[Molvis-list] Re: adding hydrogens to a pdb file

[Eric Martz]

Dear Jeff:

At 1/18/05, Jeff Cohlberg wrote:
>There used to be a WHAT IF web interface in which a user could submit a 
>PDB ID number and get back an "hadded.pdb" file with hydrogen atoms 
>added.  This site no longer exists, and the WHAT IF software is now only 
>available to those who purchase it for 500 Euros (at 
>http://swift.cmbi.kun.nl/whatif/).
>
>Is there any other free software or server which can add hydrogens to a 
>PDB file?

The almost-released PE 2.45 has an answer in its Help/Index/Glossary
under hydrogen:
http://www.umass.edu/microbio/chime/beta/pe_gecko/protexpl/igloss.htm#hydrogen

where it refers you to
the Richardson Lab MolProbity server, which adds hydrogens to proteins and 
nucleic acids (but not water; same as WHATIF)
http://kinemage.biochem.duke.edu/molprobity/index-king.html
and also gives you lots of other very useful information, including 
visualization of clashes, and an overall clash score, stating where your 
case falls among published proteins of similar resolution.

PE's "Protein Structure Bioinformatics Resources" page
http://www.umass.edu/microbio/chime/beta/pe_gecko/protexpl/psbiores.htm#molprobity
states
"MolProbity conducts a new and powerful structure validation based on 
all-atom contacts analysis, producing automatic corrections (rotamer 
flips). The flips can be inspected and accepted or rejected in a java-based 
Kinemage-style viewer. The corrected PDB file, containing added hydrogen 
atoms, is provided. For secure use, free software that performs the 
all-atom contacts analysis can be downloaded and run locally. The server 
also offers very useful Ramachandran plots (identifying residues outside 
the favorable regions), C-beta deviations, and rotamer analysis."

MolProbity is featured in the new PE's External Resources page.

At the MolProbity website, some browsers may say you cannot use KiNG even 
when your java is up to date -- just ignore that error. You can use KiNG if 
you have an up to date java (from java.com).

The server cmbi.kun.nl was down in recent days but is back up. The free 
on-line version of WhatIF is available at
http://swift.cmbi.kun.nl/WIWWWI/
also linked into PE's Bioinformatics Resources page.

-Eric


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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
               http://www.umass.edu/molvis/martz
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