Hope this helps!
Patrick
Article PeptideBuilder: A simple Python library to generate model peptides
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