On Sat, Aug 21, 2010 at 5:41 PM, wrote:

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Sorry I meant to ask if there was any way to use phenix.ready_set "old".  I don't know the syntax but I read that it would output hydgrogens with a nomenclature that was compatable with coot library.

Hi Yarrow, PHENIX uses the PDB version 3.x naming conventions, and Coot does not always conform to this standard, which is the problem you are running into. It is the hope that eventually all programs will use the PDB standard, and we do so as part of our goal to make sure files generated by PHENIX are ready for deposition to the PDB. (As an aside, if you refine your structure with H atoms attached it is good practice to deposit your final model with H atoms present.) If you need to go back to a the PDB version 2.3 standard, there is a program called "Remediator" that converts between the two standards available here: http://kinemage.biochem.duke.edu/software/remediator.php I recommend using the Python version (more robust), and if you run into any trouble with it please let me know. Thanks, Jeff

On Sat, Aug 21, 2010 at 5:41 PM, wrote:

...

...

Sorry I meant to ask if there was any way to use phenix.ready_set "old".  I don't know the syntax but I read that it would output hydgrogens with a nomenclature that was compatable with coot library.

Hi Yarrow,

PHENIX uses the PDB version 3.x naming conventions, and Coot does not always conform to this standard, which is the problem you are running into. It is the hope that eventually all programs will use the PDB standard, and we do so as part of our goal to make sure files generated by PHENIX are ready for deposition to the PDB. (As an aside, if you refine your structure with H atoms attached it is good practice to deposit your final model with H atoms present.)

If you need to go back to a the PDB version 2.3 standard, there is a program called "Remediator" that converts between the two standards available here: http://kinemage.biochem.duke.edu/software/remediator.php

I recommend using the Python version (more robust), and if you run into any trouble with it please let me know.

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

Thanks Jeff! I am an idiot. I forgot you have to type python first. It worked like a charm. -Yarrow

On Aug 22, 2010, at 6:51 AM, Pavel Afonine wrote:

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After reading many posts on the phenix and coot boards I realize that the hydrogens produced by phenix.ready_set are not compatable with coot.

well, may be COOT is not compatible with PHENIX: just to turn the words around to be neutral: a cool program should be compatible with everything -:)

This is absolutely true but, how about adding an option that would allow to (also) output a PDB version 2-formatted coordinate file at the end of a phenix.refine run? That way, one could read it directly into Coot for further model building, without hydrogens "exploding" at the first touch... BTW, I think I already brought this up some time ago, but an option to output coordinate/map coefficients not only at the end of the refinement run, but also at the end of every intermediate macro cycle, would also be an useful addition to have. Best, Luca

Hi Pavel:

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This is absolutely true but, how about adding an option that would allow to (also) output a PDB version 2-formatted coordinate file at the end of a phenix.refine run? That way, one could read it directly into Coot for further model building, without hydrogens "exploding" at the first touch...

I guess (not entirely sure) that if you use a recent Coot version then you shouldn't have problems with hydrogens. At least they don't fly away at the first touch. I just tried myself.

Well, I have the latest Fink version for OS X (0.6.2-pre-1-65), and they definitely do fly on my machine! Have you tried regularizing a Tyr residue, for example?

Also, only a few gurus know about PDB format versions (2 or 3). Most of people will get confused seeing two PDB files at the end of refinement run, and they will flood us with questions about the differences between these two files and why and so on ... So I would just stick to the latest and wait a bit when the others adjust.

Actually, phenix.reduce can output v2 formatted PDB. I guess it is "-OLDpdb" keyword. So if you really like to stick to the older format you can.

Yeah, sure, no big deal.

...

BTW, I think I already brought this up some time ago, but an option to output coordinate/map coefficients not only at the end of the refinement run, but also at the end of every intermediate macro cycle, would also be an useful addition to have.

I'm wondering why? Imagine you refine a huge model and do 20 macro-cycles... You will get a bunch of huge files...

True, but occasionally one gets a quite clear "minimum" at - say - cycle 7... and then you have to re-run the whole thing again. Also, in this case, it's not a problem to just fire un another job... but if one would have this feature as an optional switch (off by default), it wouldn't hurt either. No? Best, Luca

I guess (not entirely sure) that if you use a recent Coot version then you shouldn't have problems with hydrogens. At least they don't fly away at the first touch. I just tried myself.

There are still some hydrogen atoms that will fly off into space in Coot. The naming changes in proteins that seem most effected are those atom sets where the numbering changed, such as HB1 and HB2 in PDB version 2.3 to HB2 and HB3 in PDB version 3.x. DNA hydrogens also will fly off into space, as can some ligands.

Actually, phenix.reduce can output v2 formatted PDB. I guess it is "-OLDpdb" keyword. So if you really like to stick to the older format you can.

This option doesn't entirely solve the problem because it doesn't change the heavy atom naming conventions. Not a huge deal in proteins, but a bigger problem in RNA/DNA. When using the "-OLD" flag in Reduce it is expecting that the heavy atoms conform to PDB 2.3, so the hydrogen atoms won't be added correctly if you mix and match nor will any changes to the heavy atoms be made. Jeff