On Thu, Feb 9, 2012 at 4:16 PM, Nigel Moriarty wrote:

Its true that ReadySet! does not handle the glycans as well as it should. Its on my list of things to fix, but you can delete the hydrogens by hand for a short time. This actually brings up an interesting point. I believe its better to add the hydrogens once and use that model for all subsequent refinements. In this scenario, you use ReadySet! once and the addition of hydrogens is a "checkpoint" in the refinement process.

This only makes sense if you assume that no more atoms which might contain hydrogens will be added during refinement - which is very rarely the case until the very end. It would be helpful if ReadySet didn't add hydrogens to ligands that already have one or more built, since this will both avoid the replacement of spurious hydrogens on glycans and also make subsequent runs much faster. -Nat

Hi, just to second this... In refinement hydrogens are treated as "riding" (unless you are refining against neutron or ultra-high resolution X-ray data). Since Reduce (or ReadySet! that uses it) builds hydrogen atoms in a smart way (optimizes hydrogen bonds, for example) it's a good idea to rebuild hydrogens from time to time because it may build better hydrogens starting form a better model. I was even thinking to rebuild hydrogens during refinement every macro-cycle by calling Reduce internally but I haven't done it yet because of numerous technical troubles, including inconsistencies in geometry libraries used by Reduce and Monomer Library, different naming conventions, etc etc etc. Pavel On 2/10/12 8:36 AM, Jianghai Zhu wrote:

Exactly my point. The structure actually changes a lot during building, especially for low-resolution structures. Also another thing about keeping the hydrogen is that COOT runs very slow in the presence of hydrogens. And regularization with hydrogen in COOT often gives different result than without hydrogen.

-- Jianghai

On Feb 9, 2012, at 7:21 PM, Nathaniel Echols wrote:

...

On Thu, Feb 9, 2012 at 4:16 PM, Nigel Moriarty wrote:

...

Its true that ReadySet! does not handle the glycans as well as it should. Its on my list of things to fix, but you can delete the hydrogens by hand for a short time. This actually brings up an interesting point. I believe its better to add the hydrogens once and use that model for all subsequent refinements. In this scenario, you use ReadySet! once and the addition of hydrogens is a "checkpoint" in the refinement process. This only makes sense if you assume that no more atoms which might contain hydrogens will be added during refinement - which is very rarely the case until the very end. It would be helpful if ReadySet didn't add hydrogens to ligands that already have one or more built, since this will both avoid the replacement of spurious hydrogens on glycans and also make subsequent runs much faster.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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A problem for this workaround is that not all HO4 should be removed. Manually removing individual atoms would be tedious since I have a lot of glycans. -- Jianghai On Feb 10, 2012, at 3:10 AM, Christian Roth wrote:

Hi, a workaround for this special case at the moment is to use after ready set the pdbtools to remove the wrongly placed atoms.

phenix.pdbtools file.pdb remove="name HO4" Or remove whatever atom should be removed. Its a bit more work for the moment, but it works well for me

Am Freitag 10 Februar 2012 01:05:49 schrieb Jianghai Zhu:

...

Hi,

I am using phenix.ready_set (version 1.7.3) to add hydrogens to my structure. I found out that it makes a few mistakes when dealing with glycans. It adds hydrogens to C1, O4, O3, O6 even when these atoms have formed covalent bonds with other sugars and residues. Subsequent phenix.refine aborts because of these incorrect hydrogens. However, when I use phenix.reduce directly, all hydrogens are placed correctly. I assume something went wrong in phenix.ready_set. The problem with phenix.reduce is that it doesn't know how to deal with ligand whereas phenix.ready_set does when a cif file is provided.

-- Jianghai

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-- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319