Can we also count, say the total number of alanine residues in a PDB file or any other other residue for that matter?
Ricardo J Ferreira
Hi,
if you are using Linux, is easy:
" cat file.pdb | grep OW | wc" -> gives you the total number of waters (number to the left). Basically is the number of lines that contains an atom named "OW", that should correspond to each one of the waters.
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Surajit Kalita
In addition to the previous answer, similarly you can grep the residue name ALA for Alanine and expected to get the same results.
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Ravi Ramalingam
Hi Prathvi,
In Chimera you can go to Tools -> General Controls -> Command Line
Here you can pass the command "select :HOH", which will select the water molecule and at the bottom of the window you can see the selected atom numbers too.
Hope this helps
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