Hi Nicholas,
Thank you for your reply.
it seems that we are trying to deposit one model to satisfy two
different purposes - one for model validation and the other for model
interpretation (use in docking etc), and what's good for one purpose
might not be necessarily good for the other.
Th
Hi Ethan,
> > mainly because (a) the calculation of likelihood is only based on a
> > subset of the 'data' that are obtained from an X-ray diffraction
> > experiment (for example, we ignore diffuse scattering as Ian
> > pointed-out),
>
> I do not think that is a valid criticism. In any field
On Saturday 18 September 2010, Nicholas M Glykos wrote:
>
> > it seems that we are trying to deposit one model to satisfy two
> > different purposes - one for model validation and the other for model
> > interpretation (use in docking etc), and what's good for one purpose
> > might not be neces
> it seems that we are trying to deposit one model to satisfy two
> different purposes - one for model validation and the other for model
> interpretation (use in docking etc), and what's good for one purpose
> might not be necessarily good for the other.
This has been discussed before on thi
Very interesting discussion. I wonder if the "inexperienced user" of PDB really
exists? I don't know anyone off-hand who would really make use of information
from hydrogen positions but not understand the issues. Although I hear they
have been sighted in the Everglades http://en.wikipedia.o
As a relatively inexperienced scientist, I find this discussion
fascinating.
I wonder if NMR and EM people are also worried about depositing enough
"modeled info" to allow back calculation of data.
Regarding the original discussion of whether to deposit riding
hydrogens used in the refineme
Dirk,
- Imagine a (not very uncommon, unfortunately) situation when someone
obtains the final model and Fcalc, and then, right before the PDB
deposition does a final check in Coot, and moves/removes a few atoms
(a few waters, or instance) here and there. Or may be does a
real-space fit of a
> Oh, goodness, I see: even here, we would need clear rules what the
> calculated structure factors are, which weights are were, which bulk solvent
> correction was applied ... a maze, too!
Fortunately the X-ray & restraint weights/target values are not an
issue here: varying them changes the refi
Dear Ian,
Am 17.09.10 12:30, schrieb Ian Tickle:
Dirk
Personally I wouldn't make use of the deposited Fcalcs, I would insist
on having the refined model, not only for the reasons Pavel gave, but
also because it's never clear which mathematical model was used to
produce the deposited Fcalcs. T
Dirk
Personally I wouldn't make use of the deposited Fcalcs, I would insist
on having the refined model, not only for the reasons Pavel gave, but
also because it's never clear which mathematical model was used to
produce the deposited Fcalcs. There are 2 problem areas (at least 2 I
can think of r
Hi Pavel,
Am 16.09.10 17:56, schrieb Pavel Afonine:
Hi Dirk,
so, wouldn't be the deposition of the final model's Fcalc, Phic (and
their weights) along with the final coordinates be the best solution?
The final Fcalc are our best model and can be used to reproduce the
final statistics (whi
On Thursday 16 September 2010 10:34:14 am Dr. Mark Mayer wrote:
> >Huh? That's not a cif fragment. What file are you looking at?
> >In my experience the PDB feeds back to you a cif format structure factor
> >file with a name like rcsb054058-sf.cif
> >Near the top of that file you should find a d
Huh? That's not a cif fragment. What file are you looking at?
In my experience the PDB feeds back to you a cif format structure factor
file with a name like rcsb054058-sf.cif
Near the top of that file you should find a description of the data
columns. The columns present depend on what you fed
On Thu, Sep 16, 2010 at 10:19:14AM -0700, Ethan Merritt wrote:
> [...]
> > What's a structural biologist to do?
>
> The empiricist's approach.
> Experiment till you find a procedure that works, then stick to it :-)
... or the social approach: communicate with the person at the PDB responsible
fo
On Thursday 16 September 2010 09:56:14 am Dr. Mark Mayer wrote:
> Ethan wrote
>
> >I believe that deposition of Fc Phic FOM should be required.
> >Certainly it should be the recommended practice.
> >
>
> For the same series of structures I just deposited, which started the
> the riding H discuss
Hi Mark,
I assume you deposited the mtz? This is what Ethan was referring to - the pdb
does not do well with maintaining all the relevant columns when submitting the
mtz file. However, if you convert your mtz to cif yourself and make sure it
has all the columns you would like to include and
Ethan wrote
I believe that deposition of Fc Phic FOM should be required.
Certainly it should be the recommended practice.
For the same series of structures I just deposited, which started the
the riding H discussion, my mtz file had Fc Phic FOM + other data put
out by Phenix - pavel can ela
On Thursday 16 September 2010 01:25:12 am Dirk Kostrewa wrote:
>
> > so, wouldn't be the deposition of the final model's Fcalc, Phic (and
> > their weights) along with the final coordinates be the best solution?
> > The final Fcalc are our best model and can be used to reproduce the
> > final s
Hi Dirk,
so, wouldn't be the deposition of the final model's Fcalc, Phic (and
their weights) along with the final coordinates be the best solution?
The final Fcalc are our best model and can be used to reproduce the
final statistics (which would remove the sfcheck annoyance) and to
reproduce
On Thursday 16 September 2010 01:25:12 am Dirk Kostrewa wrote:
> so, wouldn't be the deposition of the final model's Fcalc, Phic (and
> their weights) along with the final coordinates be the best solution?
> The final Fcalc are our best model and can be used to reproduce the
> final statistics
Dear Ian and contributors to this interesting thread,
(please, scroll down a little bit)
Am 15.09.10 23:34, schrieb Ian Tickle:
I should just like to point out that the main source of the
disagreement here seems to be that people have very different ideas
about what a 'model' is or should be.
Dear Ed,
no, if you start with model that has no hydrogens, they will not be
generated internally.
Pavel.
On 9/15/10 2:58 PM, Ed Pozharski wrote:
Sure. But if I start with model that has no hydrogens, they will be
generated but not passed to the output, right. just like refmac.
On Wed, 2
Sure. But if I start with model that has no hydrogens, they will be
generated but not passed to the output, right. just like refmac.
On Wed, 2010-09-15 at 14:52 -0700, Pavel Afonine wrote:
> Dear Ed,
>
> On 9/15/10 2:47 PM, Ed Pozharski wrote:
> > On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey
Dear Ed,
On 9/15/10 2:47 PM, Ed Pozharski wrote:
On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote:
So the riding hydrogen model is imperfect. At least with
phenix.refine
you can measure it, unlike the default behavior of REFMAC. (But you
can
tell it to write hydrogens out, I believe).
On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote:
> So the riding hydrogen model is imperfect. At least with
> phenix.refine
> you can measure it, unlike the default behavior of REFMAC. (But you
> can
> tell it to write hydrogens out, I believe).
>
My impression is that default behavior
I should just like to point out that the main source of the
disagreement here seems to be that people have very different ideas
about what a 'model' is or should be. Strictly a model is a purely
mathematical construct, in this case it consists of the appropriate
equation for the calculated structu
On Wed, 2010-09-15 at 13:13 -0700, Pavel Afonine wrote:
> I can't agree with this, sorry. A change to a model content
> (especially
> the one that changes Fcalc) is a model manipulation.
>
That is not what I asked. Do you agree that using the riding model does
not add additional refinable parame
On 9/15/10 3:54 PM, Ed Pozharski wrote:
Don't you agree that using the riding model does not add
additional refinable parameters?
(snip)
instance, when hydrogens are added, the average N-H distance is
1.1(5), but upon refinement the value is down to 0.85998(4). I
So the riding hydrogen
Dear Ed,
On 9/15/10 12:54 PM, Ed Pozharski wrote:
On Wed, 2010-09-15 at 10:50 -0700, Pavel Afonine wrote:
I wouldn't dare calling a model manipulation that typically changes
the
R-factor by 0.5 ... ~2% as "nothing". Although, you are may be right
-
"who cares"?
It's not a manipulation becau
On Wed, 2010-09-15 at 10:50 -0700, Pavel Afonine wrote:
> I wouldn't dare calling a model manipulation that typically changes
> the
> R-factor by 0.5 ... ~2% as "nothing". Although, you are may be right
> -
> "who cares"?
It's not a manipulation because no parameters were manipulated in the
mo
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