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

[Dale Tronrud]

   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 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 the diversity of software packages out there for reading PDB files and the 
historical lack of any standard way of dealing with this issue.  Even if the file format 
is hacked there is no way to force all the existing software out 

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

[James Holton]

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 the diversity of software 
packages out there for reading PDB files and the historical lack of 
any standard way of dealing with this issue.  Even if the file 
format is hacked there is no way to force all the existing software 
out there to understand the hack.  A file format that isn't designed 
with this sort of feature from day one is not going to be fixable as 
a practical matter after so much legacy code has accumulated.


-Eric



On Apr 3, 2011, at 2:20 PM, Jacob Keller wrote:


To the delete-the-atom-nik's: do you propose deleting the whole
residue or just the side chain? I can understand deleting the whole
residue, but deleting only the side chain seems to me to be placing a
stumbling block also, and even possibly confusing for an experienced
crystallographer: the .pdb says "lys" but it looks like an ala? Which
is it? I could imagine a lot of frustration-hours arising from this
practice, with people cross-checking sequences, looking in the methods
sections for mutations...

JPK

Re: [ccp4bb] OT: PCR instrument

[Artem Evdokimov]

"I am too poor to afford cheap things"
(I am not sure where quote comes from but it's relevant).

The answer depends on whether time is considered expensive or not. Sometimes
(e.g. when free labor such as graduate students) time is not an issue. And
sometimes it is. Reagent costs are fairly low now.

For time, one cannot beat the Robocycler. It's a funny looking design, but
it's really fast and quite accurate (since the blocks do not change
temperature throughout the process).

Artem

On Sun, Apr 3, 2011 at 2:42 PM, VAN RAAIJ , MARK JOHAN <
mjvanra...@cnb.csic.es> wrote:

> if the PCR machine is just to be used for standard sub-cloning (amplifying
> fragments from other plasmids, cloned cDNA etc.), I would go for the
> cheapest one I could find. I guess there are few crystallography projects
> were the first PCR step turned out to be the most difficult.
> For more sophisticated applications there are probably forums where more
> knowledgeable people reside (on PCR that is...)
> Mark
>
> Quoting "Bernhard Rupp (Hofkristallrat a.D.)":
>
> > Dear All,
> >
> > I was polled for a  recommendation for a  good PCR instrument,
> > but I am not much of a molecular biology person - if someone could
> > please help and kindly send some recommendations to
> >
> > Eric W. Reinheimer 
> >
> > Best regards, BR
> > -
> > Bernhard Rupp
> > 001 (925) 209-7429
> > +43 (676) 571-0536
> > b...@ruppweb.org
> > hofkristall...@gmail.com
> > http://www.ruppweb.org/
> > -
> > No animals were hurt or killed during the
> > production of this email.
> > -
> >
>
> Mark J van Raaij
> Laboratorio M-4
> Dpto de Estructura de Macromoléculas
> Centro Nacional de Biotecnología - CSIC
> c/Darwin 3, Campus Cantoblanco
> 28049 Madrid
> tel. 91 585 4616
> email: mjvanra...@cnb.csic.es
>

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

[Maia Cherney]

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 the diversity of software packages out there for reading PDB files and the 
historical lack of any standard way of dealing with this issue.  Even if the file format 
is hacked there is no way to force all the existing software out there to understand the 
hack.  A file format that isn't designed with this sort of feature from day one is not 
going to be fixable as a practical matter after so much legacy code has accumulated.

-Eric



On Apr 3, 2011, at 2:20 PM, Jacob Keller wrote:



To the delete-the-atom-nik's: do you propose deleting the whole
residue or just the side chain? I can understand deleting the whole
residue, but deleting only the side chain seems to me to be placing a
stumbling block also, and even possibly confusing for an experienced
crystallographer: the .pdb says "lys" but it looks like an ala? Which
is it? I could imagine a lot of frustration-hours arising from this
practice, with people cross-checking sequences, looking in the methods
sections for mutations...

JPK

  




  

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

[Jacob Keller]

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 the diversity of software packages out there for reading 
> PDB files and the historical lack of any standard way of dealing with this 
> issue.  Even if the file format is hacked there is no way to force all the 
> existing software out there to understand the hack.  A file format that isn't 
> designed with this sort of feature from day one is not going to be fixable as 
> a practical matter after so much legacy code has accumulated.
>
> -Eric
>
>
>
> On Apr 3, 2011, at 2:20 PM, Jacob Keller wrote:
>
>> To the delete-the-atom-nik's: do you propose deleting the whole
>> residue or just the side chain? I can understand deleting the whole
>> residue, but deleting only the side chain seems to me to be placing a
>> stumbling block also, and even possibly confusing for an experienced
>> crystallographer: the .pdb says "lys" but it looks like an ala? Which
>> is it? I could imagine a lot of frustration-hours arising from this
>> practice, with people cross-checking sequences, looking in the methods
>> sections for mutations...
>>
>> JPK
>>
>



-- 
***
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

[Eric Bennett]

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 the diversity of software packages out there for reading PDB 
files and the historical lack of any standard way of dealing with this issue.  
Even if the file format is hacked there is no way to force all the existing 
software out there to understand the hack.  A file format that isn't designed 
with this sort of feature from day one is not going to be fixable as a 
practical matter after so much legacy code has accumulated.

-Eric



On Apr 3, 2011, at 2:20 PM, Jacob Keller wrote:

> To the delete-the-atom-nik's: do you propose deleting the whole
> residue or just the side chain? I can understand deleting the whole
> residue, but deleting only the side chain seems to me to be placing a
> stumbling block also, and even possibly confusing for an experienced
> crystallographer: the .pdb says "lys" but it looks like an ala? Which
> is it? I could imagine a lot of frustration-hours arising from this
> practice, with people cross-checking sequences, looking in the methods
> sections for mutations...
> 
> JPK
> 

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

[Bernhard Rupp (Hofkristallrat a.D.)]

I vote for the electron density irrespective of side chains, main chains,
ligands, dark matter. The PDB is a collection of experimentally determined
structures per its own definition. If density supports it high B is fine -
B-factor simply is a parameter of a probability distribution. If you extend
that to no density - it becomes problematic. After all, coordinates imply
that an atom is actually at some specified place with a certain probability.
We may know that the atom necessarily has to be someplace lest it got chewed
off for some reason. The experiment just tells you that you do not know
where the atom is. 

Or in Rumsfeldic: Better a known unknown than a unknown known.

Cheers, BR

-Original Message-
From: Boaz Shaanan [mailto:bshaa...@exchange.bgu.ac.il] 
Sent: Sunday, April 03, 2011 11:02 AM
To: hofkristall...@gmail.com; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] what to do with disordered side chains

The original posting that started this thread referred to side-chains, as
the subject still suggests. Do you propose to omit only side-chain atoms, in
which case you end up with different residues, as pointed out by quite a few
people,or do you suggest also to omit the main-chain atoms of the
problematic residues ?

Besides, as mentioned by Phoebe and others, many users
(non-crystallographers) of PDB's know already  the meaning of the B-factor
and will know how to interpret a very high B. It is our task (the
crystallographers) to enllighten those who don't know what the B column in a
PDB entry stands for. I certainly do and I'm sure many of us do so too. I
voted for high B and would vote for it again, if asked.

Cheers,

   Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Sent: Sunday, April 03, 2011 7:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] what to do with disordered side chains

Thus my feeling is that if one does NOT see the coords in the electron
density, they should NOT be included, and let someone else try to model them
in, but they should be aware that they are modeling them.
Joel L. Sussman

Concur.  BMC p 680 'How to handle missing parts'

Best wishes, BR

On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:

Doing something sensible in the major software packages, both for graphics
and for other analysis of the structure, could solve the problem for most
users.

But nobody knows what other software is out there being used by individuals
or small groups.  And the more remote the authors of that software are from
protein structure solution the more likely it is that they have not/will not
properly handle atoms with zero occupancy or high B values, for example.

I am absolutely positive that there is software that does its voodoo on
ATOM/HETATM records and pays absolutely no attention to anything beyond the
x, y, z coordinates (i.e. beyond column 54).

   Frances Bernstein

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
 *   ***
f...@bernstein-plus-sons.com
*** *
 *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Sat, 2 Apr 2011, Jacob Keller wrote:

I guess I missed it in the flurry of replies to this thread over the last
few days, but what exactly is so terrible about keeping the atoms (since you
have chemical evidence from protein sequence that they are there, and even
if there is X-ray damage they were originally there and are likely still
there in a subset of the molecules), but changing occupancy to zero as an
acknowledgment that your data does not provide evidence to support a
specific atomic position for these atoms?

Some users might pull up the structure, see those atoms, and think their
positions were based on data, which they were not, and then draw conclusions
based on them. I agree that occ=0 is tantamount to the suggestion you
queried, however.

A somewhat key question might be: across the various molecular visualization
programs, what is the default way to handle atoms with occ=0? Perhaps those
programs might be the best place to fix the problem...

JPK


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

Re: [ccp4bb] OT: PCR instrument

[VAN RAAIJ , MARK JOHAN]

if the PCR machine is just to be used for standard sub-cloning (amplifying 
fragments from other plasmids, cloned cDNA etc.), I would go for the cheapest 
one I could find. I guess there are few crystallography projects were the first 
PCR step turned out to be the most difficult. 
For more sophisticated applications there are probably forums where more 
knowledgeable people reside (on PCR that is...) 
Mark 

Quoting "Bernhard Rupp (Hofkristallrat a.D.)":

> Dear All,
>
> I was polled for a  recommendation for a  good PCR instrument,
> but I am not much of a molecular biology person - if someone could
> please help and kindly send some recommendations to
>
> Eric W. Reinheimer 
>
> Best regards, BR
> -
> Bernhard Rupp
> 001 (925) 209-7429
> +43 (676) 571-0536
> b...@ruppweb.org
> hofkristall...@gmail.com
> http://www.ruppweb.org/ 
> -
> No animals were hurt or killed during the
> production of this email.
> -
>

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

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

[Dale Tronrud]

   Clearly there are strong feelings held by the advocates of the
several solutions to the problem of what to do about atoms that
cannot be reliably placed based on the electron density map.  I
certainly understand since I passionately support my own favorite
solution.

   Why is it that a community of generally reasonable people keep
coming back to this same issue and yet fail to find a solution
that can reach some kind of consensus?

   My 2 cents on this, more fundamental, issue:

   A model created by someone who believes that all atoms (for a
residue with any atoms) must be built will contain two kinds of
atoms.  Those placed based on the appearance of the electron
density and those placed in some convenient location simply to
fill out the atom count.  I think most everyone agrees that a
full residue is a convenience for some users of our models.  What
those of us who favor partial models want is an absolutely clear
distinction between the two classes of atoms.

   All this needs is a bit.  Literally, one bit of data that flags
those atoms added to the model simply to complete the set.

   Why can't we come to a solution that satisfies?  Because we
continue to use a non-extensible file format that does not allow
us a place to put this bit.

   Some people want to put the bit in the occupancy column by
defining a special value (occ=0) that would be the flag.  Some
people want to put it in the B factor column by defining a special
value there (a couple possibilities here, B=1000.00, B=500.00,
B varying but larger than that of any atom built into density).

   The B factor and occupancy columns in the PDB file have been
precisely defined back when the mmCIF dictionary was created and
to change their definitions now would require opening that process
again.  I am pretty sure that committee in charge will never allow
a definition for these items that includes the phrase "... except when
the value is equal too ...".  You can't run a database that way.

   Each piece of information has to have its own tag and definition.
Once it is defined we can embrace the task of educating software
developers and our collaborators who use our models in its meaning.

   There is just no place to put this bit in a PDB format file.
mmCIF - its trivial.  PDB format - no way.  As long as we insist that
this format is the preferred means of distributing our models we
will continue to return to this argument again and again with no
possibility of coming to a solution.

Dale Tronrud

P.S. I've even thought about using the model of the "REMARK" statement,
where all sorts of information have been added by the hack of
"standardized remarks".  I thought that one could create a
"standardized footnote" that would mark the atoms as "imaginary".
I found that, unfortunately, footnotes were removed from the PDB
format many years ago.



On 4/3/2011 11:01 AM, Boaz Shaanan wrote:

The original posting that started this thread referred to side-chains, as the 
subject still suggests. Do you propose to omit only side-chain atoms, in which 
case you end up with different residues, as pointed out by quite a few 
people,or do you suggest also to omit the main-chain atoms of the problematic 
residues ?

Besides, as mentioned by Phoebe and others, many users (non-crystallographers) 
of PDB's know already  the meaning of the B-factor and will know how to 
interpret a very high B. It is our task (the crystallographers) to enllighten 
those who don't know what the B column in a PDB entry stands for. I certainly 
do and I'm sure many of us do so too. I voted for high B and would vote for it 
again, if asked.

 Cheers,

Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp 
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Sent: Sunday, April 03, 2011 7:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] what to do with disordered side chains

Thus my feeling is that if one does NOT see the coords in the electron
density, they should NOT be included, and let someone else try to model
them in, but they should be aware that they are modeling them.
Joel L. Sussman

Concur.  BMC p 680 ‘How to handle missing parts’

Best wishes, BR

On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:

Doing something sensible in the major software packages, both
for graphics and for other analysis of the structure, could
solve the problem for most users.

But nobody knows what other software is out there being used by
individuals or small groups.  And the more remote the authors
of that software are from protein structure solution the more
likely it is that they have not/will not properly handle atoms
with zero occupancy or high B values, for example.

I am absolutely positive that there is

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

[Tommi Kajander]

Hi,
it is quite possible to truncate say Lys residue isnt it? so why not  
do this, this doesn't change
the identity of the residue but precisely draws attention to the fact  
that atoms are missing due to lack

of density.

And if you click on an atom in Pymol, at least i dont see the b-factor  
displayed anywhere - i would suspect
its the same case with other mol. graphics visualization software to  
fair extent. or its some small print somewhere...
+ can you actually tell by just looking at the B-factor whether there  
is any density or not? if the wilson b
is high i suspect you can see density and the B-factor will be high  
where as if Wilson B is low same b-factor
will probably mean you dont see density at same sigma cutoff/contour  
level. or i may be wrong but suspect
this is the casewhich is why i think its better probably to  
truncate (not to ala/gly, but to truncate) them if
you don't see the density for the side chain at all. OR model the 5  
most like conformers then - or 4 - 6 ? 3?


well, this can go on forever --or rather hopefully NOT, but really i  
don't think this quite so simple as what comes to
B-factors and later analysis ---in particular if that will be in  
anyway automated and will deal with say a larger set of
coordinate files. is it really a good idea to leave an active site  
residue side chain with high B (=no density what so ever)

in, in _one_ defined conformation? i am not so dead certain...

cheers,
Tommi


On Apr 3, 2011, at 9:01 PM, Boaz Shaanan wrote:

The original posting that started this thread referred to side- 
chains, as the subject still suggests. Do you propose to omit only  
side-chain atoms, in which case you end up with different residues,  
as pointed out by quite a few people,or do you suggest also to omit  
the main-chain atoms of the problematic residues ?


Besides, as mentioned by Phoebe and others, many users (non- 
crystallographers) of PDB's know already  the meaning of the B- 
factor and will know how to interpret a very high B. It is our task  
(the crystallographers) to enllighten those who don't know what the  
B column in a PDB entry stands for. I certainly do and I'm sure many  
of us do so too. I voted for high B and would vote for it again, if  
asked.


   Cheers,

  Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of  
Bernhard Rupp (Hofkristallrat a.D.) [hofkristall...@gmail.com]

Sent: Sunday, April 03, 2011 7:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] what to do with disordered side chains

Thus my feeling is that if one does NOT see the coords in the electron
density, they should NOT be included, and let someone else try to  
model

them in, but they should be aware that they are modeling them.
Joel L. Sussman

Concur.  BMC p 680 ‘How to handle missing parts’

Best wishes, BR

On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:

Doing something sensible in the major software packages, both
for graphics and for other analysis of the structure, could
solve the problem for most users.

But nobody knows what other software is out there being used by
individuals or small groups.  And the more remote the authors
of that software are from protein structure solution the more
likely it is that they have not/will not properly handle atoms
with zero occupancy or high B values, for example.

I am absolutely positive that there is software that does its
voodoo on ATOM/HETATM records and pays absolutely no attention
to anything beyond the x, y, z coordinates (i.e. beyond column 54).

  Frances Bernstein

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
*   ***  f...@bernstein-plus-sons.com

*** *
*   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Sat, 2 Apr 2011, Jacob Keller wrote:

I guess I missed it in the flurry of replies to this thread over the
last few days, but what exactly is so terrible about keeping the atoms
(since you have chemical evidence from protein sequence that they are
there, and even if there is X-ray damage they were originally there  
and

are likely still there in a subset of the molecules), but changing
occupancy to zero as an acknowledgment that your data does not provide
evidence to support a specific atomic position for these atoms?

Some users might pull up the structure, see those atoms, and think
their positions were based on data, which they were not, and then draw
conclusions based on them. I agree that occ=0 is tantamount to the
suggestion y

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

[Ethan Merritt]

On Sunday, April 03, 2011, Jacob Keller wrote:
> To the delete-the-atom-nik's: do you propose deleting the whole
> residue or just the side chain? 

Omit the atoms beyond CB for which there is no apparent density.
Always place CB if the backbone trace is reasonable, because its
location is fixed a priori by known stereochemistry.
As a practical matter, I use Coot's "stub" command.

Ethan



> I can understand deleting the whole
> residue, but deleting only the side chain seems to me to be placing a
> stumbling block also, and even possibly confusing for an experienced
> crystallographer: the .pdb says "lys" but it looks like an ala? Which
> is it? I could imagine a lot of frustration-hours arising from this
> practice, with people cross-checking sequences, looking in the methods
> sections for mutations...
> 
> JPK
> 
> On Sun, Apr 3, 2011 at 11:42 AM, Bernhard Rupp (Hofkristallrat a.D.)
>  wrote:
> > Thus my feeling is that if one does NOT see the coords in the electron
> >
> > density, they should NOT be included, and let someone else try to model
> >
> > them in, but they should be aware that they are modeling them.
> >
> > Joel L. Sussman
> >
> >
> >
> > Concur.  BMC p 680 ‘How to handle missing parts’
> >
> >
> >
> > Best wishes, BR
> >
> >
> >
> > On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:
> >
> >
> >
> > Doing something sensible in the major software packages, both
> > for graphics and for other analysis of the structure, could
> > solve the problem for most users.
> >
> > But nobody knows what other software is out there being used by
> > individuals or small groups.  And the more remote the authors
> > of that software are from protein structure solution the more
> > likely it is that they have not/will not properly handle atoms
> > with zero occupancy or high B values, for example.
> >
> > I am absolutely positive that there is software that does its
> > voodoo on ATOM/HETATM records and pays absolutely no attention
> > to anything beyond the x, y, z coordinates (i.e. beyond column 54).
> >
> >Frances Bernstein
> >
> > =
> > Bernstein + Sons
> > *   *   Information Systems Consultants
> > 5 Brewster Lane, Bellport, NY 11713-2803
> > *   * ***
> >  *Frances C. Bernstein
> >  *   ***  f...@bernstein-plus-sons.com
> > *** *
> >  *   *** 1-631-286-1339FAX: 1-631-286-1999
> > =
> >
> > On Sat, 2 Apr 2011, Jacob Keller wrote:
> >
> > I guess I missed it in the flurry of replies to this thread over the
> >
> > last few days, but what exactly is so terrible about keeping the atoms
> >
> > (since you have chemical evidence from protein sequence that they are
> >
> > there, and even if there is X-ray damage they were originally there and
> >
> > are likely still there in a subset of the molecules), but changing
> >
> > occupancy to zero as an acknowledgment that your data does not provide
> >
> > evidence to support a specific atomic position for these atoms?
> >
> >
> >
> > Some users might pull up the structure, see those atoms, and think
> >
> > their positions were based on data, which they were not, and then draw
> >
> > conclusions based on them. I agree that occ=0 is tantamount to the
> >
> > suggestion you queried, however.
> >
> >
> >
> > A somewhat key question might be: across the various molecular
> >
> > visualization programs, what is the default way to handle atoms with
> >
> > occ=0? Perhaps those programs might be the best place to fix the
> >
> > problem...
> >
> >
> >
> > JPK
> >
> >
> >
> >
> >
> > ***
> >
> > 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

[Jacob Keller]

To the delete-the-atom-nik's: do you propose deleting the whole
residue or just the side chain? I can understand deleting the whole
residue, but deleting only the side chain seems to me to be placing a
stumbling block also, and even possibly confusing for an experienced
crystallographer: the .pdb says "lys" but it looks like an ala? Which
is it? I could imagine a lot of frustration-hours arising from this
practice, with people cross-checking sequences, looking in the methods
sections for mutations...

JPK

On Sun, Apr 3, 2011 at 11:42 AM, Bernhard Rupp (Hofkristallrat a.D.)
 wrote:
> Thus my feeling is that if one does NOT see the coords in the electron
>
> density, they should NOT be included, and let someone else try to model
>
> them in, but they should be aware that they are modeling them.
>
> Joel L. Sussman
>
>
>
> Concur.  BMC p 680 ‘How to handle missing parts’
>
>
>
> Best wishes, BR
>
>
>
> On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:
>
>
>
> Doing something sensible in the major software packages, both
> for graphics and for other analysis of the structure, could
> solve the problem for most users.
>
> But nobody knows what other software is out there being used by
> individuals or small groups.  And the more remote the authors
> of that software are from protein structure solution the more
> likely it is that they have not/will not properly handle atoms
> with zero occupancy or high B values, for example.
>
> I am absolutely positive that there is software that does its
> voodoo on ATOM/HETATM records and pays absolutely no attention
> to anything beyond the x, y, z coordinates (i.e. beyond column 54).
>
>    Frances Bernstein
>
> =
>     Bernstein + Sons
> *   *   Information Systems Consultants
>     5 Brewster Lane, Bellport, NY 11713-2803
> *   * ***
>  *    Frances C. Bernstein
>  *   ***  f...@bernstein-plus-sons.com
> *** *
>  *   *** 1-631-286-1339    FAX: 1-631-286-1999
> =
>
> On Sat, 2 Apr 2011, Jacob Keller wrote:
>
> I guess I missed it in the flurry of replies to this thread over the
>
> last few days, but what exactly is so terrible about keeping the atoms
>
> (since you have chemical evidence from protein sequence that they are
>
> there, and even if there is X-ray damage they were originally there and
>
> are likely still there in a subset of the molecules), but changing
>
> occupancy to zero as an acknowledgment that your data does not provide
>
> evidence to support a specific atomic position for these atoms?
>
>
>
> Some users might pull up the structure, see those atoms, and think
>
> their positions were based on data, which they were not, and then draw
>
> conclusions based on them. I agree that occ=0 is tantamount to the
>
> suggestion you queried, however.
>
>
>
> A somewhat key question might be: across the various molecular
>
> visualization programs, what is the default way to handle atoms with
>
> occ=0? Perhaps those programs might be the best place to fix the
>
> problem...
>
>
>
> JPK
>
>
>
>
>
> ***
>
> Jacob Pearson Keller
>
> Northwestern University
>
> Medical Scientist Training Program
>
> cel: 773.608.9185
>
> email: j-kell...@northwestern.edu
>
> ***
>
>
>
>



-- 
***
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

[Boaz Shaanan]

The original posting that started this thread referred to side-chains, as the 
subject still suggests. Do you propose to omit only side-chain atoms, in which 
case you end up with different residues, as pointed out by quite a few 
people,or do you suggest also to omit the main-chain atoms of the problematic 
residues ?

Besides, as mentioned by Phoebe and others, many users (non-crystallographers) 
of PDB's know already  the meaning of the B-factor and will know how to 
interpret a very high B. It is our task (the crystallographers) to enllighten 
those who don't know what the B column in a PDB entry stands for. I certainly 
do and I'm sure many of us do so too. I voted for high B and would vote for it 
again, if asked.

Cheers,

   Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp 
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Sent: Sunday, April 03, 2011 7:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] what to do with disordered side chains

Thus my feeling is that if one does NOT see the coords in the electron
density, they should NOT be included, and let someone else try to model
them in, but they should be aware that they are modeling them.
Joel L. Sussman

Concur.  BMC p 680 ‘How to handle missing parts’

Best wishes, BR

On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:

Doing something sensible in the major software packages, both
for graphics and for other analysis of the structure, could
solve the problem for most users.

But nobody knows what other software is out there being used by
individuals or small groups.  And the more remote the authors
of that software are from protein structure solution the more
likely it is that they have not/will not properly handle atoms
with zero occupancy or high B values, for example.

I am absolutely positive that there is software that does its
voodoo on ATOM/HETATM records and pays absolutely no attention
to anything beyond the x, y, z coordinates (i.e. beyond column 54).

   Frances Bernstein

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
 *   ***  f...@bernstein-plus-sons.com
*** *
 *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Sat, 2 Apr 2011, Jacob Keller wrote:

I guess I missed it in the flurry of replies to this thread over the
last few days, but what exactly is so terrible about keeping the atoms
(since you have chemical evidence from protein sequence that they are
there, and even if there is X-ray damage they were originally there and
are likely still there in a subset of the molecules), but changing
occupancy to zero as an acknowledgment that your data does not provide
evidence to support a specific atomic position for these atoms?

Some users might pull up the structure, see those atoms, and think
their positions were based on data, which they were not, and then draw
conclusions based on them. I agree that occ=0 is tantamount to the
suggestion you queried, however.

A somewhat key question might be: across the various molecular
visualization programs, what is the default way to handle atoms with
occ=0? Perhaps those programs might be the best place to fix the
problem...

JPK


***
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

[Bernhard Rupp (Hofkristallrat a.D.)]

Thus my feeling is that if one does NOT see the coords in the electron

density, they should NOT be included, and let someone else try to model 

them in, but they should be aware that they are modeling them.

Joel L. Sussman

 

Concur.  BMC p 680 'How to handle missing parts'

 

Best wishes, BR

 

On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:

 

Doing something sensible in the major software packages, both
for graphics and for other analysis of the structure, could
solve the problem for most users.

But nobody knows what other software is out there being used by
individuals or small groups.  And the more remote the authors
of that software are from protein structure solution the more
likely it is that they have not/will not properly handle atoms
with zero occupancy or high B values, for example.

I am absolutely positive that there is software that does its
voodoo on ATOM/HETATM records and pays absolutely no attention
to anything beyond the x, y, z coordinates (i.e. beyond column 54).

   Frances Bernstein

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
 *   ***  f...@bernstein-plus-sons.com
*** *
 *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Sat, 2 Apr 2011, Jacob Keller wrote:



I guess I missed it in the flurry of replies to this thread over the

last few days, but what exactly is so terrible about keeping the atoms

(since you have chemical evidence from protein sequence that they are

there, and even if there is X-ray damage they were originally there and

are likely still there in a subset of the molecules), but changing

occupancy to zero as an acknowledgment that your data does not provide

evidence to support a specific atomic position for these atoms?

 

Some users might pull up the structure, see those atoms, and think

their positions were based on data, which they were not, and then draw

conclusions based on them. I agree that occ=0 is tantamount to the

suggestion you queried, however.

 

A somewhat key question might be: across the various molecular

visualization programs, what is the default way to handle atoms with

occ=0? Perhaps those programs might be the best place to fix the

problem...

 

JPK

 

 

***

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

[Quyen Hoang]

If these users exist (I don't doubt that they do), then they would also might 
think that lysine residues sometimes look identical to alanine - if the atoms 
after beta carbon of the lysine are deleted in the PDB due to lack of density.

So, I guess, if one's objectives in solving structures are to provide these 
users with coordinates that they could us, then it would make more sense to me 
to find out what one's "customers" want, rather than speculating about it. Or 
at least, train one's "customers" how to use one's products - I believe that's 
what people in business do.

However, I think that many people solve structures for their own consumption - 
they are their own customers - therefore, it's really up to them to cook it 
anyway they find most tasteful. Others can agree or disagree, but we know that 
not everybody has the same taste.

Cheers,
Quyen


On Apr 3, 2011, at 12:54 AM, Prof. Joel L. Sussman wrote:

> I think Frances is right, i.e. most non crystallographers ignore 
> "anything beyond the x, y, z coordinates (i.e. beyond column 54)"
> [as Frances wrote]. 
> Thus if a crystallographer put in coords that he/she does NOT see,
> even with OCC=0, or an enormously large Bfactor, these coords are usually 
> treated in just the same way that experimentally observed coords are treated. 
> Thus my feeling is that if one does NOT see the coords in the electron
> density, they should NOT be included, and let someone else try to model 
> them in, but they should be aware that they are modeling them.
> Joel L. Sussman
> 
> 
> 
> On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote:
> 
>> Doing something sensible in the major software packages, both
>> for graphics and for other analysis of the structure, could
>> solve the problem for most users.
>> 
>> But nobody knows what other software is out there being used by
>> individuals or small groups.  And the more remote the authors
>> of that software are from protein structure solution the more
>> likely it is that they have not/will not properly handle atoms
>> with zero occupancy or high B values, for example.
>> 
>> I am absolutely positive that there is software that does its
>> voodoo on ATOM/HETATM records and pays absolutely no attention
>> to anything beyond the x, y, z coordinates (i.e. beyond column 54).
>> 
>>Frances Bernstein
>> 
>> =
>> Bernstein + Sons
>> *   *   Information Systems Consultants
>> 5 Brewster Lane, Bellport, NY 11713-2803
>> *   * ***
>>  *Frances C. Bernstein
>>  *   ***  f...@bernstein-plus-sons.com
>> *** *
>>  *   *** 1-631-286-1339FAX: 1-631-286-1999
>> =
>> 
>> On Sat, 2 Apr 2011, Jacob Keller wrote:
>> 
 I guess I missed it in the flurry of replies to this thread over the
 last few days, but what exactly is so terrible about keeping the atoms
 (since you have chemical evidence from protein sequence that they are
 there, and even if there is X-ray damage they were originally there and
 are likely still there in a subset of the molecules), but changing
 occupancy to zero as an acknowledgment that your data does not provide
 evidence to support a specific atomic position for these atoms?
>>> 
>>> Some users might pull up the structure, see those atoms, and think
>>> their positions were based on data, which they were not, and then draw
>>> conclusions based on them. I agree that occ=0 is tantamount to the
>>> suggestion you queried, however.
>>> 
>>> A somewhat key question might be: across the various molecular
>>> visualization programs, what is the default way to handle atoms with
>>> occ=0? Perhaps those programs might be the best place to fix the
>>> problem...
>>> 
>>> JPK
>>> 
>>> 
>>> ***
>>> Jacob Pearson Keller
>>> Northwestern University
>>> Medical Scientist Training Program
>>> cel: 773.608.9185
>>> email: j-kell...@northwestern.edu
>>> ***
>>> 
> 

[ccp4bb] Call for paper

[Dr. Imtiyaz Hassan]

Dear colleagues,

 

The Centre for Interdisciplinary Research
in Basic Sciences, Jamia Millia Islamia is organising the International
Interdisciplinary Science Conference 2011, on “Bioinformatics: An Interface
between Computer Science and Biology".
The Conference will be held during November 15-17, 2011 in the University
premises. The purpose of this conference is to provide an opportunity to
Ph. D. scholars and M. Sc. students of both basic sciences and life sciences to
listen to and interact with established researcher s (Bioinformatists, System
Biologists, Microbiologists, Immunologists, Molecular Biologists and Clinicians)
who are making use of computer science in understanding biological problems. In
addition to this, they will also have an opportunity to meet representatives
and policy makers from the pharmaceutical and biotechnological industries. Your
research scholars and M. Sc. students are encouraged to send their abstracts
for poster presentation. Some of the accepted posters will be selected for oral
presentation.  

For
details about registration and abstract submission in the I-ISC2011, please
visit our website: http://www.i-isc.com/


With warm regards,


 

Yours
sincerely,







Dr. M. I. Hassan

Organizing Secretary

I-ISC-2011
E-mail: mihas...@jmi.ac.in

=Md. Imtiyaz Hassan, Ph.D. 
Assistant Professor (Biophysics)
Centre for Interdisciplinary Research In Basic Saciences 
Jamia Millia Islamia 
New Delhi 10025, INDIA 
TeleFax: +91 11 26983409 
Mob-9311323414 & 9990323217
E-mail: mihas...@jmi.ac.in
http://www.jmi.nic.in/cirbs/cirbs.htm

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

[John R Helliwell]

Dear Ed,
Many thanks for this careful explanation, which I appreciate.

I realise in my own practise on such matters I have two situations :-

(i) where, albeit limited, electron density evidence, coupled with
chemical evidence, leads to an attempted model atomic fit but the B
factors there sky rocket.

(ii) there is no electron density evidence and even though the
chemical evidence is sound one can in fact add nothing. Here I simply
concede that there is nothing one can do. The issue here is not
whether to keep these atoms but simply you really cannot make a start
finding them.

Greetings,
John


On Fri, Apr 1, 2011 at 4:03 PM, Ed Pozharski  wrote:
> Dear John,
>
> there may be reasons to disagree with both options.  This has been a
> recurring discussion for many years, and in my mind the most convincing
> arguments for both sides are as follows:
>
> "Keepers":
>
> I know the side chain is there and the high ADP is a good approximation
> of reality.  Removing atoms causes such a mess for the end user.
>
> "Deleters":
>
> We don't model missing loops, termini, ligands and waters when there is
> no density, and side chains should not be treated differently.  Most end
> users think ADP is a nucleotide and will over-interpret the model.
>
> I am a "keeper" when it comes to end user treatment, but a recently
> converted "deleter" when it comes to modeling (a rather stressful
> position).  So I am not taking sides really, but rather looking for a
> middle way. (Have to admit that my secret goal was to knock down the
> zero occupancy fallacy :)
>
> Perhaps these ideas are worth exploring:
>
> 1.  Provide dual representation - a crystallographic model and an
> end-user model, both downloadable from the PDB.
> 2.  Model missing side chains "NMR-way"
> 3.  A new data file format is needed (mmCIF?) that combines atomic model
> with electron density, and visualization/analysis software shall be
> modified to always utilize the experimental data
> 4.  Implement reduced ADP restraints for disordered side chains to
> further reduce model bias
>
> But ultimately, as long as experimental data is deposited, I believe
> that people are free to interpret their data the way they see fit.
> Others are then free to look at the electron density and become outraged
> at the interpretation.
>
> Cheers,
>
> Ed.
>
> On Thu, 2011-03-31 at 23:25 +0100, Jrh wrote:
>> Dear Ed,
>> Thankyou for this and apologies for late reply.
>> If one has chemical evidence for the presence of residues but these
>> residues are disordered I find the delete atoms option disagreeable.
>> Such a static disorder situation should be described by a high atomic
>> displacement parameter, in my view. (nb the use of ADP is better than
>> B factor terminology).
>> Yours sincerely,
>> John
>> Prof John R Helliwell DSc
>>
>
> --
> "I'd jump in myself, if I weren't so good at whistling."
>                               Julian, King of Lemurs
>
>



-- 
Professor John R Helliwell DSc