Re: [ccp4bb] what to do with disordered side chains

[Robbie Joosten]

Hi Jacob,

The PDB header has a record for missing atoms. Coot has an option to find them 
and any decent validation software will warn about incomplete residues. There 
are PDBREPORT entries for every PDB file with a list of incomplete residues. If 
a user makes a very small effort, he doesn't have to go around clicking every 
'alanine'.

Cheers,
Robbie

> Date: Mon, 4 Apr 2011 16:15:58 -0500
> From: j-kell...@fsm.northwestern.edu
> Subject: Re: [ccp4bb] what to do with disordered side chains
> To: CCP4BB@JISCMAIL.AC.UK
> 
> I like your IMGATM proposal, but wouldn't it also potentially break
> some of the programs? Also--and this is a problem with deleting only
> sidechain atoms in general--it seems that many, myself included, might
> totally miss that an apparent "alanine" is really a trunco-lysine.
> What I like is that it does get around the problem of people
> over-interpreting bogus sidechains, but it falls short, perhaps, in
> misleading people about what residue is there. I, for one, would not
> feel that I had to click on all the alanines in a model to verify that
> they were not lysines, and would be surprised and puzzled for a while
> about why this ala said lys when I clicked on it. Wouldn't you be
> surprised? (Well, maybe not after this thread...)
> 
> JPK
> 
> 
> 
> On Mon, Apr 4, 2011 at 1:55 AM, Dale Tronrud  
> wrote:
> >   The definition of _atom_site.occupancy is
> >
> >  The fraction of the atom type present at this site.
> >  The sum of the occupancies of all the atom types at this site
> >  may not significantly exceed 1.0 unless it is a dummy site.
> >
> > When an atom has an occupancy equal to zero that means that the
> > atom is NEVER present at that site - and that is not what you
> > intend to say.  Setting the occupancy to zero does not mean that
> > a full atom is located somewhere in this area.  Quite the opposite.
> >
> >   (The reference to a dummy site is interesting and implies to
> > me that mmCIF already has the mechanism you wish for.)
> >
> >   Having some experience with refining low occupancy atoms and
> > working with dummy marker atoms I'm quite confident that you can
> > never define a B factor cutoff that would work.  No matter what
> > value you choose you will find some atoms in density that refine
> > to values greater than the cutoff, or the limit you choose is so
> > high that you will find marker atoms that refine to less than the
> > limit.  A B factor cutoff cannot work - no matter the value you
> > choose you will always be plagued with false positives or false
> > negatives.
> >
> >   If you really want to stuff this bit into one of these fields
> > you have to go all out.  Set the occupancy of a marker atom to -99.99.
> > This will unambiguously mark the atom as an imaginary one.  This
> > will, of course, break every program that reads PDB format files,
> > but that is what should happen in any case.  If you change the
> > definition of the columns in the file you must mandate that all
> > programs be upgraded to recognized the new definitions.  I don't
> > know how you can do that other than ensuring that the change will
> > cause programs to cough.  To try to slide it by with a magic value
> > that will be silently accepted by existing programs is to beg for
> > bugs and subtle side-effects.
> >
> >   Good luck getting the maintainers of the mmCIF standard to accept
> > a magic value in either of these fields.
> >
> >   How about this: We already have the keywords ATOM and HETATM
> > (and don't ask me why we have two).  How about we create a new
> > record in the PDB format, say IMGATM, that would have all the
> > fields of an ATOM record but would be recognized as whatever the
> > marker is for "dummy" atoms in the current mmCIF?  Existing programs
> > would completely ignore these atoms, as they should until they are
> > modified to do something reasonable with them.  Those of us who
> > have no use for them can either use a switch in the program to
> > ignore them or just grep them out of the file.  Someone could write
> > a program that would take a model with only ATOM and HETATM records
> > and fill out all the desired IMGATM records (Let's call that program
> > WASNIAHC, everyone would remember that!).
> >
> >   This solution is unambiguous.  It can be represented in current
> > mmCIF, I think.  The PDB could run WASNIAHC themselves after deposition
> > but before acceptance by the depositor so people like me would not
> > have to deal with them during refinement but would be able to see
> > them before our precious works of art are unleashed on the world.
> >
> >   Seems like a win-win solution to me.
> >
> > Dale Tronrud
> >
> >
> > On 4/3/2011 9:17 PM, Jacob Keller wrote:
> >>
> >> Well, what about getting the default settings on the major molecular
> >> viewers to hide atoms with either occ=0 or b>cutoff ("novice mode?")?
> >> While the b cutoff is still be tricky, I assume we could eventually
> >> come to consensus on some reasonable cu

Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?

[Poul Nissen]

Deng,
You need a good synchrotron source with a low point spread detector, but not 
least a careful consideration in crystal mounting so that your crystal rotates 
apprx around the long axis during data collection to optimise the separation of 
reflections on the detector
besides checking that the long axis is not a result of bad cryo and crystal 
deterioration during flash cooling
Poul



On 05/04/2011, at 07.05, dengzq1987  wrote:

> hello all,
> does anyone have the experience of   Collecting Data from Long Unit Cell Axes 
> ? I have a crystal that diffracts to about 4 A. in some direction  the spots 
> overlap. we can't use the data to index .we think it is because that there is 
> a long unit cell axes. so  is there any method to solve this problem?
>  
> best wishes.
>  
> 2011-04-05
> dengzq1987

[ccp4bb] how to Collecting Data from Long Unit Cell Axes ?

[dengzq1987]

hello all,
does anyone have the experience of  Collecting Data from Long Unit Cell Axes ? 
I have a crystal that diffracts to about 4 A. in some direction  the spots 
overlap. we can't use the data to index .we think it is because that there is a 
long unit cell axes. so  is there any method to solve this problem? 

best wishes.

2011-04-05 



dengzq1987 

Re: [ccp4bb] what to do with disordered side chains

[Flip Hoedemaeker]

It's nice to see that this discussion pops up every two years or so with 
exactly the same arguments :)


My vote (as always) is for leaving the atoms of disordered side chains 
in with high B values, the B values are part of the models. Its up to 
the popular Biologist's visualization software out there to properly 
display these models. I'm sure we can use all kinds of nice 4D blurry 
renderings of these disordered atoms nowadays.


Flip

On 4/4/2011 23:15, Jacob Keller wrote:

I like your IMGATM proposal, but wouldn't it also potentially break
some of the programs? Also--and this is a problem with deleting only
sidechain atoms in general--it seems that many, myself included, might
totally miss that an apparent "alanine" is really a trunco-lysine.
What I like is that it does get around the problem of people
over-interpreting bogus sidechains, but it falls short, perhaps, in
misleading people about what residue is there. I, for one, would not
feel that I had to click on all the alanines in a model to verify that
they were not lysines, and would be surprised and puzzled for a while
about why this ala said lys when I clicked on it. Wouldn't you be
surprised? (Well, maybe not after this thread...)

JPK



On Mon, Apr 4, 2011 at 1:55 AM, Dale Tronrud  wrote:

   The definition of _atom_site.occupancy is

  The fraction of the atom type present at this site.
  The sum of the occupancies of all the atom types at this site
  may not significantly exceed 1.0 unless it is a dummy site.

When an atom has an occupancy equal to zero that means that the
atom is NEVER present at that site - and that is not what you
intend to say.  Setting the occupancy to zero does not mean that
a full atom is located somewhere in this area.  Quite the opposite.

   (The reference to a dummy site is interesting and implies to
me that mmCIF already has the mechanism you wish for.)

   Having some experience with refining low occupancy atoms and
working with dummy marker atoms I'm quite confident that you can
never define a B factor cutoff that would work.  No matter what
value you choose you will find some atoms in density that refine
to values greater than the cutoff, or the limit you choose is so
high that you will find marker atoms that refine to less than the
limit.  A B factor cutoff cannot work - no matter the value you
choose you will always be plagued with false positives or false
negatives.

   If you really want to stuff this bit into one of these fields
you have to go all out.  Set the occupancy of a marker atom to -99.99.
This will unambiguously mark the atom as an imaginary one.  This
will, of course, break every program that reads PDB format files,
but that is what should happen in any case.  If you change the
definition of the columns in the file you must mandate that all
programs be upgraded to recognized the new definitions.  I don't
know how you can do that other than ensuring that the change will
cause programs to cough.  To try to slide it by with a magic value
that will be silently accepted by existing programs is to beg for
bugs and subtle side-effects.

   Good luck getting the maintainers of the mmCIF standard to accept
a magic value in either of these fields.

   How about this: We already have the keywords ATOM and HETATM
(and don't ask me why we have two).  How about we create a new
record in the PDB format, say IMGATM, that would have all the
fields of an ATOM record but would be recognized as whatever the
marker is for "dummy" atoms in the current mmCIF?  Existing programs
would completely ignore these atoms, as they should until they are
modified to do something reasonable with them.  Those of us who
have no use for them can either use a switch in the program to
ignore them or just grep them out of the file.  Someone could write
a program that would take a model with only ATOM and HETATM records
and fill out all the desired IMGATM records (Let's call that program
WASNIAHC, everyone would remember that!).

   This solution is unambiguous.  It can be represented in current
mmCIF, I think.  The PDB could run WASNIAHC themselves after deposition
but before acceptance by the depositor so people like me would not
have to deal with them during refinement but would be able to see
them before our precious works of art are unleashed on the world.

   Seems like a win-win solution to me.

Dale Tronrud


On 4/3/2011 9:17 PM, Jacob Keller wrote:


Well, what about getting the default settings on the major molecular
viewers to hide atoms with either occ=0 or b>cutoff ("novice mode?")?
While the b cutoff is still be tricky, I assume we could eventually
come to consensus on some reasonable cutoff (2 sigma from the mean?),
and then this approach would allow each free-spirited crystallographer
to keep his own preferred method of dealing with these troublesome
sidechains and nary a novice would be led astray

JPK

On Sun, Apr 3, 2011 at 2:58 PM, Eric Bennettwrote:


Most non-structural users are familiar with the 

Re: [ccp4bb] what to do with disordered side chains

[Jacob Keller]

I like your IMGATM proposal, but wouldn't it also potentially break
some of the programs? Also--and this is a problem with deleting only
sidechain atoms in general--it seems that many, myself included, might
totally miss that an apparent "alanine" is really a trunco-lysine.
What I like is that it does get around the problem of people
over-interpreting bogus sidechains, but it falls short, perhaps, in
misleading people about what residue is there. I, for one, would not
feel that I had to click on all the alanines in a model to verify that
they were not lysines, and would be surprised and puzzled for a while
about why this ala said lys when I clicked on it. Wouldn't you be
surprised? (Well, maybe not after this thread...)

JPK



On Mon, Apr 4, 2011 at 1:55 AM, Dale Tronrud  wrote:
>   The definition of _atom_site.occupancy is
>
>  The fraction of the atom type present at this site.
>  The sum of the occupancies of all the atom types at this site
>  may not significantly exceed 1.0 unless it is a dummy site.
>
> When an atom has an occupancy equal to zero that means that the
> atom is NEVER present at that site - and that is not what you
> intend to say.  Setting the occupancy to zero does not mean that
> a full atom is located somewhere in this area.  Quite the opposite.
>
>   (The reference to a dummy site is interesting and implies to
> me that mmCIF already has the mechanism you wish for.)
>
>   Having some experience with refining low occupancy atoms and
> working with dummy marker atoms I'm quite confident that you can
> never define a B factor cutoff that would work.  No matter what
> value you choose you will find some atoms in density that refine
> to values greater than the cutoff, or the limit you choose is so
> high that you will find marker atoms that refine to less than the
> limit.  A B factor cutoff cannot work - no matter the value you
> choose you will always be plagued with false positives or false
> negatives.
>
>   If you really want to stuff this bit into one of these fields
> you have to go all out.  Set the occupancy of a marker atom to -99.99.
> This will unambiguously mark the atom as an imaginary one.  This
> will, of course, break every program that reads PDB format files,
> but that is what should happen in any case.  If you change the
> definition of the columns in the file you must mandate that all
> programs be upgraded to recognized the new definitions.  I don't
> know how you can do that other than ensuring that the change will
> cause programs to cough.  To try to slide it by with a magic value
> that will be silently accepted by existing programs is to beg for
> bugs and subtle side-effects.
>
>   Good luck getting the maintainers of the mmCIF standard to accept
> a magic value in either of these fields.
>
>   How about this: We already have the keywords ATOM and HETATM
> (and don't ask me why we have two).  How about we create a new
> record in the PDB format, say IMGATM, that would have all the
> fields of an ATOM record but would be recognized as whatever the
> marker is for "dummy" atoms in the current mmCIF?  Existing programs
> would completely ignore these atoms, as they should until they are
> modified to do something reasonable with them.  Those of us who
> have no use for them can either use a switch in the program to
> ignore them or just grep them out of the file.  Someone could write
> a program that would take a model with only ATOM and HETATM records
> and fill out all the desired IMGATM records (Let's call that program
> WASNIAHC, everyone would remember that!).
>
>   This solution is unambiguous.  It can be represented in current
> mmCIF, I think.  The PDB could run WASNIAHC themselves after deposition
> but before acceptance by the depositor so people like me would not
> have to deal with them during refinement but would be able to see
> them before our precious works of art are unleashed on the world.
>
>   Seems like a win-win solution to me.
>
> Dale Tronrud
>
>
> On 4/3/2011 9:17 PM, Jacob Keller wrote:
>>
>> Well, what about getting the default settings on the major molecular
>> viewers to hide atoms with either occ=0 or b>cutoff ("novice mode?")?
>> While the b cutoff is still be tricky, I assume we could eventually
>> come to consensus on some reasonable cutoff (2 sigma from the mean?),
>> and then this approach would allow each free-spirited crystallographer
>> to keep his own preferred method of dealing with these troublesome
>> sidechains and nary a novice would be led astray
>>
>> JPK
>>
>> On Sun, Apr 3, 2011 at 2:58 PM, Eric Bennett  wrote:
>>>
>>> Most non-structural users are familiar with the sequence of the proteins
>>> they are studying, and most software does at least display residue identity
>>> if you select an atom in a residue, so usually it is not necessary to do any
>>> cross checking besides selecting an atom in the residue and seeing what its
>>> residue name is.  The chance of somebody misinterpreting a truncated Lys as
>>>

[ccp4bb] ICSG 2011 May 10-14, 2011, Toronto

[Thomas C. Terwilliger]

Dear Colleagues,

We hope that you are planning to join us in Toronto, Canada for the
International Conference on Structural Genomics 2011 which will be held on
May 10-14, 2011.  We have an excellent scientific program prepared which
includes both oral and poster presentations (please see:
http://www.icsg2011.org/scientific_program.php ). Participants will also
enjoy the fabulous view of the city of Toronto during the banquet to be
held at the revolving 360 Restaurant at the top of the CN tower. An
optional post-conference tour to Niagara Falls will also be available. We
invite you to register on line by April 15, 2011 at 11:59 pm EST.  A
limited number of late poster abstracts will be accepted until April 12,
2011 at 11:59 pm EST

In addition to the main ICSG meeting, there will be a whole day of
concurrent satellite workshops (May 10, 2011) that are free for ICSG 2011
registrants, including:

Small Molecule Screening Workshop- This hands-on workshop will allow
participants to screen a protein of their choice for binding of selected
compounds, using thermal shift assays.

iSee: Interactive 3D Documents for the Dissemination of Structural Biology
- This hands-on workshop will familiarize participants with the iSEE 3D
graphical software which allows interactive viewing of 3 dimensional
molecular structures and is currently used by journals such as Nature
Structural & Molecular Biology and PLoS Biology and PLoS ONE
Eukaryotic Gene Expression Systems Workshop - This workshop will provide
participants with a detailed understanding of the state-of-the-art for
production of eukaryotic proteins destined for biochemical, biophysical,
and structural analyses..

Workshop on NMR Methods for Structural Biology- This workshop will survey
technologies for structure/function investigations of proteins, developed
in (or in collaboration with) structural genomics projects, that are ready
for widespread use by the wider biological community.

Phenix Crystallography Software Workshop - This workshop will introduce
the PHENIX software for macromolecular structure determination and the
core algorithms that it uses. It will provide hands-on tutorials for
crystallographers of all levels.

The workshop registration deadline is Monday April 11, 2011 at 11:59 pm EST

Please visit http://www.icsg2011.org    for ICSG
2011 meeting and workshop registration details and to submit your poster
abstract.


We hope to see you there!


Best regards,

Cheryl Arrowsmith
ICSG 2011 Organizer

Ted Baker
Stephen Burley
Dino Moras
Joel Sussman
Shigeyuki Yokoyama
Tom Terwilliger
ISGO Executive Committee

Re: [ccp4bb] what to do with disordered side chains

[Ed Pozharski]

On Mon, 2011-04-04 at 09:38 -0500, Jacob Keller wrote:
> Could it be that they are not normal because of all of the outlier,
> huge-b-factor sidechains? 

That is part of it

> If every exposed sidechain without real
> density gets a b-factor of 150, wouldn't that make a sizeable and
> illegitimate non-normal population?

It will surely skew the standard deviation to higher values

>  I would actually be curious about
> normality of b-factors--is there such a study/figure out there
> somewhere, with, say, histograms of b-factors of many individual
> structures? 

Well, technically speaking they cannot possibly obey normal distribution
since they are always positive.  Another reason is, of course, that
there are different atom types (e.g. side chains versus backbone) and
you have at best multi-modal distribution.  In my experience, the
B-factor distributions always fail normality tests even when you break
atoms to groups (the most "normal" are, somewhat expectedly, waters, yet
they fail too).

Cheers,

Ed.

PS.  If you keep going at this - start a new thread

-- 
"I'd jump in myself, if I weren't so good at whistling."
   Julian, King of Lemurs

Re: [ccp4bb] what to do with disordered side chains

[Pavel Afonine]

Hi Robbie,

 I updated my stripper program to remove all atoms with occ<0.00 instead of
> 0.00
>

- I used to do it in the past in phenix.model_vs_data but then I found it
too boring since it was silently swallowing the problem cases -:) so I
reverted it back to the "naive mode" when it takes what's in PDB as "God
given" and computes the stats using it. This in turn points out problem
cases, which is instructive, and which one can take care of on a second
walk-through.

- Also, you will be missing things like this:

>  http://www.rcsb.org/pdb/files/3otj.pdb
http://www.rcsb.org/pdb/files/3kcj.pdb
(.. and so on, I have a full list)
where, I guess, "D" with negative occupancy actually means H -:)

All the best!
Pavel.

Re: [ccp4bb] what to do with disordered side chains

[Robbie Joosten]

Nice one Pavel. PDB_REDO actually runs on these files but it's not pretty. I 
updated my stripper program to remove all atoms with occ<0.00 instead of 0.00
 
Cheers,
Robbie
 


Date: Mon, 4 Apr 2011 07:26:23 -0700
From: pafon...@gmail.com
Subject: Re: [ccp4bb] what to do with disordered side chains
To: CCP4BB@JISCMAIL.AC.UK

Hi Dale,



 Set the occupancy of a marker atom to -99.99.
This will unambiguously mark the atom as an imaginary one.  This
will, of course, break every program that reads PDB format files,


may be not every -:)


phenix.model_vs_data works just fine with


http://www.rcsb.org/pdb/files/1BQU.pdb
http://www.rcsb.org/pdb/files/1azr.pdb


(Um... I guess I just created some work for PDB_REDO folks, sorry -:) )


All the best!
Pavel.


  

Re: [ccp4bb] what to do with disordered side chains

[Robbie Joosten]

Dear James,
 
You make a very good point. So far we only discussed the option of removing 
alls side chain atoms except for CB. What if only a few side chain atoms are 
outside the density? Should we just remove those? If we use the argument that 
we should remove the atoms we cannot see, then surely we should keep the ones 
we can see. 
A problem is that if someone else recalculates the maps and inspects them 
(which is the point of the EDS), some atoms may very well fall inside or 
outside the density differently than in the original crystallographic study: 
software changes, other reflections are included (remember the recent I/sigI 
discussion), and last (but not least) when atoms are removed the solvent mask 
changes. 
 
Anyway, I don't think that the side chain discussion will be solved in this 
thread. PDB users are not all the same and treat the options that are proposed 
differently. They are all used in the PDB and that complicates matters for the 
users. In PDB_REDO (plug, plug ;) we build all missing side chains (and rebuild 
the zero-occupancy ones) and let the B-factor sort it out. Not everyone will 
agree with this, but at least it is consistent. If anyone studies a single 
structure properly, he should use the density and there is no problem. For 
statistics studies the first thing people do is filter by resolution and 
B-factor (and sequence identity) so the really bad side chains are removed from 
the testset anyway.
 
Cheers,
Robbie
 

 
> Date: Sun, 3 Apr 2011 23:45:10 -0700
> From: jmhol...@lbl.gov
> Subject: Re: [ccp4bb] what to do with disordered side chains
> To: CCP4BB@JISCMAIL.AC.UK
> 
> At the risk of throwing a little gasoline on the flame war, what about 
> side chains that will ALWAYS poke outside of the electron density? For 
> example, pretty much any terminal aliphatic at 3.5 A resolution? I 
> first learned this about 15 years ago when I made this movie:
> 
> http://bl831.als.lbl.gov/~jamesh/movies/resolution.mpeg
> 
> For those of you whose browser no longer supports MPEG-1, this is a 
> movie of a calculated (aka noise-free) electron density map, contoured 
> at "1 sigma", but cut to the resolution shown after applying an overall 
> B factor sufficient to suppress series-termination. By that I mean the 
> maps don't look all that different with or without the cutoff. The 
> coordinates shown are the "correct" model used to calculate the map. At 
> about 3.5 A you start to see side chains poking out of the density, and 
> at 6 A, all the side chains are "gone". Does this mean they should be 
> modeled with zero occupancy? ;)
> 
> -James Holton
> MAD Scientist
> 
> 
> On 4/3/2011 9:57 PM, Maia Cherney wrote:
> > I guess, most hydrophilic side chains on the surface are flexible, 
> > they don't keep the same conformation. If you cut those side chains 
> > off, the surface will be looking pretty hydrophobic and misleading 
> > (and very horrible). I prefer to see them intact. I know, most of them 
> > are flexible and don't have one exact position, but it's OK. I know 
> > they are there not far from the main chain. Usually, their exact 
> > position is irrelevant.
> >
> > Maia
> >
> >
> >
> > Jacob Keller wrote:
> >> Well, what about getting the default settings on the major molecular
> >> viewers to hide atoms with either occ=0 or b>cutoff ("novice mode?")?
> >> While the b cutoff is still be tricky, I assume we could eventually
> >> come to consensus on some reasonable cutoff (2 sigma from the mean?),
> >> and then this approach would allow each free-spirited crystallographer
> >> to keep his own preferred method of dealing with these troublesome
> >> sidechains and nary a novice would be led astray
> >>
> >> JPK
> >>
> >> On Sun, Apr 3, 2011 at 2:58 PM, Eric Bennett  wrote:
> >>> Most non-structural users are familiar with the sequence of the 
> >>> proteins they are studying, and most software does at least display 
> >>> residue identity if you select an atom in a residue, so usually it 
> >>> is not necessary to do any cross checking besides selecting an atom 
> >>> in the residue and seeing what its residue name is. The chance of 
> >>> somebody misinterpreting a truncated Lys as Ala is, in my 
> >>> experience, much much lower than the chance they will trust the xyz 
> >>> coordinates of atoms with zero occupancy or high B factors.
> >>>
> >>> What worries me the most is somebody designing a whole biological 
> >>> experiment around an over-interpretation of details that are implied 
> >>> by xyz coordinates of atoms, even if those atoms were not resolved 
> >>> in the maps. When this sort of error occurs it is a level of pain 
> >>> and wasted effort that makes the "pain" associated with having to 
> >>> build back in missing side chains look completely trivial.
> >>>
> >>> As long as the PDB file format is the way users get structural data, 
> >>> there is really no good way to communicate "atom exists with no 
> >>> reliable coordinates" to the user, given t

Re: [ccp4bb] what to do with disordered side chains

[Jacob Keller]

> Not likely - the distribution of ADPs is not normal, so you can't easily
> convert Z-scores to probabilities.

Could it be that they are not normal because of all of the outlier,
huge-b-factor sidechains? If every exposed sidechain without real
density gets a b-factor of 150, wouldn't that make a sizeable and
illegitimate non-normal population? I would actually be curious about
normality of b-factors--is there such a study/figure out there
somewhere, with, say, histograms of b-factors of many individual
structures?




-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] what to do with disordered side chains

[Pavel Afonine]

Hi Dale,

 Set the occupancy of a marker atom to -99.99.
> This will unambiguously mark the atom as an imaginary one.  This
> will, of course, break every program that reads PDB format files,


may be not every -:)

phenix.model_vs_data works just fine with

http://www.rcsb.org/pdb/files/1BQU.pdb
http://www.rcsb.org/pdb/files/1azr.pdb

(Um... I guess I just created some work for PDB_REDO folks, sorry -:) )

All the best!
Pavel.

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

[Quyen Hoang]

This could be my last post ...

I am now leaving mercury
It's surface was safe and free
Meet a mystical gryphon and some alien mosquitos
They gave me some protein crystals
Which tried to shoot like 007
Missed them all but the heaven
Will try again with my new X8
Which 007 would surely hate
Now approaching pluto
Visibility is really low
My landing site had became flatter
And the uncertainty perimeter around it had turned into darkmatter
If I miss the apex of my landing site
Will I disappear right out of sight
Will I turn into an infinite spaghetti
Which I am sure the novice users would get all gitty

Cheers,
Quyen


On Apr 4, 2011, at 5:19 AM, Eleanor Dodson wrote:


Very clever..
Eleanor


On 04/01/2011 03:19 PM, Quyen Hoang wrote:
Will this affect my reprocessing of the data with D*TREK on my  
journey

to XPLORE the planets MERCURY and rPLUTO in my ENDEAVOUR to find and
BUSTER some CRYSTALS with my on-board TNT into XPOWDER?
I am still trying to GRASP the idea of AUTODOCKing on precise HKL
locations based on the SHARP but CONVX images produced by CRYSTAL  
STUDIO.


Quyen


On Apr 1, 2011, at 2:06 AM, Ethan Merritt wrote:


Hi to all on ccp4bb:

What better day to announce the availability of a breakthrough  
technique

in macromolecular crystallography?

Given recent discussion and in particular James Holton's  
suggestion that
the problem of disordered sidechains is a problem akin to the  
difficulty

of describing dark matter and dark energy...

I am happy to announce a new crystallographic tool that can  
improve your
model by accounting for an often-neglected physical property. A  
detailed
explanation, references, and a preliminary implementation of the  
program

can be downloaded from

http://skuld.bmsc.washington.edu/DarkMatter

--
Ethan A Merritt
Karmic Diffraction Project
Fine crystallography since April 1, 2011
"What goes around, comes around - usually as a symmetry equivalent"

Re: [ccp4bb] what to do with disordered side chains

[Ed Pozharski]

On Sun, 2011-04-03 at 23:17 -0500, Jacob Keller wrote:
> While the b cutoff is still be tricky, I assume we could eventually
> come to consensus on some reasonable cutoff (2 sigma from the mean?) 

Not likely - the distribution of ADPs is not normal, so you can't easily
convert Z-scores to probabilities.  

-- 
"I'd jump in myself, if I weren't so good at whistling."
   Julian, King of Lemurs

[ccp4bb] CCP4MG Version 2.5.0

[Stuart McNicholas]

Dear All,

  Version 2.5.0 of the CCP4 Molecular Graphics Program
(CCP4MG) has just been placed on the downloads page:

http://www.ccp4.ac.uk/MG/download/

This version includes many bug fixes and improvements over 2.4.3, including:

### General bug fixes
  * Fix very serious Vista/Windows 7 crash upon loading most pdb files.
  * Fix some crashes in Movie Editor.
  * Fix some crashes when closing windows or data files, or deleting 
atom selections.

  * Workaround lighting initialization crash with some onboard chipsets.

### Render Module
  * Fix glitches when there is a transparent background in rendered files.
  * Fix clipping of text labels in rendered files.
  * Fix position of text labels when rendering.
  * Fix a problem with batch rendering and -norestore flag.
  * Compress tiff output from render.

### Sequence Viewer
  * Only populate/update sequence viewer when it is shown.
  * Residues selected in sequence viewer appear in Display Table so 
that style/colouring/selection can be user edited.

  * Do not show waters in sequence view or sequences without AA/NA.
  * Residues are correctly highlighted in sequence viewer at restart 
and after alignment.

  * Colour models by sequence conservation from an alignment.
  * Sequence alignment is restored at program restart.
  * Undo a sequence alignment.
  * Font size in Sequence Viewer can be changed.

### General Enhancements
  * Ask user if he/she wishes to restore status at restart.
  * Escape exits full-screen mode.
  * Show edit zoom factor in status bar.
  * Make some large widgets (e.g. residue type colours) scrollable.
  * The compact docked display table now has a usable slider for 
electron density contour level, etc.


The full list of changes can be found at:
http://www.ccp4.ac.uk/MG/download/#release_notes

Please report problems to ccp...@ysbl.york.ac.uk.

Best Wishes,
CCP4MG

Re: [ccp4bb] metal binds?

[vincent Chaptal]

Hi,

we recently published a method that could be just what you need, and 
easy to implement.
It detects covalent modifications of cysteines, and mercury, gold and 
some platinums target cysteines...


have a look at this paper.
feel free to contact me if you want more information.
vincent


Fluorescence Detection of Heavy Atom Labeling (FD-HAL): A rapid method 
for identifying covalently modified cysteine residues by phasing atoms.


Chaptal V, Ujwal R, Nie Y, Watanabe A, Kwon S, Abramson J.

J Struct Biol. 2010 Feb 10.






Le 3/25/11 8:39 AM, Careina Edgooms a écrit :

Dear ccp4 users

I would like to know, is there a way to check that heavy metal has 
bound to crystals before I take it to synchrotron which is far away?


thanks
Careina



--

Vincent Chaptal, PhD

Institut de Biologie et Chimie des Protéines

Drug-resistance modulation and mechanism Laboratory

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.ibcp.fr

Re: [ccp4bb] Comparing conformations using LSQKAB

[Eleanor Dodson]

Well - I usually work in confunction with the graphics, so you can look 
at the regions which differ.


I start with the rms difference. If that is > 2, I think there are 
significant changes. So then you have to decide what Q you are asking, 
and why. Is it that you want to use a model for Molecular replacement, 
or gain insight into possibly different biology and so on?


Is there a loop which is very different?
 Are there domains which shift relative to each other?
Is one structure more reliable than the other?

And so on..
Eleanor

On 04/04/2011 08:29 AM, Sandro Renato Dias wrote:

Dear all,

I´m doing some comparissons of main chain conformations using LSQKAB
and I would like to know from you how can I quantify a delta atom
result.
For instance, when I compare two identicals main chains I have the
following result:
  0.0011C   A 1C   A
  0.0012N   A 2N   A
  0.0012CA  A 2CA  A
  0.0012C   A 2C   A
  0.0012O   A 2O   A
  0.0003N   A 3N   A
  0.000  101C   A   101C   A
  0.000  102N   A   102N   A
  0.000  102CA  A   102CA  A
  0.000  102C   A   102C   A
  0.001  102O   A   102O   A
  0.000  103N   A   103N   A

But when I compare two different ones I can get something like this:
  1.3121C   A 1C   A
  1.3992N   A 2N   A
  1.7252CA  A 2CA  A
  3.0792C   A 2C   A
  5.2932O   A 2O   A
  2.2803N   A 3N   A
  1.327  101C   A   101C   A
  1.226  102N   A   102N   A
  1.858  102CA  A   102CA  A
  2.928  102C   A   102C   A
  2.875  102O   A   102O   A
  4.038  103N   A   103N   A

My main objective is to define how similar these conformations are.
But I don´t know how many angstroms is sufficient to affirm that the
both are identical or very closer so I can exchange each other.


Thanks for any suggestions.

Sandro


---
M.Sc. Sandro Renato Dias
PhD. Student in Bioinformatics
Laboratório de Biologia Estrutural
Instituto de Ciências Biológicas
Universidade Federal de Minas Gerais
http://lattes.cnpq.br/5300421458375793

[ccp4bb] Comparing conformations using LSQKAB

[Sandro Renato Dias]

Dear all,

I´m doing some comparissons of main chain conformations using LSQKAB
and I would like to know from you how can I quantify a delta atom
result.
For instance, when I compare two identicals main chains I have the
following result:
 0.0011C   A 1C   A
 0.0012N   A 2N   A
 0.0012CA  A 2CA  A
 0.0012C   A 2C   A
 0.0012O   A 2O   A
 0.0003N   A 3N   A
 0.000  101C   A   101C   A
 0.000  102N   A   102N   A
 0.000  102CA  A   102CA  A
 0.000  102C   A   102C   A
 0.001  102O   A   102O   A
 0.000  103N   A   103N   A

But when I compare two different ones I can get something like this:
 1.3121C   A 1C   A
 1.3992N   A 2N   A
 1.7252CA  A 2CA  A
 3.0792C   A 2C   A
 5.2932O   A 2O   A
 2.2803N   A 3N   A
 1.327  101C   A   101C   A
 1.226  102N   A   102N   A
 1.858  102CA  A   102CA  A
 2.928  102C   A   102C   A
 2.875  102O   A   102O   A
 4.038  103N   A   103N   A

My main objective is to define how similar these conformations are.
But I don´t know how many angstroms is sufficient to affirm that the
both are identical or very closer so I can exchange each other.


Thanks for any suggestions.

Sandro


---
M.Sc. Sandro Renato Dias
PhD. Student in Bioinformatics
Laboratório de Biologia Estrutural
Instituto de Ciências Biológicas
Universidade Federal de Minas Gerais
http://lattes.cnpq.br/5300421458375793