hydrogens in low resolution structure refinement
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Dear all! I am refining two structures at 3.0 and 2.7 A. In some older threads on this board I found that you recommended adding hydrogens to the pdb file even at this resolution. I tried that (adding hydrogens with reduce and refine with riding hydrogens) but inspite of what I read in your postings, my R-Factors went up by 1% (not down as was predicted). Are there any other keywords which could be changed or do you have any other ideas why this could be? Thanks in advance! Stefanie
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Hej
AFAIK R-factors should go up as they did. But if you look at the clash scores, they are now
way better because
hydrogens are taken into account in the anti-bumping restraints. Soo - do you want better
model or lower
Rfactors is the key question.
~L~
_______________________________________
Lari Lehtiö
Structural Genomics Consortium
Medical Biochemistry & Biophysics Dept.
Karolinska Institute
Stockholm, Sweden
_______________________________________
----- Original Message -----
From: Stefanie Krieg
Dear all!
I am refining two structures at 3.0 and 2.7 A. In some older threads on this board I found that you recommended adding hydrogens to the pdb file even at this resolution. I tried that (adding hydrogens with reduce and refine with riding hydrogens) but inspite of what I read in your postings, my R-Factors went up by 1% (not down as was predicted). Are there any other keywords which could be changed or do you have any other ideas why this could be?
Thanks in advance! Stefanie
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Hi, with the next PHENIX version you will be able to set this flag "hydrogens.contribute_to_f_calc" to "False" that will most likely fix the R-factors problem (it's not available in the current version). Pavel. On 11/16/2007 6:31 AM, Stefanie Krieg wrote:
Dear all!
I am refining two structures at 3.0 and 2.7 A. In some older threads on this board I found that you recommended adding hydrogens to the pdb file even at this resolution. I tried that (adding hydrogens with reduce and refine with riding hydrogens) but inspite of what I read in your postings, my R-Factors went up by 1% (not down as was predicted). Are there any other keywords which could be changed or do you have any other ideas why this could be?
Thanks in advance! Stefanie _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Lari Lehtio
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Pavel Afonine
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Stefanie Krieg