[ccp4bb] paper from mol microbiol

[Ronnie Berntsson]

Dear all,

I'm looking for a pdf of the paper
Atomic structure and specificity of bacterial periplasmic receptors  
for active transport and chemotaxis: variation of common themes


Florante Quiocho, P Ledvina
Mol Microbiol. 1996 Apr: 20(1)17-25

Our library only has electronic access from 1997 and onwards, and  
unfortunately the librarys printed copy is somewhat difficult to  
localize... If someone has it lying around I'd be very grateful!


With regards,
Ronnie Berntsson

--
Ph.D. Student
Department of Biochemistry
Groningen Biomolecular Sciences and Biotechnology Institute
& Zernike Institute for Advanced Materials
University of Groningen
Nijenborgh 4, 9747 AG
Groningen, The Netherlands

telephone: +31 50 363 4195
telefax: +31 50 363 4165
e-mail: [EMAIL PROTECTED]
homepage: http://www.rug.nl/gbb/research/researchgroups/enzymology/index

Re: [ccp4bb] problems with map quality, refinement and R/Rfree

[Axel T. Brunger]

Mark,

The bulk solvent model in CNS 1.2 is now perfectly stable at low 
resolution.  No need

to fix the solvent parameters anymore.


Axel

Mark A. White wrote:

Joe,

1) The bulk solvent models in CNS and REFMAC are not stable at low 
resolution.  Fixing the bulk solvent B-factor can improve this behavior.


2) With low resolution data model-bias becomes a serious issue when 
working with a MR solution.  I have found that DM (with or withou NCS) 
can improve low resolution maps significantly.  I routinely use 
RESOLVE to phase improve my model maps as I build new models (I use my 
PMB program to do this automatically for me using a combination of 
CNS/CCP4/RESOLVE http://xray.utmb.edu/PMB 
).  In one low resolution MR case at 3.5A 
we had an entire domain in the wrong orientation and DM gave clear and 
unambiguous density for the correct orientation (caveat: 70% solvent 
does wonders for phase improvement).


Good luck,

Mark


On Fri, 2007-10-19 at 11:39 -0400, Joe Smith wrote:

Hi all,

We have data sets for a protein-RNA complex at 3.2 A resolution. . The
data belong to the space group I4122 and contains one molecule of
Protein-RNA complex (300AA and 16nt; 66% solvent content) in the asym
unit. We have managed to get phases using Se-SAD and the present model
contains 60% of the protein atoms (250 residues many of them build as
Ala) and almost complete RNA (16nt).  We could not locate ~20 % of the
residues (present in various loops as well as at N- and C-terminal
ends). First 120 residues present at N-terminal end seem to have poor
relatively main-chain density and almost no side chain density. RNA
and 130 residues present at the C-terminal end have good electron
density for main-chain as well as side chain.

The solution seems to be correct as molecular replacement trials with
this model gave same solution in Phaser, Molrep and AMoRe. Solution
seems to be also correct because as expected one RNA strand present in
asym unit pairs with another one coming from symmetry related
molecule.

We have checked data in space group I4122 with CCP4 (SFCHECK,
cumulative intensity distribution), Yeates server as well as
Phenix.xtriage. In all the cases it indicates no twinning. However if
I process the data in lower symmetry space group it does indicate
presence of almost perfect twin. We realize that this could be just
because of processing data in lower symmetry space group and data in
all probability may still be fine.

The problem is now with refinement and model building. Refinement with
CNS and Refamc gave considerably higher value of R and R free. In
CNS1.1, refinement with small changes in the model some time leads to
large shift in R and R-free value.
 Refmac: R=36; Rfree=47
CNS1.1:  R=40-59; R-free=45-63
However in both the cases map looks more or less same (with reasonably
good density for the main-chain as well as RNA)

I tried refining with phenix.refine and there is some improvement in
the R(34%) and Rfree(40%) values. I think may be robust bulk solvent
correction incorporated in phenix.refine has helped in this case.
However, I still see no improvement in the map quality for the first
120 residues.

In the absence of any clear density I am unable to build any further.
I feel N-terminal domain is bit flexible and may have overall poor
density. I have used Se position as well as predicted secondary
structure in assigning the amino acid in the map but due to few breaks
in the N-terminal domain as well as poor density I am unable to assign
any amino acid into the poly ala main chain.

Frankly speaking, I do not know how to proceed further. I welcome any
kind of suggestions which could help us in this case.

Regards
Joe


Yours sincerely,

Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics 
X-ray Crystallography Laboratory,

Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Fax. (409) 747-4745
mailto://[EMAIL PROTECTED]
http://xray.utmb.edu
http://xray.utmb.edu/~white




--
Axel T. Brunger
Investigator,  Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University

Web:http://atb.slac.stanford.edu
Email:  [EMAIL PROTECTED]  
Phone:  +1 650-736-1031

Fax:+1 650-745-1463

[ccp4bb] Ohio Valley Crystallography and Biophysics Symposium

[Artem Evdokimov]

Dear Colleagues,

 

We would like extend an invitation to you for the 3rd annual Ohio Valley
Crystallography and Biophysics Symposium (now with more biophysics!), to be
held this year at the University of Toledo, Ohio on Friday, November 9th. In
addition to talks on macromolecular structure determination, there will also
be poster presentations and vendor displays, as well as tours of College of
Arts and Sciences Instrumentation Center. 

 

The cost of registration and meals is underwritten by our sponsors, and some
travel grants are available for undergraduate students. For more information
and registration please visit:

 

 http://www.xtals.org/2007_conference.html

 

The Organizing Committee

 

Re: [ccp4bb] problems with map ->-> refmac SAD function

[Bryan W. Lepore]

On Fri, 19 Oct 2007, Kay Diederichs wrote:

Acta Cryst. (2004). D60, 2196-2201
Direct incorporation of experimental phase information in model refinement
P. Skub?k, G. N. Murshudov and N. S. Pannu


the refmac documentation(s) mention Rice, MLHL, etc., but i didn't see 
explicit mention of SAD - is this something that refmac will 'know' once 
it sees the labels?  i.e, which keyword is used how, to do simultaneous 
SAD/model refinement?


-bryan

Re: [ccp4bb] problems with map quality, refinement and R/Rfree

[James Holton]

Merge in the lower symmetry space group you mentioned and refine with a 
twinning operator. 

xtriage can tell you what the twinning operator is and phenix.refine can 
do the twinned refinement.


In my experience, these kinds of stats almost always indicate an 
incorrect symmetry choice somewhere (usually the space group choice, but 
it can be twinning too).  In general, it never hurts to re-merge your 
data in P1 and then use PDBSET to expand your model into the P1 cell.  
In cases like yours with centering you can use TRACER to tell you what 
operators to use to get to a primitive cell.  This should never make 
your Rcryst any worse.  If rigid body and/or further refinement gives 
you better stats and significant difference features, then you had the 
wrong symmetry.


-James Holton
MAD Scientist

Joe Smith wrote:

Hi all,

We have data sets for a protein-RNA complex at 3.2 A resolution. . The
data belong to the space group I4122 and contains one molecule of
Protein-RNA complex (300AA and 16nt; 66% solvent content) in the asym
unit. We have managed to get phases using Se-SAD and the present model
contains 60% of the protein atoms (250 residues many of them build as
Ala) and almost complete RNA (16nt).  We could not locate ~20 % of the
residues (present in various loops as well as at N- and C-terminal
ends). First 120 residues present at N-terminal end seem to have poor
relatively main-chain density and almost no side chain density. RNA
and 130 residues present at the C-terminal end have good electron
density for main-chain as well as side chain.

The solution seems to be correct as molecular replacement trials with
this model gave same solution in Phaser, Molrep and AMoRe. Solution
seems to be also correct because as expected one RNA strand present in
asym unit pairs with another one coming from symmetry related
molecule.

We have checked data in space group I4122 with CCP4 (SFCHECK,
cumulative intensity distribution), Yeates server as well as
Phenix.xtriage. In all the cases it indicates no twinning. However if
I process the data in lower symmetry space group it does indicate
presence of almost perfect twin. We realize that this could be just
because of processing data in lower symmetry space group and data in
all probability may still be fine.

The problem is now with refinement and model building. Refinement with
CNS and Refamc gave considerably higher value of R and R free. In
CNS1.1, refinement with small changes in the model some time leads to
large shift in R and R-free value.
 Refmac: R=36; Rfree=47
CNS1.1:  R=40-59; R-free=45-63
However in both the cases map looks more or less same (with reasonably
good density for the main-chain as well as RNA)

I tried refining with phenix.refine and there is some improvement in
the R(34%) and Rfree(40%) values. I think may be robust bulk solvent
correction incorporated in phenix.refine has helped in this case.
However, I still see no improvement in the map quality for the first
120 residues.

In the absence of any clear density I am unable to build any further.
I feel N-terminal domain is bit flexible and may have overall poor
density. I have used Se position as well as predicted secondary
structure in assigning the amino acid in the map but due to few breaks
in the N-terminal domain as well as poor density I am unable to assign
any amino acid into the poly ala main chain.

Frankly speaking, I do not know how to proceed further. I welcome any
kind of suggestions which could help us in this case.

Regards
Joe
  

Re: [ccp4bb] problems with map quality, refinement and R/Rfree

[Eleanor Dodson]

These problems are horrible!

1) I usually try to run refinement using the exptl phases as restraints.

It is worth getting the best possible phases before you start - DM with 
66% solvent should make a great improvement..


Then these cam be used  as restraints for the refinement, and your FWT 
maps will include that phase info.


Try first to build the side chains wherever possible - I look at both 
the exptl map and the FWT map to do this. Of course the FWT map is 
biased towards what you have built..


Once you have improved the existing model as much as possible you should 
also have improved the map to see the missing parts. You will prob. have 
to drop the contour level quite a bit..


But these problems are very tricky always - better crystal?

eleanor


Joe Smith wrote:

Hi all,

We have data sets for a protein-RNA complex at 3.2 A resolution. . The
data belong to the space group I4122 and contains one molecule of
Protein-RNA complex (300AA and 16nt; 66% solvent content) in the asym
unit. We have managed to get phases using Se-SAD and the present model
contains 60% of the protein atoms (250 residues many of them build as
Ala) and almost complete RNA (16nt).  We could not locate ~20 % of the
residues (present in various loops as well as at N- and C-terminal
ends). First 120 residues present at N-terminal end seem to have poor
relatively main-chain density and almost no side chain density. RNA
and 130 residues present at the C-terminal end have good electron
density for main-chain as well as side chain.

The solution seems to be correct as molecular replacement trials with
this model gave same solution in Phaser, Molrep and AMoRe. Solution
seems to be also correct because as expected one RNA strand present in
asym unit pairs with another one coming from symmetry related
molecule.

We have checked data in space group I4122 with CCP4 (SFCHECK,
cumulative intensity distribution), Yeates server as well as
Phenix.xtriage. In all the cases it indicates no twinning. However if
I process the data in lower symmetry space group it does indicate
presence of almost perfect twin. We realize that this could be just
because of processing data in lower symmetry space group and data in
all probability may still be fine.

The problem is now with refinement and model building. Refinement with
CNS and Refamc gave considerably higher value of R and R free. In
CNS1.1, refinement with small changes in the model some time leads to
large shift in R and R-free value.
 Refmac: R=36; Rfree=47
CNS1.1:  R=40-59; R-free=45-63
However in both the cases map looks more or less same (with reasonably
good density for the main-chain as well as RNA)

I tried refining with phenix.refine and there is some improvement in
the R(34%) and Rfree(40%) values. I think may be robust bulk solvent
correction incorporated in phenix.refine has helped in this case.
However, I still see no improvement in the map quality for the first
120 residues.

In the absence of any clear density I am unable to build any further.
I feel N-terminal domain is bit flexible and may have overall poor
density. I have used Se position as well as predicted secondary
structure in assigning the amino acid in the map but due to few breaks
in the N-terminal domain as well as poor density I am unable to assign
any amino acid into the poly ala main chain.

Frankly speaking, I do not know how to proceed further. I welcome any
kind of suggestions which could help us in this case.

Regards
Joe


  

Re: [ccp4bb] problems with map quality, refinement and R/Rfree

[Juergen Bosch]

Hi Joe,

have you tried to process the data in different programs ? This can 
sometimes make a dramatic difference, being completely unbiased I would 
recommend XDS over Mosflm or HKL2000. Was your data carefully collected 
? How many rejections, overlaps do you have ?


Juergen

--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

[ccp4bb] Reminder : SRS AP50 (April - December 2008) Open for Applications

[Ellis, MJ (Mark)]

> Dear SRS Users,
> 
> Applications are now invited for beam-time in allocation period 50 (April - 
> December 2008) on PX station 10.1 at the SRS. The deadline for submission of 
> proposals is Thursday 1st November.
> 
> Further details on how to apply for beamtime can be found here :- 
> http://www.srs.ac.uk/srs/userSR/AP50_announcement.htm
> 
> Station 10.1 (http://www.biophysics.dl.ac.uk/srsbl10.html) at the SRS 
> Daresbury is a world competitive high throughput PX/XAFS structural biology 
> facility. It has a XAFS capable sagittal focussing monochromator (tuneable 
> between 5 and 14 keV) a state-of-the-art MarMosaic CCD225 detector and a 
> state of the art low-profile monolithic 4-element x-ray fluorescence Ge 
> detector, with an energy resolution of 170-200 eV. This is the first time 
> that such a high quality fluorescence detector is included as an integral 
> part of a PX beamline. A crystal microspectrophotometer for measuring optical 
> data is also available on-line. Station 10.1 is therefore ideally suited for 
> combining optical, PX and XAFS data collection on the same protein crystal, 
> identifying metal redox states of crystals in-situ, anomalous diffraction 
> measurements, monitoring crystals for radiation damage and long wavelength 
> (up to 2.3Å) SAD phasing experiments. In addition, automated cryogenic sample 
> changing allows high-throughput crystal screening and data collection. 
> 
> Please feel free to contact me ([EMAIL PROTECTED]) or Richard Strange ([EMAIL 
> PROTECTED]) if you have any questions.
> 
> Yours sincerely,
> 
> Mark Ellis
> ---
> Dr. Mark Ellis
> SRS Station Scientist 10.1
> Researcher Molecular Biophysics Group
> Science and Technology Facilities Council
> Daresbury Laboratory
> Daresbury Science and Innovation Campus
> Warrington
> Cheshire
> WA4 4AD, UK
> 
> tel : +44 (0)1925 603830  http://www.stfc.ac.uk
> fax : +44 (0)1925 603748 http://www.biophysics.dl.ac.uk
> 
> 

Re: [ccp4bb] DM NCS averaging

[Kevin Cowtan]

User error I'm afraid.

You are using the 'add domain' button in the GUI, you should be using 
the 'add operator' button instead.


Kevin

Bernhard Rupp wrote:

Thanks to Pete and Juergen - seems that the
GUI sticks the offending 


domain 1 -
domain 2 -

line in the script. Both the linux and windows versions did that.
Is this a GUI error or is user error?

Thx, br
-
Dear All,

trying to run DM in NCS averaging mode from GUI.
Problem is error message:
 dm:   (RCARDS) AVER: enter indentity matrix first

There are 2 domains (monomers) related by NCS
The same message appears irrespective of whether
a) I do enter 0,0,0, 0,0,0 for the first domain
and then the second one with the NCS operator
or 
b)only one domain and the operator.


Script follows
--- 
 mode -

SOLV -
SAYR -
AVER
combine PERT
scheme ALL
ncycles -
AUTO
solc 0.48
average -
domain 1 -
REFI
rota EULER -
0.0 0.0 0.0
tran 0.0 0.0 0.0
average -
domain 2 -
REFI
rota EULER -
-179.16 150.31 -0.84
tran 12.82 226.45 60.88
ncsmask -
nmer 2 -
update 2
LABIN  FP=FB-sharp PHIO=PHIB-sharp FOMO=FOM-sharp
LABOUT  FDM=FDM-2 PHIDM=PHIDM-2 FOMDM=FOMDM-2


This seems quite right according to example scripts

Thx, br
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
[EMAIL PROTECTED]
[EMAIL PROTECTED] 
http://www.ruppweb.org/ 
-

Every day above ground is a good day.
-

Re: [ccp4bb] problems with map quality, refinement and R/Rfree

[Mark A. White]

Joe,

1) The bulk solvent models in CNS and REFMAC are not stable at low
resolution.  Fixing the bulk solvent B-factor can improve this behavior.

2) With low resolution data model-bias becomes a serious issue when
working with a MR solution.  I have found that DM (with or withou NCS)
can improve low resolution maps significantly.  I routinely use RESOLVE
to phase improve my model maps as I build new models (I use my PMB
program to do this automatically for me using a combination of
CNS/CCP4/RESOLVE http://xray.utmb.edu/PMB).  In one low resolution MR
case at 3.5A we had an entire domain in the wrong orientation and DM
gave clear and unambiguous density for the correct orientation (caveat:
70% solvent does wonders for phase improvement).

Good luck,

Mark


On Fri, 2007-10-19 at 11:39 -0400, Joe Smith wrote:

> Hi all,
> 
> We have data sets for a protein-RNA complex at 3.2 A resolution. . The
> data belong to the space group I4122 and contains one molecule of
> Protein-RNA complex (300AA and 16nt; 66% solvent content) in the asym
> unit. We have managed to get phases using Se-SAD and the present model
> contains 60% of the protein atoms (250 residues many of them build as
> Ala) and almost complete RNA (16nt).  We could not locate ~20 % of the
> residues (present in various loops as well as at N- and C-terminal
> ends). First 120 residues present at N-terminal end seem to have poor
> relatively main-chain density and almost no side chain density. RNA
> and 130 residues present at the C-terminal end have good electron
> density for main-chain as well as side chain.
> 
> The solution seems to be correct as molecular replacement trials with
> this model gave same solution in Phaser, Molrep and AMoRe. Solution
> seems to be also correct because as expected one RNA strand present in
> asym unit pairs with another one coming from symmetry related
> molecule.
> 
> We have checked data in space group I4122 with CCP4 (SFCHECK,
> cumulative intensity distribution), Yeates server as well as
> Phenix.xtriage. In all the cases it indicates no twinning. However if
> I process the data in lower symmetry space group it does indicate
> presence of almost perfect twin. We realize that this could be just
> because of processing data in lower symmetry space group and data in
> all probability may still be fine.
> 
> The problem is now with refinement and model building. Refinement with
> CNS and Refamc gave considerably higher value of R and R free. In
> CNS1.1, refinement with small changes in the model some time leads to
> large shift in R and R-free value.
>  Refmac: R=36; Rfree=47
> CNS1.1:  R=40-59; R-free=45-63
> However in both the cases map looks more or less same (with reasonably
> good density for the main-chain as well as RNA)
> 
> I tried refining with phenix.refine and there is some improvement in
> the R(34%) and Rfree(40%) values. I think may be robust bulk solvent
> correction incorporated in phenix.refine has helped in this case.
> However, I still see no improvement in the map quality for the first
> 120 residues.
> 
> In the absence of any clear density I am unable to build any further.
> I feel N-terminal domain is bit flexible and may have overall poor
> density. I have used Se position as well as predicted secondary
> structure in assigning the amino acid in the map but due to few breaks
> in the N-terminal domain as well as poor density I am unable to assign
> any amino acid into the poly ala main chain.
> 
> Frankly speaking, I do not know how to proceed further. I welcome any
> kind of suggestions which could help us in this case.
> 
> Regards
> Joe

Yours sincerely,

Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology, 
Manager, Sealy Center for Structural Biology and Molecular Biophysics
X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Fax. (409) 747-4745
mailto://[EMAIL PROTECTED]
http://xray.utmb.edu
http://xray.utmb.edu/~white

[ccp4bb] problems with map quality, refinement and R/Rfree

[Joe Smith]

Hi all,

We have data sets for a protein-RNA complex at 3.2 A resolution. . The
data belong to the space group I4122 and contains one molecule of
Protein-RNA complex (300AA and 16nt; 66% solvent content) in the asym
unit. We have managed to get phases using Se-SAD and the present model
contains 60% of the protein atoms (250 residues many of them build as
Ala) and almost complete RNA (16nt).  We could not locate ~20 % of the
residues (present in various loops as well as at N- and C-terminal
ends). First 120 residues present at N-terminal end seem to have poor
relatively main-chain density and almost no side chain density. RNA
and 130 residues present at the C-terminal end have good electron
density for main-chain as well as side chain.

The solution seems to be correct as molecular replacement trials with
this model gave same solution in Phaser, Molrep and AMoRe. Solution
seems to be also correct because as expected one RNA strand present in
asym unit pairs with another one coming from symmetry related
molecule.

We have checked data in space group I4122 with CCP4 (SFCHECK,
cumulative intensity distribution), Yeates server as well as
Phenix.xtriage. In all the cases it indicates no twinning. However if
I process the data in lower symmetry space group it does indicate
presence of almost perfect twin. We realize that this could be just
because of processing data in lower symmetry space group and data in
all probability may still be fine.

The problem is now with refinement and model building. Refinement with
CNS and Refamc gave considerably higher value of R and R free. In
CNS1.1, refinement with small changes in the model some time leads to
large shift in R and R-free value.
 Refmac: R=36; Rfree=47
CNS1.1:  R=40-59; R-free=45-63
However in both the cases map looks more or less same (with reasonably
good density for the main-chain as well as RNA)

I tried refining with phenix.refine and there is some improvement in
the R(34%) and Rfree(40%) values. I think may be robust bulk solvent
correction incorporated in phenix.refine has helped in this case.
However, I still see no improvement in the map quality for the first
120 residues.

In the absence of any clear density I am unable to build any further.
I feel N-terminal domain is bit flexible and may have overall poor
density. I have used Se position as well as predicted secondary
structure in assigning the amino acid in the map but due to few breaks
in the N-terminal domain as well as poor density I am unable to assign
any amino acid into the poly ala main chain.

Frankly speaking, I do not know how to proceed further. I welcome any
kind of suggestions which could help us in this case.

Regards
Joe

Re: [ccp4bb] problems with map quality, refinement and R/Rfree

[Kay Diederichs]

I'd try to
1) make sure your data reduction is optimal - try at least one other program, 
and not only your favourite one!
2) as this is SAD: use SHARP to get the best experimental phases, plus density 
modification for a map without model bias
3) incorporate the experimental phase information into the refinement - can be 
done in all programs you mention, but maybe optimally in the procedure published 
in Acta Cryst. (2004). D60, 2196-2201

Direct incorporation of experimental phase information in model refinement
P. Skubák, G. N. Murshudov and N. S. Pannu
- have not tried this myself, but it sounds fairly convincing.

HTH,
Kay

Joe Smith schrieb:

Hi all,

We have data sets for a protein-RNA complex at 3.2 A resolution. . The
data belong to the space group I4122 and contains one molecule of
Protein-RNA complex (300AA and 16nt; 66% solvent content) in the asym
unit. We have managed to get phases using Se-SAD and the present model
contains 60% of the protein atoms (250 residues many of them build as
Ala) and almost complete RNA (16nt).  We could not locate ~20 % of the
residues (present in various loops as well as at N- and C-terminal
ends). First 120 residues present at N-terminal end seem to have poor
relatively main-chain density and almost no side chain density. RNA
and 130 residues present at the C-terminal end have good electron
density for main-chain as well as side chain.

The solution seems to be correct as molecular replacement trials with
this model gave same solution in Phaser, Molrep and AMoRe. Solution
seems to be also correct because as expected one RNA strand present in
asym unit pairs with another one coming from symmetry related
molecule.

We have checked data in space group I4122 with CCP4 (SFCHECK,
cumulative intensity distribution), Yeates server as well as
Phenix.xtriage. In all the cases it indicates no twinning. However if
I process the data in lower symmetry space group it does indicate
presence of almost perfect twin. We realize that this could be just
because of processing data in lower symmetry space group and data in
all probability may still be fine.

The problem is now with refinement and model building. Refinement with
CNS and Refamc gave considerably higher value of R and R free. In
CNS1.1, refinement with small changes in the model some time leads to
large shift in R and R-free value.
 Refmac: R=36; Rfree=47
CNS1.1:  R=40-59; R-free=45-63
However in both the cases map looks more or less same (with reasonably
good density for the main-chain as well as RNA)

I tried refining with phenix.refine and there is some improvement in
the R(34%) and Rfree(40%) values. I think may be robust bulk solvent
correction incorporated in phenix.refine has helped in this case.
However, I still see no improvement in the map quality for the first
120 residues.

In the absence of any clear density I am unable to build any further.
I feel N-terminal domain is bit flexible and may have overall poor
density. I have used Se position as well as predicted secondary
structure in assigning the amino acid in the map but due to few breaks
in the N-terminal domain as well as poor density I am unable to assign
any amino acid into the poly ala main chain.

Frankly speaking, I do not know how to proceed further. I welcome any
kind of suggestions which could help us in this case.

Regards
Joe



--
Kay Diederichs  http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED]  Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz



smime.p7s
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[ccp4bb] Gerard Bunick )posted on behalf of Leif Hanson(

[Artem Evdokimov]

Dear Colleagues,

 

It is with sorrow I report the passing of Gerard (Gerry) Bunick on September
19, 2007 in Oak Ridge, Tennessee after an 11 year struggle with cancer. In
addition to other significant research, Gerry was one of the architects of
the resurgence in neutron protein crystallography. He is survived by his
wife, son and daughter-in-law, and daughter and son-in-law. He will be
missed.

 

Leif Hanson