Re: [phenixbb] how to remove hydrogen from pdb

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Nat, On 02/06/2014 10:26 PM, Nathaniel Echols wrote:

On Thu, Feb 6, 2014 at 1:07 PM, Edward A. Berry wrote:

...

Maybe a specialized tool like phenix.refine is safest!

At the risk of sounding like a broken record again: Unix shell tricks are great *if you already know how to use these tools* and have a detailed knowledge of the PDB format specification. For everyone else, I do not recommend trying to edit models with anything other than a tool specifically designed for this purpose. This is going to be especially important as the field slowly migrates to mmCIF.

some time ago (about 6 months), Eugene Krissinel sported a similar argument together with the statement that if a program does not exist to do a particular job, it was the developers' task to fix it. At that time I described a problem a student of mine had in data mining, but I never received a response. I am glad somebody else here wrote a little script to sort out the problem, because the numbers were important. With the warning above and the implicit concept to wait for developers, I still would not know. So I am happy about the availability and possibility to use scripting to push my research forward and not having to wait for someone to adjust my ideas to some API. Cheers, Tim P.S.: I checked the command on some output from phenix and noticed that the element type correctly is the last character of the line. Some (older) PDB files from the PDB show two blank spaces, the the regular expression does not work.

For the record, I had to add parentheses to get the egrep command to work on my Mac:

egrep -v '^(ATOM|HETATM).*H$' m.pdb

which does the job. But I do not think this solution is preferable to using phenix.reduce or phenix.pdbtools (or any number of other utilities).

A final note: in my experience, if you deposit a file containing hydrogens to the PDB, they're just going to delete them for you (whether you want this or not!), so it is not necessary to do any additional preparation. In fact, I just did this last week, so we'll see what happens.

-Nat

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