Hi Tim,
no, in the cases I remember there was no significant difference in geometry - of course, we do tend to work on rather stable, rocky proteins...
Mark
On 9 Aug 2013, at 16:33, Tim Gruene wrote:
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> Hi Mark,
>
> does your experience also include the geometry of the model? There
> might be improvements, as e.g. reported from molprobity, because of a
> better modelling of the temperature factors.
>
> I am asking because you mention improvements of the electron density,
> whereas some improvements in the geometry, like the Ramachandran plot,
> may not be directly visible in the electron density.
>
> Cheers,
> Tim
>
> On 08/09/2013 04:27 PM, Mark J van Raaij wrote:
>> Omid, how necessary is it that you do TLS refinement? I.e. are you
>> just doing it to improve your Rs a bit or is the density really
>> getting better? If the density is not improving, I would just
>> refine without TLS and avoid any posterior temperature factor
>> analysis difficulties. While I am sure there are cases where TLS
>> refinement really helps (cf. published examples), my experience in
>> our structures is that it does not really make a difference. Also,
>> in my opinion the TLS model you define must make some physical
>> sense, i.e. some logical explanation why your structure or domains
>> of your structure may have internally consistent anisotropic Bs.
>> Mark
>>
>>
>>
>>
>> On 8 Aug 2013, at 23:01, Ethan Merritt wrote:
>>
>>> On Thursday, August 08, 2013 01:51:34 pm Omid Haji-Ghassemi
>>> wrote:
>>>> Dear Robbie, Marcus and Reginald,
>>>>
>>>> Thanks again for your replies, I truly appreciate the help.
>>>>
>>>> The B-factors was set to 20 when performing TLS refinement so I
>>>> don't think that is the problem.
>>>>
>>>> I also tried Marcus's suggestion using output from coot, with
>>>> no luck.
>>>>
>>>> The only thing left to try is to test alternative TLS group as
>>>> Reginald have suggested.
>>>
>>> You have only told us about an increase in average B, not whether
>>> it is uniformly inflated. Possibly the output from analysis by
>>> the Parvati server http://skuld.bmsc.washington.edu/parvati would
>>> indicate specific parts of your structure that are behaving badly
>>> during refinement.
>>>
>>> Ethan
>>>
>>>>
>>>> Cheers Omid
>>>>
>>>>> Hi Omid,
>>>>>
>>>>> Sometimes the choice of TLS groups and to a lesser extent the
>>>>> initial B-factor matter a lot. You should try a few other TLS
>>>>> group selections and see if these give nicer results. Things
>>>>> to try: TLSMD, including or excluding ligands and
>>>>> carbohydrates, other common-sense or gut-feeling structure
>>>>> partitionings. If you have a lot of different groupings to
>>>>> test, you can reset the B-factor and do pure TLS refinement
>>>>> (i.e. 0 cycles of restrained refinement) for all of them. You
>>>>> can then use the best one for your 'final' refinement. It's
>>>>> much faster then trying your final refinement with all TLS
>>>>> groups selections.
>>>>>
>>>>> Cheers, Robbie
>>>>>
>>>>> Sent from my Windows Phone ________________________________
>>>>> Van: Omid Haji-Ghassemi Verzonden: 8-8-2013 21:55 Aan:
>>>>> [log in to unmask] Onderwerp: Re: [ccp4bb] TLS refinement
>>>>> and ANISOU records
>>>>>
>>>>> Dear Ethan,
>>>>>
>>>>> Thank you for your reply.
>>>>>
>>>>> I will try to review my refinement protocol once more;
>>>>> however, I am still perplexed at what lies at the heart of
>>>>> the problem.
>>>>>
>>>>> Overestimation of average B-factor using TLS is perfectly
>>>>> sound, but I am not sure why all my structures the average
>>>>> increases tremendously.
>>>>>
>>>>> In one case it increases from 16.36 to 73.02 for a 2.3Ang
>>>>> structure.
>>>>>
>>>>> I already tried changing weights and number of TLS rounds,
>>>>> which resulting in only a small change in average B.
>>>>>
>>>>> Omid
>>>>>
>>>>>> On Thursday, August 08, 2013 11:39:22 am Omid Haji-Ghassemi
>>>>>> wrote:
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I was about to deposit a few structures to the pdb when I
>>>>>>> noticed the mean B-factors were larger than one might
>>>>>>> expect.
>>>>>>>
>>>>>>> All the structures were refined using TLS refinement.
>>>>>>>
>>>>>>> During refinement in Refmac the average temperature
>>>>>>> factors for each structure is reasonable. For example, a
>>>>>>> structure at 2.75� has a mean B-factor of 40; however,
>>>>>>> after adding the ANISOU records as required by the PDB, I
>>>>>>> noticed the average B-factors double.
>>>>>>
>>>>>> Please see my paper: E. A. Merritt (2011). "Some Beq are
>>>>>> more equivalent than others". Acta Cryst. A67, 512-516.
>>>>>> <http://skuld.bmsc.washington.edu/parvati/ActaA_67_512.pdf>
>>>>>>
>>>>>>
>>>>>>
> In short, the quantity stored in the "B" field of a PDB file after TLS
>>>>>> refinement is Beq, which overestimates what the isotropic B
>>>>>> factor would have been if you had refined without TLS. So
>>>>>> in general the "average B" after TLS refinement is always
>>>>>> higher than the "average B" without TLS. The problem is
>>>>>> that the two quantities marked "average B" are not directly
>>>>>> comparable.
>>>>>>
>>>>>> Having said that, the overestimate is not usually as much
>>>>>> as a factor of 2. So something else may indeed be causing a
>>>>>> problem in your case.
>>>>>>
>>>>>> Ethan
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> Is this normal?
>>>>>>>
>>>>>>> Sincerely, Omid
>>>>>>>
>>>>>>> ---------------------------------------------------
>>>>>>> --------------------------------------------------- Omid
>>>>>>> Haji-Ghassemi, Graduate Student Department of
>>>>>>> Biochemistry & Microbiology University of Victoria PO Box
>>>>>>> 3055 STN CSC Victoria, BC, V8W 3P6 CANADA
>>>>>>>
>>>>>>> Tel: 250-721-8945 Fax: 250-721-8855
>>>>>>>
>>>>>>
>>>>>> -- Ethan A Merritt Biomolecular Structure Center, K-428
>>>>>> Health Sciences Bldg University of Washington, Seattle
>>>>>> 98195-7742
>>>>>>
>>>>>
>>>>
>>>
>>> -- Ethan A Merritt Biomolecular Structure Center, K-428 Health
>>> Sciences Bldg University of Washington, Seattle 98195-7742
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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