Re: [modeller_usage] Building missing atoms using MODELLER

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 10/16/20 4:16 AM, Zeineb Si Chaib wrote:
> I have a PDB file with missing atoms and residues. I would like to build 
> the missing atoms only without touching the rest.

The easiest way to do this is to use the complete_pdb script, then write 
out the model. No need to build an alignment and do the whole 
comparative modeling run, unless you need to optimize the coordinates of 
the missing atoms:
https://salilab.org/modeller/9.25/manual/node456.html
https://salilab.org/modeller/9.25/manual/node181.html

> It seems that Modeller built the missing atoms (4) but I am ending up 
> with a new model that has fewer atoms than the original one (1512 vs 
> 1558) although they both have the same number of residues.

When you build a model in Modeller it builds a single conformation using 
all heavy atoms. If atoms are missing in your input file, it adds them; 
if there are extra atoms they are removed. These extra atoms could be 
alternate conformations for some residues (with an alternate location 
indicator in column 17 in the PDB file, as per 
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM), 
extra atoms such as hydrogens, or perhaps modified residues. But you 
would have to look in the file to be sure.

	Ben Webb, Modeller Caretaker
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