Simon, You should always include H atoms in refinement whatever the resolution, I can't think of any reason for not doing so. They are not refined independently but 'ride' on the parent atom, so don't contribute to the parameter and restraint counts, and as you say it is essential that they are included when running Molprobity, you won't get sensible results without them.
-- Ian > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Simon Kolstoe > Sent: 12 May 2008 12:08 > To: [email protected] > Subject: Validation Question > > Dear ccp4bb, > > I have heard from many people that molprobity is the gold > standard as > far as validation is concerned. As I am just about to deposit a > structure I therefore figured it was best to use molprobity > in guiding > the final stages of my refinement. I do not have enough data to > justify adding hydrogens in my refinement, however as molprobity > suggests adding hydrogens for validation purposes I > obediently did so > and (surprise surprise) found that I had a number of clashes > (clashcore 17.6). Just as an experiment I re-ran refmac including > hydrogens and this time my clash score was much lower and apparently > acceptable (6.27), whilst my R factors were pretty much identical to > before. So my question is this - do I ignore the normal obs:params > calculation and just refine my structure with hydrogens (resolution > 1.9, 99.9% complete) as according to molprobity this gives me a > "better" structure, or do I just ignore the clashscore targets in > molprobity based upon not having enough data to justify > refining this > component? > > Thanks, > > Simon > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
