Hi Engin, this is for your first question and I hope someone knows a better solution for the second one: First of all, sorry for the problem. As it is now, if "ordered_solvent=true" is used phenix.refine treats water the way that it can be removed any time if it does not satisfy the selection criteria; or/and the water can be added as well. There is no way to fix particular waters (unless you re-name them somehow like WT1, WT2, ... ). The idea behind this seeming inflexibility is that the selection criteria are for the purpose to not let a wrong water be in your structure. If you believe the selection criteria are too strict you may loosen them till they keep your favorite water molecules. I now realize that it's possible that one may want to keep certain waters even though they are beyond the selection criteria and lowering the criteria (to keep those waters) may add some spurious "waters". On the other hand, fixing selected waters will make it a user's responsibility to monitor their quality (which is dangerous in general and is against the idea of automation). Anyway, I will provide a functionality to keep selected waters in future (this will require some code modifications) (it's on my list already but I'm not sure when I get to it); although a long-term goal is to make water updating procedure smarter so there will be no need to manually fix anything. As for the second question (I don't really know the best solution..., just something that would practically work...), I would manually create a custom CIF file and give a name to that complex (so the waters that make it are not treated as real waters anymore). So basically this is what you did already... Please let know if you have any other questions or problems! Pavel. On 11/24/2008 3:16 PM, Engin Ozkan wrote:
Hi,
Is there a way to shut off solvent checking for a few waters? I have what looks like sodium-coordinating waters that get taken out by ordered solvent filtering, even as I am loosely restraining them to be at distances expected for sodium. These waters -I have 4 NCS-related copies- are taken out by filtering, which messes up water numbering, and makes my restraint descriptions irrelevant. I have tried putting them in a separate chain, but they get fused to the solvent chain by phenix. My other option is to describe those waters as a different type of atom (not HOH), but they are water molecules, so I am reluctant. And I want to keep ordered_solvent True.
For cif files already available in the default ccp4 library, NA seems to be elemental sodium, NAW, NA5 and NA6 seem to be specific sodium+water complexes with three, five and six waters coordinating (where they are no longer HOH, obviously). So, I have created bond/angle restraints specifically to my atoms, but is there an easy way to do this? Or should I just create a two-water NA (NA2.cif) specific for my case and call waters as some O atom? That's easy, but I wonder if that's the common practice (or I am missing something completely).
Any ideas?
Thanks
Engin _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb