[phenixbb] riding model and deposition

Pavel Afonine PAfonine at lbl.gov
Thu Feb 18 11:07:56 PST 2010


PS: I was talking about command line version of phenix.refine. If you 
use the GUI then there is an option to add H.
Pavel.


On 2/18/10 11:05 AM, Pavel Afonine wrote:
> Hi Carsten,
>
> phenix.refine does not add hydrogens. If you want to use H atoms in 
> refinement then you need to add them first, before going into refinement.
>
> You can add hydrogens using phenix.reduce or phenix.ready_set.
>
> Pavel.
>
>
> On 2/18/10 11:00 AM, Schubert, Carsten [PRDUS] wrote:
>>
>> Hi Pavel,
>>
>>  
>>
>> if I understand Christina's question correctly, she was stating that 
>> when phenix.refine runs with riding hydrogens enabled using a pdb 
>> file, which does not contain hydrogens, the final hydrogens are not 
>> written out. I presume this is the case, since a phenix.reduce run is 
>> required to add hydrogens prior to refinement, phenix.refine does not 
>> add hydrogens, correct?
>>
>>  
>>
>> Cheers,
>>
>>  
>>
>>                 Carsten
>>
>>  
>>
>>  
>>
>> *From:* phenixbb-bounces at phenix-online.org 
>> [mailto:phenixbb-bounces at phenix-online.org] *On Behalf Of *Pavel Afonine
>> *Sent:* Thursday, February 18, 2010 12:36 PM
>> *To:* PHENIX user mailing list
>> *Subject:* Re: [phenixbb] riding model and deposition
>>
>>  
>>
>> Hi Christina,
>>
>> if H atoms were used in refinement then they should not be removed 
>> from the model you are going to PDB deposit. Post-refinement model 
>> manipulation is bad. This makes the reported statistics 
>> irreproducible. The R-factor computed for a model with and without H 
>> atoms is different.
>>
>> Different programs use different libraries of ideal X-H parameters 
>> (some put them at longer "neutron" X-H distances, and some place at 
>> the position where the electron cloud is expected - shorter X-H 
>> distance). The B-factors of H atoms can be inherited from atoms they 
>> are bonded to or can be multiplied by a scale from 1 to 1.5. There is 
>> a class of X-H geometries where this position of H atoms is not 
>> unique: for example, C-O-H group in Tyrosine residue, where H can 
>> rotate around C-O axis. Some programs optimize the position of H atom 
>> to accommodate potential hydrogen bond and some doesn't.
>>
>> Destroying is always easier than building: removing existing 
>> hydrogens is a matter of running one command :
>>
>> phenix.reduce -trim model.pdb > model_noH.pdb
>>
>> and takes 1 or 2 seconds. However, to build the H atoms back the 
>> *exact* same way they were before is not that straightforward.
>>
>> It's just counterintuitive why you need to manipulate the refined 
>> model for which you have obtained all the statistics numbers? If you 
>> remove hydrogen atoms then you need to update the statistics. By 
>> stripping off H atoms you will get somewhat smaller file, but does 
>> the file size matter these days?  
>>
>> Pavel.
>>
>>
>> On 2/18/10 6:55 AM, Christina Bourne wrote:
>>
>> Alex, Pavel,
>> In my experience when using a riding hydrogen model they are not 
>> included in the output pdb file.  It is only when they are added 
>> explicitly that they are given output coordinates, which should of 
>> course be kept unchanged.  Can you please verify this??
>> -Christina
>>
>>  
>>
>> ------------------------------------------------------------------------
>>
>> *From:* Pavel Afonine <PAfonine at lbl.gov> <mailto:PAfonine at lbl.gov>
>> *To:* PHENIX user mailing list <phenixbb at phenix-online.org> 
>> <mailto:phenixbb at phenix-online.org>
>> *Sent:* Wed, February 17, 2010 8:06:40 PM
>> *Subject:* Re: [phenixbb] riding model and deposition
>>
>> Hi Alex,
>>
>> > I have refined a 1.3A structure using individual anisotropic 
>> B-factors (Rfactor, 15.5%; Rfree, 17.7%). Additional use of the 
>> riding model during refinement has improvement the R values (Rf, 
>> 14.5%; Rfree, 16.6%),
>>
>> this is not surprising at all -- hydrogens do contribute to the 
>> scattering.
>>
>> > although bond length and angle outliers did increase (anyone know 
>> why that would be?).
>> > 
>>
>> Different model - slightly different Xray/Restraints weights - 
>> slightly different statistics.
>>
>> > I have decided to deposit the model obtained using the riding model, 
>> but am unsure whether to include the hydrogen coordinates in the 
>> deposition.
>> > 
>>
>> If H atoms were used in refinement and final statistics calculation 
>> (such as R-factors, etc), then the H atoms have to be included into 
>> depositing model. Otherwise your statistics will not be reproducible.
>>
>> > The Phenix.refine documentation advises that they are left in, as 
>> they are needed to reproduce the  refinement statistics. However, 
>> reviewing the high resolution structures in the PDB I found that:
>> > 
>>
>> Reviewing statistics in the PDB you can find many interesting things, 
>> such as Fobs labeled as Iobs (and Iobs labeled as Fobs), atoms with 
>> unknown scattering types labeled X (which makes R-factor impossible 
>> to compute), O-H distances in water longer than 10A, etc. one can go 
>> on for a long list.
>>
>> > 1. In the case of structures refined using REFMAC or SHELX, the 
>> riding model does not seem to be included, although its use during 
>> refinement is mentioned in the pdb header.
>> > 
>>
>> Which is, in my opinion, not good.
>>
>> > 2. In the case of structures refined using PHENIX, use of the riding 
>> model is sometimes indicated in the header, but hydrogen coordinates 
>> only appear to be included in the pdb in the case of structures 
>> refined to a resolution better than 1.3A.
>> > 
>>
>> This most likely indicates a manipulation with a file contained 
>> refined model, which is, again, in my opinion, not good.
>>
>> > As far as I can understand the purpose of the riding model is to 
>> provide additional restraints for refinement, so as long as its use 
>> is made evident in the pdb header (and maybe the methods section of 
>> the publication) that should be enough. Inclusion of hydrogens in the 
>> model, when you can't see them seems inappropriate.
>> > 
>>
>> Different programs use different libraries of ideal X-H parameters. 
>> Depending on the program, the B-factors of H atoms can be inherited 
>> from atoms they are bonded to or can be multiplied by a scale from 1 
>> to 1.5. These all makes adding H program-dependent, and therefore 
>> statistics from such models may vary.
>>
>> I believe that any manipulation on the refined structure is bad.
>>
>> Pavel.
>>
>>
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>>
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