Re: [ccp4bb] "resolution" on PDB web page

[Jan Dohnalek]

There have been other manipulations with user-input values. We could not
input solvent content 83% for 3cg8 (the real value!!!) as "being out of the
allowed range".
The resulting value in the PDB is "NULL" not showing the actually
interesting feature of the structure.

I also noticed that the reported resolution values are nonsensically
advertised with three decimal positions after the point which is not the
way we would put it, is it?

Either fight it or live with it ...

Jan Dohnalek




On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice  wrote:

> I just noticed that the PDB has changed the stated resolution for one of
> my old structures!  It was refined against a very anisotropic data set that
> extended to 2.2 in the best direction only.  When depositing I called the
> resolution 2.5 as a rough average of resolution in all 3 directions, but
> now PDB is advertising it as 2.2, which is misleading.
>
> I'm afraid I may not have paid enough attention to the fine print on this
> issue - is the PDB now automatically advertising the "resolution" of a
> structure as that of the outermost flyspeck used in refinement, regardless
> of more cautious assertions by the authors?  If so, I object!
>
> =
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
>
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>



-- 
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

Re: [ccp4bb] "resolution" on PDB web page

[Mark J van Raaij]

Phoebe, Jan, PDB,
is this something particular to the US portal of the PDB, or general?
We always use the European portal pdbe and have not had such "problems".
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



On 25 Apr 2012, at 09:41, Jan Dohnalek wrote:

> There have been other manipulations with user-input values. We could not 
> input solvent content 83% for 3cg8 (the real value!!!) as "being out of the 
> allowed range".
> The resulting value in the PDB is "NULL" not showing the actually interesting 
> feature of the structure.
> 
> I also noticed that the reported resolution values are nonsensically 
> advertised with three decimal positions after the point which is not the way 
> we would put it, is it?
> 
> Either fight it or live with it ...
> 
> Jan Dohnalek
> 
> 
> 
> 
> On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice  wrote:
> I just noticed that the PDB has changed the stated resolution for one of my 
> old structures!  It was refined against a very anisotropic data set that 
> extended to 2.2 in the best direction only.  When depositing I called the 
> resolution 2.5 as a rough average of resolution in all 3 directions, but now 
> PDB is advertising it as 2.2, which is misleading.
> 
> I'm afraid I may not have paid enough attention to the fine print on this 
> issue - is the PDB now automatically advertising the "resolution" of a 
> structure as that of the outermost flyspeck used in refinement, regardless of 
> more cautious assertions by the authors?  If so, I object!
> 
> =
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> http://www.rsc.org/shop/books/2008/9780854042722.asp
> 
> 
> 
> -- 
> Jan Dohnalek, Ph.D
> Institute of Macromolecular Chemistry
> Academy of Sciences of the Czech Republic
> Heyrovskeho nam. 2
> 16206 Praha 6
> Czech Republic
> 
> Tel: +420 296 809 340
> Fax: +420 296 809 410

[ccp4bb] REMINDER *CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC*

[David Flot]

*CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC*

Proposal Deadline **1st May 2012**


There will be beam time available at the ESRF for MX data collectionwith 
a setup that allows online monitoring of UV/VIS absorbance 
orfluorescence spectral changes of the crystal during the 
X-raydiffraction experiment. Users who are interested in using this beam 
time(including those who are members of BAG Groups) should use the 
followingmechanism:_http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal_and 
*it must be clearly indicated in the title of the proposal form 
that**the online monitoring of spectral changes is necessary for the 
project*. A brief description of the device is given below however users 
areencouraged to consult the web pages for detailed 
information:_http://www.esrf.fr/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/Run_Your_Experiment/Microspectrophotometer_User_Guide_The 
device is also described in: McGeehan, J., Ravelli, R.B., Murray,J.W., 
Owen, R.L., Cipriani, F., McSweeney, S., Weik, M. and Garman, E.F.(2009) 
Colouring cryo-cooled crystals: online microspectrophotometry. 
JSynchrotron Radiat., 16, 163-172.


As this is not a standard set-up, it might take a significant amount 
oftime to train users, align the device, and analyze the data in order 
toderive relevant data collection schemes. *We will therefore schedule 
24**hours for each project*. The *deadline *for this specific 
application is*Tuesday 1st**May 2012*.


It is strongly recommended to, beforehand, record an 
absorption(fluorescence) spectrum of the crystal on a home 
microspectrophotometersuch as the 4dx one, or at an off-line facility 
such as the ESRFCryobench, and to provide it in the application form. 
Such a spectrumwould greatly help to determine the feasibility of the 
experiment. Foroptimal experimental conditions, crystals should be 
frozen in minimalamounts of cryosolution, especially when the crystals 
are small.Finally, please note that *the ESRF sample changer cannot be 
operated at**the same time as the on-line microspec*.The use of specific 
LASER is possible if the device is compliant withthe beam line safety 
system (interlock on device power).



Dates of beam-time: *13th June - 17th June 2012*
Storage Ring: Uniform (200mA)
Beamline: ID14-1
Energy: 13.27 keV (not tunable)


Specifications:
UV/VIS-range: 250-1100 nm
Light source: Mikropack DH-2000-BAL (Deuterium/Halogen)
Fluorescence/Actinic excitation wavelength: 405, 440, 473, 532, 561, 671 nm
ODmax for UV-vis absorbance spectra: 2-2.5
Monitoring light size: 0.03 (min) - 0.15mm(max)
Sampling freq (to disk): 10Hz or lower





--


Dr David FLOT
Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63
Structural Biology GroupFax : (+33) 4 76 88 26 24
ESRF
B.P. 220, 6 rue Jules Horowitz  e-mail :david.f...@esrf.fr
F-38043 GRENOBLE CEDEX  http://www.esrf.eu

Re: [ccp4bb] "resolution" on PDB web page

[Jan Dohnalek]

We indeed used the US portal for deposition which may be "the difference".
Nevertheless the recent reported resolution values etc. are projected also
to the PDBe portal.

Jan


On Wed, Apr 25, 2012 at 10:10 AM, Mark J van Raaij
wrote:

> Phoebe, Jan, PDB,
> is this something particular to the US portal of the PDB, or general?
> We always use the European portal pdbe and have not had such "problems".
> Mark
> Mark J van Raaij
> Laboratorio M-4
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.cnb.csic.es/~mjvanraaij
>
>
>
> On 25 Apr 2012, at 09:41, Jan Dohnalek wrote:
>
> > There have been other manipulations with user-input values. We could not
> input solvent content 83% for 3cg8 (the real value!!!) as "being out of the
> allowed range".
> > The resulting value in the PDB is "NULL" not showing the actually
> interesting feature of the structure.
> >
> > I also noticed that the reported resolution values are nonsensically
> advertised with three decimal positions after the point which is not the
> way we would put it, is it?
> >
> > Either fight it or live with it ...
> >
> > Jan Dohnalek
> >
> >
> >
> >
> > On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice 
> wrote:
> > I just noticed that the PDB has changed the stated resolution for one of
> my old structures!  It was refined against a very anisotropic data set that
> extended to 2.2 in the best direction only.  When depositing I called the
> resolution 2.5 as a rough average of resolution in all 3 directions, but
> now PDB is advertising it as 2.2, which is misleading.
> >
> > I'm afraid I may not have paid enough attention to the fine print on
> this issue - is the PDB now automatically advertising the "resolution" of a
> structure as that of the outermost flyspeck used in refinement, regardless
> of more cautious assertions by the authors?  If so, I object!
> >
> > =
> > Phoebe A. Rice
> > Dept. of Biochemistry & Molecular Biology
> > The University of Chicago
> > phone 773 834 1723
> >
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> > http://www.rsc.org/shop/books/2008/9780854042722.asp
> >
> >
> >
> > --
> > Jan Dohnalek, Ph.D
> > Institute of Macromolecular Chemistry
> > Academy of Sciences of the Czech Republic
> > Heyrovskeho nam. 2
> > 16206 Praha 6
> > Czech Republic
> >
> > Tel: +420 296 809 340
> > Fax: +420 296 809 410
>
>


-- 
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

Re: [ccp4bb] "resolution" on PDB web page

[Edward A. Berry]

We also use the US portal. Can't speak to the solvent content as we never
had a value much over 70%.

As for the resolution range, I never saw any place to enter this
user-defined resolution of the structure.
As far as i know it comes from the record:
REMARK 200  RESOLUTION RANGE HIGH  (A) : 1.200
which should be the high resolution used in refinement.

I suppose in an "additional remark" you could give the
optical resolution or the resolution of 90% complete at I/sig=2.
Or the title could be "The 2.2A resolution structure of protein x",
never mind that there were a few reflections used at 1.7A.
eab

Mark J van Raaij wrote:

Phoebe, Jan, PDB,
is this something particular to the US portal of the PDB, or general?
We always use the European portal pdbe and have not had such "problems".
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



On 25 Apr 2012, at 09:41, Jan Dohnalek wrote:


There have been other manipulations with user-input values. We could not input solvent 
content 83% for 3cg8 (the real value!!!) as "being out of the allowed range".
The resulting value in the PDB is "NULL" not showing the actually interesting 
feature of the structure.

I also noticed that the reported resolution values are nonsensically advertised 
with three decimal positions after the point which is not the way we would put 
it, is it?

Either fight it or live with it ...

Jan Dohnalek




On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice  wrote:
I just noticed that the PDB has changed the stated resolution for one of my old 
structures!  It was refined against a very anisotropic data set that extended 
to 2.2 in the best direction only.  When depositing I called the resolution 2.5 
as a rough average of resolution in all 3 directions, but now PDB is 
advertising it as 2.2, which is misleading.

I'm afraid I may not have paid enough attention to the fine print on this issue - is the 
PDB now automatically advertising the "resolution" of a structure as that of 
the outermost flyspeck used in refinement, regardless of more cautious assertions by the 
authors?  If so, I object!

=
Phoebe A. Rice
Dept. of Biochemistry&  Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp



--
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

Re: [ccp4bb] "resolution" on PDB web page

[Mike Sleutel]

Curious that 83% solvent content would be out of range; A quick search in
the pdb indicates that there are 43 entries with solvent content >85% ...

Op 25 april 2012 09:41 schreef Jan Dohnalek  het
volgende:

> There have been other manipulations with user-input values. We could not
> input solvent content 83% for 3cg8 (the real value!!!) as "being out of the
> allowed range".
> The resulting value in the PDB is "NULL" not showing the actually
> interesting feature of the structure.
>
> I also noticed that the reported resolution values are nonsensically
> advertised with three decimal positions after the point which is not the
> way we would put it, is it?
>
> Either fight it or live with it ...
>
> Jan Dohnalek
>
> --
>
>
> Vrije Universiteit Brussel (VUB)
> Vlaams Interuniversitair Instituut voor Biotechnologie (VIB)
> Instituut Moleculaire Biologie & Biotechnologie (IMOL)
> Ultrastructuur (ULTR)
> Oefenplein, Gebouw E (4.16)
> Pleinlaan 2, 1050 Brussel
> e-mail: msleu...@vub.ac.be
> Tel:  ++32-(0)2-629-1923
> Fax: ++32-(0)2-629-1963
>
>
>
>

Re: [ccp4bb] "resolution" on PDB web page

[Miller, Mitchell D.]

I too believe that the value is set from the
high resolution limit form data collection or refinement.
All three numbers (high resolution limit in remark 2, remark 3 
and Remark 200) are supposed to be consistent and are
defined as the highest resolution reflection used.
http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_reflns.d_resolution_high.html
http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html

 Looking at the PDB specification, it shows that there is an option 
to add a free text comment to the remark 2 resolution --
"Additional explanatory text may be included starting with the third line of 
the REMARK 2 record. For example, depositors may wish to qualify the resolution 
value provided due to unusual experimental conditions."
http://www.wwpdb.org/documentation/format33/remarks1.html 

  We have not done this, but we have in a number of cases 
qualified the resolution by using a lower resolution in the 
title of the entry and further detailing this "nominal"
resolution in the remark 3 other refinement remarks. E.g. see
http://www.rcsb.org/pdb/explore/explore.do?structureId=1vr0 
http://www.rcsb.org/pdb/explore/explore.do?structureId=1vkk 

Regards,
Mitch

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. 
Berry
Sent: Wednesday, April 25, 2012 6:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] "resolution" on PDB web page

We also use the US portal. Can't speak to the solvent content as we never
had a value much over 70%.

As for the resolution range, I never saw any place to enter this
user-defined resolution of the structure.
As far as i know it comes from the record:
REMARK 200  RESOLUTION RANGE HIGH  (A) : 1.200
which should be the high resolution used in refinement.

I suppose in an "additional remark" you could give the
optical resolution or the resolution of 90% complete at I/sig=2.
Or the title could be "The 2.2A resolution structure of protein x",
never mind that there were a few reflections used at 1.7A.
eab

Mark J van Raaij wrote:
> Phoebe, Jan, PDB,
> is this something particular to the US portal of the PDB, or general?
> We always use the European portal pdbe and have not had such "problems".
> Mark
> Mark J van Raaij
> Laboratorio M-4
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.cnb.csic.es/~mjvanraaij
>
>
>
> On 25 Apr 2012, at 09:41, Jan Dohnalek wrote:
>
>> There have been other manipulations with user-input values. We could not 
>> input solvent content 83% for 3cg8 (the real value!!!) as "being out of the 
>> allowed range".
>> The resulting value in the PDB is "NULL" not showing the actually 
>> interesting feature of the structure.
>>
>> I also noticed that the reported resolution values are nonsensically 
>> advertised with three decimal positions after the point which is not the way 
>> we would put it, is it?
>>
>> Either fight it or live with it ...
>>
>> Jan Dohnalek
>>
>>
>>
>>
>> On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice  wrote:
>> I just noticed that the PDB has changed the stated resolution for one of my 
>> old structures!  It was refined against a very anisotropic data set that 
>> extended to 2.2 in the best direction only.  When depositing I called the 
>> resolution 2.5 as a rough average of resolution in all 3 directions, but now 
>> PDB is advertising it as 2.2, which is misleading.
>>
>> I'm afraid I may not have paid enough attention to the fine print on this 
>> issue - is the PDB now automatically advertising the "resolution" of a 
>> structure as that of the outermost flyspeck used in refinement, regardless 
>> of more cautious assertions by the authors?  If so, I object!
>>
>> =
>> Phoebe A. Rice
>> Dept. of Biochemistry&  Molecular Biology
>> The University of Chicago
>> phone 773 834 1723
>> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>> http://www.rsc.org/shop/books/2008/9780854042722.asp
>>
>>
>>
>> --
>> Jan Dohnalek, Ph.D
>> Institute of Macromolecular Chemistry
>> Academy of Sciences of the Czech Republic
>> Heyrovskeho nam. 2
>> 16206 Praha 6
>> Czech Republic
>>
>> Tel: +420 296 809 340
>> Fax: +420 296 809 410
>

Re: [ccp4bb] "resolution" on PDB web page

[Edward A. Berry]

My apologies, I guess there is a separate entry for resolution,
and in my depositions it gets filled from the remark 200 records
from CNS xtal_pdb_submission and I never thought to change it.
I guess now the PDB is enforcing the requirement that it
should be "the highest resolution used" and hence the same
as remark 200 and hence redundant.

I guess if you want to qualify the resolution on line 3 of
remark 2 you need to ask the annotator to do it for you.
(We have some structures that really should be qualified.)

Miller, Mitchell D. wrote:

I too believe that the value is set from the
high resolution limit form data collection or refinement.
All three numbers (high resolution limit in remark 2, remark 3
and Remark 200) are supposed to be consistent and are
defined as the highest resolution reflection used.
http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_reflns.d_resolution_high.html
http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html

  Looking at the PDB specification, it shows that there is an option
to add a free text comment to the remark 2 resolution --
"Additional explanatory text may be included starting with the third line of the 
REMARK 2 record. For example, depositors may wish to qualify the resolution value 
provided due to unusual experimental conditions."
http://www.wwpdb.org/documentation/format33/remarks1.html

   We have not done this, but we have in a number of cases
qualified the resolution by using a lower resolution in the
title of the entry and further detailing this "nominal"
resolution in the remark 3 other refinement remarks. E.g. see
http://www.rcsb.org/pdb/explore/explore.do?structureId=1vr0
http://www.rcsb.org/pdb/explore/explore.do?structureId=1vkk 

Regards,
Mitch

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. 
Berry
Sent: Wednesday, April 25, 2012 6:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] "resolution" on PDB web page

We also use the US portal. Can't speak to the solvent content as we never
had a value much over 70%.

As for the resolution range, I never saw any place to enter this
user-defined resolution of the structure.
As far as i know it comes from the record:
REMARK 200  RESOLUTION RANGE HIGH  (A) : 1.200
which should be the high resolution used in refinement.

I suppose in an "additional remark" you could give the
optical resolution or the resolution of 90% complete at I/sig=2.
Or the title could be "The 2.2A resolution structure of protein x",
never mind that there were a few reflections used at 1.7A.
eab

Mark J van Raaij wrote:

Phoebe, Jan, PDB,
is this something particular to the US portal of the PDB, or general?
We always use the European portal pdbe and have not had such "problems".
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



On 25 Apr 2012, at 09:41, Jan Dohnalek wrote:


There have been other manipulations with user-input values. We could not input solvent 
content 83% for 3cg8 (the real value!!!) as "being out of the allowed range".
The resulting value in the PDB is "NULL" not showing the actually interesting 
feature of the structure.

I also noticed that the reported resolution values are nonsensically advertised 
with three decimal positions after the point which is not the way we would put 
it, is it?

Either fight it or live with it ...

Jan Dohnalek




On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice   wrote:
I just noticed that the PDB has changed the stated resolution for one of my old 
structures!  It was refined against a very anisotropic data set that extended 
to 2.2 in the best direction only.  When depositing I called the resolution 2.5 
as a rough average of resolution in all 3 directions, but now PDB is 
advertising it as 2.2, which is misleading.

I'm afraid I may not have paid enough attention to the fine print on this issue - is the 
PDB now automatically advertising the "resolution" of a structure as that of 
the outermost flyspeck used in refinement, regardless of more cautious assertions by the 
authors?  If so, I object!

=
Phoebe A. Rice
Dept. of Biochemistry&   Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp



--
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

Re: [ccp4bb] "resolution" on PDB web page

[Phoebe Rice]

What freaked me out is that REMARK 2 seems to have changed over time:  I have a 
version of 1ihf.pdb (deposited around 1995) that was apparently downloaded in 
1998, where remark 2 says 2.5, and a version downloaded yesterday where remark 
2 says 2.2.
The whole thing actually started because the newer file has some odd LINK 
records as well, which I've written to PDB about (my fault, sort of: I 
apparently modeled 2 close but alternate positions of the same Cd++ ion as two 
different ions with low occupancy. PDB has now put a LINK between them, which 
makes no chemical sense).

=
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp


 Original message 
>Date: Wed, 25 Apr 2012 11:08:52 -0400
>From: CCP4 bulletin board  (on behalf of "Edward A. 
>Berry" )
>Subject: Re: [ccp4bb] "resolution" on PDB web page  
>To: CCP4BB@JISCMAIL.AC.UK
>
>My apologies, I guess there is a separate entry for resolution,
>and in my depositions it gets filled from the remark 200 records
>from CNS xtal_pdb_submission and I never thought to change it.
>I guess now the PDB is enforcing the requirement that it
>should be "the highest resolution used" and hence the same
>as remark 200 and hence redundant.
>
>I guess if you want to qualify the resolution on line 3 of
>remark 2 you need to ask the annotator to do it for you.
>(We have some structures that really should be qualified.)
>
>Miller, Mitchell D. wrote:
>> I too believe that the value is set from the
>> high resolution limit form data collection or refinement.
>> All three numbers (high resolution limit in remark 2, remark 3
>> and Remark 200) are supposed to be consistent and are
>> defined as the highest resolution reflection used.
>> http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_reflns.d_resolution_high.html
>> http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html
>>
>>   Looking at the PDB specification, it shows that there is an option
>> to add a free text comment to the remark 2 resolution --
>> "Additional explanatory text may be included starting with the third line of 
>> the REMARK 2 record. For example, depositors may wish to qualify the 
>> resolution value provided due to unusual experimental conditions."
>> http://www.wwpdb.org/documentation/format33/remarks1.html
>>
>>We have not done this, but we have in a number of cases
>> qualified the resolution by using a lower resolution in the
>> title of the entry and further detailing this "nominal"
>> resolution in the remark 3 other refinement remarks. E.g. see
>> http://www.rcsb.org/pdb/explore/explore.do?structureId=1vr0
>> http://www.rcsb.org/pdb/explore/explore.do?structureId=1vkk  
>>
>> Regards,
>> Mitch
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward 
>> A. Berry
>> Sent: Wednesday, April 25, 2012 6:55 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] "resolution" on PDB web page
>>
>> We also use the US portal. Can't speak to the solvent content as we never
>> had a value much over 70%.
>>
>> As for the resolution range, I never saw any place to enter this
>> user-defined resolution of the structure.
>> As far as i know it comes from the record:
>> REMARK 200  RESOLUTION RANGE HIGH  (A) : 1.200
>> which should be the high resolution used in refinement.
>>
>> I suppose in an "additional remark" you could give the
>> optical resolution or the resolution of 90% complete at I/sig=2.
>> Or the title could be "The 2.2A resolution structure of protein x",
>> never mind that there were a few reflections used at 1.7A.
>> eab
>>
>> Mark J van Raaij wrote:
>>> Phoebe, Jan, PDB,
>>> is this something particular to the US portal of the PDB, or general?
>>> We always use the European portal pdbe and have not had such "problems".
>>> Mark
>>> Mark J van Raaij
>>> Laboratorio M-4
>>> Dpto de Estructura de Macromoleculas
>>> Centro Nacional de Biotecnologia - CSIC
>>> c/Darwin 3
>>> E-28049 Madrid, Spain
>>> tel. (+34) 91 585 4616
>>> http://www.cnb.csic.es/~mjvanraaij
>>>
>>>
>>>
>>> On 25 Apr 2012, at 09:41, Jan Dohnalek wrote:
>>>
 There have been other manipulations with user-input values. We could not 
 input solvent content 83% for 3cg8 (the real value!!!) as "being out of 
 the allowed range".
 The resulting value in the PDB is "NULL" not showing the actually 
 interesting feature of the structure.

 I also noticed that the reported resolution values are nonsensically 
 advertised with three decimal positions after the point which is not the 
 way we would put it, is it?

 Either fight it or live with it ...

 Jan Dohnalek




 On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice   

Re: [ccp4bb] "resolution" on PDB web page

[Frank von Delft]

Our policy is to request the pdb to update the stated resolution limit 
after the deposition's gone through.


That said, I suspect it did not happen for many of our structures, because:
1) it's not part of the deposition mechanism, i.e. easy to forget.
2) the various programs (especially integration & scaling) don't 
really make it obvious that anisotropic limits can be done and are a 
good idea.


The real problem is that we crystallographers have not come up with 
conventions to distinguish between "effective resolution" and "where are 
there still spots with signal" - instead we just conflate them into a 
single number.


phx.





On 25/04/2012 15:33, Miller, Mitchell D. wrote:

I too believe that the value is set from the
high resolution limit form data collection or refinement.
All three numbers (high resolution limit in remark 2, remark 3
and Remark 200) are supposed to be consistent and are
defined as the highest resolution reflection used.
http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_reflns.d_resolution_high.html
http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html

  Looking at the PDB specification, it shows that there is an option
to add a free text comment to the remark 2 resolution --
"Additional explanatory text may be included starting with the third line of the 
REMARK 2 record. For example, depositors may wish to qualify the resolution value 
provided due to unusual experimental conditions."
http://www.wwpdb.org/documentation/format33/remarks1.html

   We have not done this, but we have in a number of cases
qualified the resolution by using a lower resolution in the
title of the entry and further detailing this "nominal"
resolution in the remark 3 other refinement remarks. E.g. see
http://www.rcsb.org/pdb/explore/explore.do?structureId=1vr0
http://www.rcsb.org/pdb/explore/explore.do?structureId=1vkk 

Regards,
Mitch

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. 
Berry
Sent: Wednesday, April 25, 2012 6:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] "resolution" on PDB web page

We also use the US portal. Can't speak to the solvent content as we never
had a value much over 70%.

As for the resolution range, I never saw any place to enter this
user-defined resolution of the structure.
As far as i know it comes from the record:
REMARK 200  RESOLUTION RANGE HIGH  (A) : 1.200
which should be the high resolution used in refinement.

I suppose in an "additional remark" you could give the
optical resolution or the resolution of 90% complete at I/sig=2.
Or the title could be "The 2.2A resolution structure of protein x",
never mind that there were a few reflections used at 1.7A.
eab

Mark J van Raaij wrote:

Phoebe, Jan, PDB,
is this something particular to the US portal of the PDB, or general?
We always use the European portal pdbe and have not had such "problems".
Mark
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



On 25 Apr 2012, at 09:41, Jan Dohnalek wrote:


There have been other manipulations with user-input values. We could not input solvent 
content 83% for 3cg8 (the real value!!!) as "being out of the allowed range".
The resulting value in the PDB is "NULL" not showing the actually interesting 
feature of the structure.

I also noticed that the reported resolution values are nonsensically advertised 
with three decimal positions after the point which is not the way we would put 
it, is it?

Either fight it or live with it ...

Jan Dohnalek




On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice   wrote:
I just noticed that the PDB has changed the stated resolution for one of my old 
structures!  It was refined against a very anisotropic data set that extended 
to 2.2 in the best direction only.  When depositing I called the resolution 2.5 
as a rough average of resolution in all 3 directions, but now PDB is 
advertising it as 2.2, which is misleading.

I'm afraid I may not have paid enough attention to the fine print on this issue - is the 
PDB now automatically advertising the "resolution" of a structure as that of 
the outermost flyspeck used in refinement, regardless of more cautious assertions by the 
authors?  If so, I object!

=
Phoebe A. Rice
Dept. of Biochemistry&   Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp



--
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

[ccp4bb] how to install coot on ubuntu 11.10

[Michael Murphy]

I am trying to install Coot on a laptop that runs Ubuntu. Following the
instructions on the CCp4wiki
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Packages_for_Ubuntu


 sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 1DC81A57
 sudo add-apt-repository ppa:mok0/ppa
apt-get update && apt-get install coot <- I had to add "sudo" to the
beginning of this command and after the &&

and I received this fail message

"Package coot is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'coot' has no installation candidate"


is there some other name/link for the package other than the word "coot" or
do I need to install it by some other method other than what I have been
doing?

Re: [ccp4bb] how to install coot on ubuntu 11.10

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Michael,

the command 'aptitude search coot' could give you an answer, although
I am not sure 'aptitude' is available on Ubuntu (it is in Debian).

Tim

On 04/25/12 17:54, Michael Murphy wrote:
> I am trying to install Coot on a laptop that runs Ubuntu. Following
> the instructions on the CCp4wiki 
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Packages_for_Ubuntu
>
> 
> 
> sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys
> 1DC81A57 sudo add-apt-repository ppa:mok0/ppa apt-get update &&
> apt-get install coot <- I had to add "sudo" to the beginning of
> this command and after the &&
> 
> and I received this fail message
> 
> "Package coot is not available, but is referred to by another
> package. This may mean that the package is missing, has been
> obsoleted, or is only available from another source
> 
> E: Package 'coot' has no installation candidate"
> 
> 
> is there some other name/link for the package other than the word
> "coot" or do I need to install it by some other method other than
> what I have been doing?
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFPmB9dUxlJ7aRr7hoRAu2RAKD2lfnbMpqkM5UIdV+UPnaZ1J6ZUACePRgC
NtpuwIwxFeSvtYqC7Ya31Yw=
=Ij50
-END PGP SIGNATURE-

[ccp4bb] aimless and anisotropic scaling (and the docs?)

[Bryan Lepore]

wondering if aimless performs anisotropic scaling or "elliptical"
rejections lately.

I ask because:

[1] last I knew, scala did not
[2] I can't seem to google up the aimless manual as readily as scala

... also, what consesquence would mosflm anisotropic resolution limits
have on scaling (if aimless anisoscaling were true).

-Bryan

Re: [ccp4bb] aimless and anisotropic scaling (and the docs?)

[Phil Evans]

You can get the aimless documentation from

ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/aimless.html

pending its official release through CCP4

No it does not do anisotropic scaling as such. That needs some sort of model of 
the "ideal" intensity, probably best calculated from a model

I'm not sure that anisotropic cutoffs are a good idea. I believe Garib thinks 
they are not and I generally defer to him

Phil 

On 25 Apr 2012, at 17:00, Bryan Lepore wrote:

> wondering if aimless performs anisotropic scaling or "elliptical"
> rejections lately.
> 
> I ask because:
> 
> [1] last I knew, scala did not
> [2] I can't seem to google up the aimless manual as readily as scala
> 
> ... also, what consesquence would mosflm anisotropic resolution limits
> have on scaling (if aimless anisoscaling were true).
> 
> -Bryan

Re: [ccp4bb] aimless and anisotropic scaling (and the docs?)

[George Sheldrick]

I think that anything that irrevocably modifies the experimental data 
should be avoided whenever possible. Since anisotropic scaling is a 
relatively fast calculation and there are several ways of doing it, it 
is better to apply it locally when it is needed, e.g. in phasing (where 
it is applied by phaser and shelxe etc.) and refinement (with refmac or 
phenix_refine etc.). Provided that the standard deviations of the 
observed intensities are properly taken into account, anisotropic data 
truncation is not so important (i.e. as usual I agree with Garib and Phil).


George

On 04/25/2012 06:19 PM, Phil Evans wrote:

You can get the aimless documentation from

ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/aimless.html

pending its official release through CCP4

No it does not do anisotropic scaling as such. That needs some sort of model of the 
"ideal" intensity, probably best calculated from a model

I'm not sure that anisotropic cutoffs are a good idea. I believe Garib thinks 
they are not and I generally defer to him

Phil

On 25 Apr 2012, at 17:00, Bryan Lepore wrote:


wondering if aimless performs anisotropic scaling or "elliptical"
rejections lately.

I ask because:

[1] last I knew, scala did not
[2] I can't seem to google up the aimless manual as readily as scala

... also, what consesquence would mosflm anisotropic resolution limits
have on scaling (if aimless anisoscaling were true).

-Bryan



--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] Criteria for Ligand fitting

[Dale Tronrud]

   While I'm quite happy with all the responses this question has provoked there
is an additional point I would like to contribute.  It is not enough to say that
you can interpret your map with a model based on what you expect.  You have to
also show that you can't interpret your map with any other reasonable model.
Saying that my map is "consistent" with my model is a very weak statement in the
absence of exclusivity.

   A recent example of this sort of problem can be read about at (warning: 
tooting
my own horn)

http://www.springerlink.com/content/b8h6lg138635380v/?MUD=MP

Dale Tronrud

On 04/23/12 21:02, Naveed A Nadvi wrote:
> Dear Crystallographers,
> 
> We have obtained a 1.7 A dataset for a crystal harvested from crystallization 
> drop after 2 weeks of soaking with inhibitor. The inhibitor has an aromatic 
> ring and also an acidic tail derived from other known inhibitors. The active 
> site hydrophobic crown  had been reported to re-orient and a charged residue 
> is known to position for forming a salt-bridge with similar ligands. When 
> compared to apo strucutres, we can clearly see the re-orientation of these 
> protein residues. 
> 
> However, there are no clear density visible for the ligand in the Fo-Fc map. 
> Some density is visible in the 2Fo-Fc map with default settings in COOT. We 
> were expecting co-valent modifcations between the inhbitor, co-factor and 
> protein residues. In fact, the Fo-Fc map suggested the protein residue is no 
> longer bonded to the co-factor (red negative density) and a green positive 
> density is observed nearby for the protein residue. These observations, along 
> with the extended soaking and the pre-determined potency convince us that the 
> inhibitor is present in the complex.
> 
> When I lower the threshold of the blue 2Fo-Fc map (0.0779 e/A^3; 0.2 rmsd) we 
> can see the densities for the aromatic ring and the overall structural 
> features. These densities were observed without the cofactor and the inhibtor 
> in the initial MR search model. The R/Rfree for this dataset without 
> inhibitor was 0.20/0.24 (overall Bfactor 17.4 A^2). At 50% occupancy, 
> modeling the inhibtor showed no negative desities upon subsequent refinement. 
> With the inhibtor, the R/Rfree was 0.18/0.22  (overall Bfactor 18.8 A^2). The 
> temp factors of the inhibitor atoms (50% occ) were 15-26 A^2.
> 
> My understanding is phase from the MR search model may influence Fo-Fc maps, 
> and the 2Fo-Fc map minimizes phase bias. Since the inhibitor was absent from 
> the MR search model, can these observations be used to justify the fitting of 
> the ligand in the map? Given the low map-level used to 'see' the ligand, 
> would this be considered noise? Can I justfiy the subsequent fall in R/Rfree 
> and the absence of negative density upon ligand fitting as proof of correct 
> inhibtor modeling? I would appreciate if you could comment on this issue. Or 
> tell me that I'm dying to see the inhibitor and hence imagining things!
> 
> Kind Regards,
> 
> Naveed Nadvi.

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

[James Holton]

An effective tactic that has not been mentioned yet is simply to attach 
your coordinates and map to a blanket email and send it simultaneously 
to all of your competitors.  The key thing here is "all".  Send it to 
EVERYONE who might serve as a reviewer for your structure.  This may 
sound like madness to your paranoid "BIO-whatever" colleagues, but try 
to imagine yourself in your "evil" competitor's shoes.  You have 
crystals, you've got data sets, you might have even gotten as far as 
solving the structure and writing a draft manuscript.   And then 
"plop"!  Everything you would need to ruthlessly scoop someone who was 
kind enough to share their results with you falls in your lap.  And 
everyone in the field knows it!  How will your manuscript be received 
now?  Whom will you recommend as reviewers?  How will your next grant be 
received if you now "rush out" a structure that looks a LOT like 
something everyone knows is not your work?   Looking unethical is far 
more damaging to your career and future funding that actually being 
unethical.


In a way, the above tactic is a form of "publication".  It is just 
self-publication without any peer review to a relatively small 
audience.  Still, a "scoop" is a "scoop"?  The only problem you will 
have with your peer-reviewed publication is if your journal of choice 
has some kind of "embargo" rule because they want to be the first to 
make the "big splash".  Personally, I think all the paranoia and 
distrust in science today is rooted in this desire for notoriety.  
Sensationalism and science are a dangerous mix.  I know, I know.  
Journals need advertisers to pay for the pages, etc. etc.  
Sensationalism is unfortunately connected to the money.  But, if you 
want to make a big splash, then don't complain about being asked to leap 
from a great height.


Anonymous peer review exists because of the need to get an honest 
answer.  Non-anonymous peer review is also a good idea.  It is called 
"asking a friend to look at your manuscript".  Anyone who has tried the 
latter can attest to how difficult it can be to get comments back in a 
timely fashion, if at all!  Sometimes even offering to make them a 
co-author doesn't help.  Nevertheless, I highly recommend that everyone 
do a round of non-anonymous peer review before submitting the manuscript 
for anonymous peer review.  There is nothing more irritating to an 
"official" reviewer than someone who clearly submitted a rough draft, 
and couldn't even be bothered to check for complete sentences, spelling 
errors, having a point etc.  Remember, the anonymous reviewers (and the 
editor) are the ONLY people who will ever have to read every word of 
your manuscript.  Their comments will usually be less harsh if the MS 
has already been through non-anonymous peer review.


Then again, if a reviewer is asking for your coordinates, then perhaps 
there is something wrong with your figures?  In a way, this is like 
asking an author for a comma-separated list of their raw data points so 
that you can re-plot them in Excel.  The paper really ought to stand on 
its own, clearly showing the evidence needed to support the conclusions 
drawn.  Or at least that is what I was taught in scientist school.


-James Holton
MAD Scientist

On 4/18/2012 3:34 PM, Marc Kvansakul wrote:

Dear CCP4BBlers,

I was wondering how common it is that reviewers request to have a copy 
of the PDB coordinate file for the review purpose. I have just been 
asked to supply this by an editor after several weeks of review, after 
one of the reviewers requested a copy.


Not having ever been asked to do this before I feel just a tad 
uncomfortable about handing this over…


Your opinions would be greatly appreciated.

Best wishes

Marc

Dr. Marc Kvansakul
Laboratory Head, NHMRC CDA Fellow
Dept. of Biochemistry| La Trobe University | Bundoora
Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia
T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |

Re: [ccp4bb] how to install coot on ubuntu 11.10

[AFL]

Hi Michael,

 If I interpret the content of Morten Kjeldgaard ppa repository 
correctly the latest coot available there is for Natty Narwhal (11.04). 
Hence, installation in 11.10 or later will just not work.


Cheers, Andrzej

On 4/25/12 5:54 PM, Michael Murphy wrote:

I am trying to install Coot on a laptop that runs Ubuntu. Following the
instructions on the CCp4wiki
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Packages_for_Ubuntu

  sudo apt-key adv --keyserverkeyserver.ubuntu.com  
  --recv-keys 1DC81A57
  sudo add-apt-repository ppa:mok0/ppa
apt-get update&&  apt-get install coot<- I had to add"sudo"  to the beginning of this 
command and after the&&


and I received this fail message

"Package coot is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'coot' has no installation candidate"


is there some other name/link for the package other than the word "coot"
or do I need to install it by some other method other than what I have
been doing?




--

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

[Ethan Merritt]

On Wednesday, April 25, 2012 09:40:01 am James Holton wrote:

> If you want to make a big splash, then don't complain about 
> being asked to leap from a great height.


This gets my vote as the best science-related quote of the year.

Ethan


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] how to install coot on ubuntu 11.10

[Miguel Ortiz Lombardia]

El 25/04/12 17:54, Michael Murphy escribió:
> I am trying to install Coot on a laptop that runs Ubuntu. Following the
> instructions on the CCp4wiki
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Packages_for_Ubuntu
>  
> 
>  sudo apt-key adv --keyserver keyserver.ubuntu.com 
>  --recv-keys 1DC81A57
>  sudo add-apt-repository ppa:mok0/ppa
> apt-get update && apt-get install coot <- I had to add "sudo" to the 
> beginning of this command and after the &&
> 
> 
> and I received this fail message
> 
> "Package coot is not available, but is referred to by another package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
> 
> E: Package 'coot' has no installation candidate"
> 
> 
> is there some other name/link for the package other than the word "coot"
> or do I need to install it by some other method other than what I have
> been doing?
> 
> 

Hi Michael,

Just this weekend I installed coot on a similar computer. It's an Ubuntu
11.10 (oneiric ocelot) at 64bit. I had no much problem installing it
using Paul's autobuild script
(http://www.biop.ox.ac.uk/coot/software/build-script/build-install-coot-from-scratch)
after a couple of tweaks of that script and of the one that this script
downloads (so you may download both manually, apply de patches and
comment the if/fi lines in the first script). The tweaks are included as
diff files in the attached file.

The only other thing I had to do was to install guile-1.8 and
guile-1.8-dev from the Ubuntu repositories. Anything else compiled just
fine with Paul's script.

Good luck,


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia


cootbuilddiffs.tgz
Description: application/compressed-tar

Re: [ccp4bb] "resolution" on PDB web page

[H. Raaijmakers]

That's nothing. Once someone wrote me because the tungsten atom of my
"Tungsten containing formate dehydrogenase" had dissapeared.
Lost in translation during some autoscripted conversion.
 It was corrected soon enough.:)

Cheers,
Hans




Jan Dohnalek schreef:
> There have been other manipulations with user-input values. We could not
> input solvent content 83% for 3cg8 (the real value!!!) as "being out of
> the
> allowed range".
> The resulting value in the PDB is "NULL" not showing the actually
> interesting feature of the structure.
>
> I also noticed that the reported resolution values are nonsensically
> advertised with three decimal positions after the point which is not the
> way we would put it, is it?
>
> Either fight it or live with it ...
>
> Jan Dohnalek
>
>
>
>
> On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice  wrote:
>
>> I just noticed that the PDB has changed the stated resolution for one of
>> my old structures!  It was refined against a very anisotropic data set
>> that
>> extended to 2.2 in the best direction only.  When depositing I called
>> the
>> resolution 2.5 as a rough average of resolution in all 3 directions, but
>> now PDB is advertising it as 2.2, which is misleading.
>>
>> I'm afraid I may not have paid enough attention to the fine print on
>> this
>> issue - is the PDB now automatically advertising the "resolution" of a
>> structure as that of the outermost flyspeck used in refinement,
>> regardless
>> of more cautious assertions by the authors?  If so, I object!
>>
>> =
>> Phoebe A. Rice
>> Dept. of Biochemistry & Molecular Biology
>> The University of Chicago
>> phone 773 834 1723
>>
>> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>> http://www.rsc.org/shop/books/2008/9780854042722.asp
>>
>
>
>
> --
> Jan Dohnalek, Ph.D
> Institute of Macromolecular Chemistry
> Academy of Sciences of the Czech Republic
> Heyrovskeho nam. 2
> 16206 Praha 6
> Czech Republic
>
> Tel: +420 296 809 340
> Fax: +420 296 809 410
>

Re: [ccp4bb] "resolution" on PDB web page

[Jacob Keller]

I had heard that there was a world-wide Tungsten shortage, but this is
ridiculous!

JPK

On Wed, Apr 25, 2012 at 1:29 PM, H. Raaijmakers wrote:

> That's nothing. Once someone wrote me because the tungsten atom of my
> "Tungsten containing formate dehydrogenase" had dissapeared.
> Lost in translation during some autoscripted conversion.
>  It was corrected soon enough.:)
>
> Cheers,
> Hans
>
>
>
>
> Jan Dohnalek schreef:
> > There have been other manipulations with user-input values. We could not
> > input solvent content 83% for 3cg8 (the real value!!!) as "being out of
> > the
> > allowed range".
> > The resulting value in the PDB is "NULL" not showing the actually
> > interesting feature of the structure.
> >
> > I also noticed that the reported resolution values are nonsensically
> > advertised with three decimal positions after the point which is not the
> > way we would put it, is it?
> >
> > Either fight it or live with it ...
> >
> > Jan Dohnalek
> >
> >
> >
> >
> > On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice 
> wrote:
> >
> >> I just noticed that the PDB has changed the stated resolution for one of
> >> my old structures!  It was refined against a very anisotropic data set
> >> that
> >> extended to 2.2 in the best direction only.  When depositing I called
> >> the
> >> resolution 2.5 as a rough average of resolution in all 3 directions, but
> >> now PDB is advertising it as 2.2, which is misleading.
> >>
> >> I'm afraid I may not have paid enough attention to the fine print on
> >> this
> >> issue - is the PDB now automatically advertising the "resolution" of a
> >> structure as that of the outermost flyspeck used in refinement,
> >> regardless
> >> of more cautious assertions by the authors?  If so, I object!
> >>
> >> =
> >> Phoebe A. Rice
> >> Dept. of Biochemistry & Molecular Biology
> >> The University of Chicago
> >> phone 773 834 1723
> >>
> >>
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> >> http://www.rsc.org/shop/books/2008/9780854042722.asp
> >>
> >
> >
> >
> > --
> > Jan Dohnalek, Ph.D
> > Institute of Macromolecular Chemistry
> > Academy of Sciences of the Czech Republic
> > Heyrovskeho nam. 2
> > 16206 Praha 6
> > Czech Republic
> >
> > Tel: +420 296 809 340
> > Fax: +420 296 809 410
> >
>



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

[ccp4bb] content calculation in phaser

[Leonard Thomas]

Hello All,

We have run into a problem running Phase under both CCP4 and Phenix.   
Specifically with the Matthews calculation, which then causes Phaser  
to look for something different then what we want.  The input space  
group is R3:H after processing.   The input molecular weight of the  
model is ~16000 but Phaser for some reason thinks it is ~65000.   The  
strait Mathews calculation through CCP4 comes up with 2 molecules in  
the asymmetric unit with 51% solvent.  Phaser is coming up with a  
solvent content of 5.2% for one molecule, though it thinks the  
molecule is 65000 Da.  The pdb file only has coordinates  in it.   
Anybody else run into this problem?


We were able to get a good solution using MolRep and it turns out to  
be 2 molecules in the symmetric unit in R32:H.  If you input R32:H  
into Phaser it blows up.


Regards,
Len

Leonard Thomas Ph.D.
Macromolecular Crystallography Laboratory Manager
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019-5251

lmtho...@ou.edu
http://barlywine.chem.ou.edu
Office: (405)325-1126
Lab: (405)325-7571

Re: [ccp4bb] minimum protein concentration for NI-NTA column

[Thomas Cleveland]

Jerry,

In my experience with GE's HiTrap Chelating HP columns (which use the
tridentate IDA linkage, rather than the tetradentate NTA), capture is
usually quite good as long as the protein is well behaved and the tag
isn't occluded.  It is definitely possible to capture proteins at the
level of 0.2-0.5 mg/L, as you are describing.  With such low
concentrations, you will want to perform the binding in column mode
rather than in batch, however.  You will also need to filter your
medium through 0.22 um filters to avoid clogging the column with such
a large volume.

The bigger problem may prove to be your medium.  Most tissue culture
media contain chelators that will strip your column; your particular
medium may be OK, but you may want to contact the manufacturer (or
just try it, with the understanding that it may not work).  If your
column is stripped, when you attempt to elute with imidazole (which
normally turns your column a brighter blue), you will be able to see
that the column is partially or completely white instead.  If only a
small portion of the column turns white (it will look like a white
band at the top of the column), your capture may still work fine.  If
there is even a little bit of blue left, it may still be possible to
switch to a larger column that retains enough nickel to capture your
protein.

If the column is totally stripped, however, you will probably have no
choice but to concentrate and buffer exchange your medium.

-Tom Cleveland

Leahy Lab
Johns Hopkins University School of Medicine

On Mon, Apr 23, 2012 at 9:37 PM, Jerry McCully
 wrote:
> Dear All;
>
>    This is a sort of naive question about the NI-NTA affinity
> purification.
>
>
>    Is the Ni-NTA column from GE health able to capture proteins at
> 0.2ug/ml to 0.5ug/ml?
>
>    IF not, then it is necessary to concentrate the mammalian expression
> supernatant.
>
>   Thanks a lot and best regards,
>
> Jerry McCully
>
>