Re: [ccp4bb] Rsym problems...maybe???

[Kay Diederichs]

Am 20:59, schrieb Poul Nissen:

I very much agree - refinement will tell you if the high-res data make
sense. Another very good test is the Wilson plot - it should look
straight and reasonable. Inflated I/sigI values will not escape a
strange appearance such as the WIlson plot flattening out at higher
resolution. I normally find a very good consistency between the
resolution cut-offs indicated by the wilson plot and the refinement
statistics.



good advice


Poul
On 22/04/2010, at 19.59, Edward A. Berry wrote:


There are plenty of structures in the database with R-sym=0.99.
But something is odd here. If I understand R-pim, it should
always be bigger than Rsym, because this factor of sqrt(N/(N-1)) is
always >1
Are you saying Rpim is .30 and Rsym is 1.00?


a correction: the factor of sqrt(N/(N-1)) that you quote is for R-rim 
(same as R_meas), not for R-pim.


R-pim (more or less same as R_mrgd-I) has a factor of  sqrt(1/(N-1)) so 
a value of 30% is believable. As this is on intensities, the equivalent 
quantity calculated on amplitudes should be even less. That means that 
refinement should be happy with those data!


see the wiki: 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R-factors


HTH,

Kay



Last time I deposited a structure, Rsym and Rmerge in the last shell
are optional.
I would leave it out and rely on the excellent I/sigI in the last shell,
and use all the data (provided after refinement R-free in the last
shell is < .4).
Ed

Daniel Bonsor wrote:

Hello again.

At first I was not worry but maybe now I am. I have completed a
structure and submitted to the PDB. They queried my Rsym value in the
highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not
worried at the time as I had:

99.4% completeness
Mean(I/sdI) of 2.5
and a redundancy of 11 (which would explain the high Rsym)
Space group I422

My Rpim in this shell is 30%.

Should I reduce the resolution and start from scratch again or is
everything fine and dandy and I should stop worrying?







smime.p7s
Description: S/MIME Cryptographic Signature

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

[Garib Murshudov]

I think your procedure is good with current technology. At early  
stages twin refinement may give misleading results.


An intuitive resoning for low R factor would be: Twin is summation of  
intensities. As you sum intensities two things happen: 1) distribution  
of intensities become more symmetric (departs from wilson distribution  
or chisquared distribution with degrees of freedom 2 in case of  
acentric reflections) 2) distributions become narrower. As  
distribution becomes narrower probability that differences between  
randomly selected values from the population with this distribution is  
small will be higher. Hence R factors will be smaller. When errors in  
model becomes comparable with the errors in experiment then  
differences between observed structure and calculated structure  
factors become more "independent" and R factors become comparable. In  
practice it never happens (errors in model are always higher than  
errors in experimental data which is understandable). So "twin" R  
factor always going to be lower than corresponding non-twin R factor.


As a general rule: One should be careful in comparing R factors from  
two different crystals. R factors are not only dependent on errors in  
coordinate model. But they are dependent on many statistical  
properties of crystal, twinning is just an example of such properties.


There are some warnings about twin refinement for extreme cases on the  
presentation from www.ysbl.york.ac.uk:/y/people/garib/Presentations/ 
Refmac_February.ppt, slides number 17 and 18 (apologies if it sound  
like as self promotion)


regards
Garib



On 23 Apr 2010, at 22:56, Jon Schuermann wrote:

Hari,

   What twin tests have you run? Results? If your data really is  
P43212 and you drop to P212121 you will still have the additional  
two-fold operator in your data. An operator is a mathematical  
operator, which could be crystallographic or twin.


   I never refine a structure with twin refinement from the  
beginning (even if I suspect it is twinned). I do iterative rounds  
of model building and conventional refinement until I cannot get the  
R-factor any lower. Depending on many factors (resolution, twin  
fraction, etc.), I usually get stuck in the mid-30's. At this point  
I will investigate twin refinement or other possible SG's.


If you start using twin refinement too early in the model building  
process, I have seen programs report much too low R-factors and  
exaggerated twin fractions. Probably, a programmer like Garib or  
Peter could comment on why.


Jon



On 04/23/2010 04:28 PM, hari jayaram wrote:
I am refining a twinned dataset in possible spacegroup P212121 .  
Pointless thinks it is P43212 , but based on reading this posting (http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html 
) I think it is P212121.


The starting R/Rfree after molecular replacement  ( single site  
mutant)  was 34/38 to 2.2 A


After an initial round of restrained refinement ( without twin  
refinement) and minimal rebuilding I got the R/Rfree to 30/34


Then I did an amplitude based twin refinement - The twin fraction  
was 0.48 k,h,-l and 0.52 h,k,l and The r/rfree became 24/29


After a little more rebuilding ( a few residues out of 800 residues  
in ASU) and another twin refinement I got an r/rfree of 22/27 . Now  
the twin fraction was 0.87 (h,k,l) and 0.13 (k,h,-1)


The maps looked a little better allowing me to fix a few more  
residues


Finally the same twin refinement gives me no twin operators and the  
R/Rfree is 22/26



All the twinning tests indicate a serious twinning in my crystal.   
Any ideas why I am seeing this


Hari






--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439

email: schue...@anl.gov
Tel: (630) 252-0682
Fax: (630) 252-0687

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

[hari jayaram]

Hello Garib,
I was using the ouput from a refmac run for the next round and using what I
thought were the original fobs .
So I guess as you said at each round I was using the de-twinned result from
the previous round.

I will repeat these refinements with the original scala output mtz to get a
more accurate feel for the twin fraction.

I am using medium restraints with NCS ( I have four molecules in the asu)
and the data does also look like P43212 with fewer molecules in the ASU.

Thank you  for all your suggestions
Hari


On Fri, Apr 23, 2010 at 5:38 PM, Garib Murshudov wrote:

> You may be using output reflection data  from the previous cycle of
> refinement for the next session. After twin refinement output Fobs
> (confusingly) may be detwinned. You can try to use original reflection data
> file (e.g. after scala/truncate/freerflag) and  for refinement and it may
> clarify things a bit. If you are using original reflection data file for
> refinement then I do not knwo the reason of such peculiar behaviour.
>
> I have seen that twin fraction during refinement goes down but I am not
> sure that it would happen  substatioally if your R/Rfree were as you stated
> before twin refinement.
>
> regards
> Garib
>
> On 23 Apr 2010, at 22:28, hari jayaram wrote:
>
> I am refining a twinned dataset in possible spacegroup P212121 . Pointless
> thinks it is P43212 , but based on reading this posting (
> http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html)
> I think it is P212121.
>
> The starting R/Rfree after molecular replacement  ( single site mutant)
> was 34/38 to 2.2 A
>
> After an initial round of restrained refinement ( without twin refinement)
> and minimal rebuilding I got the R/Rfree to 30/34
>
> Then I did an amplitude based twin refinement - The twin fraction was 0.48
> k,h,-l and 0.52 h,k,l and The r/rfree became 24/29
>
> After a little more rebuilding ( a few residues out of 800 residues in ASU)
> and another twin refinement I got an r/rfree of 22/27 . Now the twin
> fraction was 0.87 (h,k,l) and 0.13 (k,h,-1)
>
> The maps looked a little better allowing me to fix a few more residues
>
> Finally the same twin refinement gives me no twin operators and the R/Rfree
> is 22/26
>
>
> All the twinning tests indicate a serious twinning in my crystal.  Any
> ideas why I am seeing this
>
> Hari
>
>
>
>
>

Re: [ccp4bb] YATQ (yet another twinning question) - may involve pirates

[Garib Murshudov]

I am getting in habit of writing double emails.

I would say that refmac overestimates at early stages and truncate  
underestimates (it is just an intuition, not based on theoretical or  
empriical results)


Garib

On 23 Apr 2010, at 23:16, Ethan Merritt wrote:


In a nutshell
=
  Is there a way to make solve/resolve behave reasonably if the data
  is twinned?  Is there a recommended alternative path to clean up and
  maybe even auto-trace a map with 4-fold NCS but twinned data?
  Maybe Pirate/Buccaneer?

In detail
=
I'm fighting with a structure that is probably/maybe in P4(2).

  2.6A data 98% complete
  Rmerge = 0.07 in P4
  Rmerge = 0.16 in P422(note the disturbingly low value)

Pointless is 88% confident it's P4(2).

  Laue GroupLklhd   NetZc  Zc+   Zc-CCCC-  Rmeas   R-

= 1  P 4/m  ***  0.916   4.68  9.36  4.67   0.94  0.47   0.09   
0.30

10  P 4/m m m   0.000   6.83  6.83  0.00   0.68  0.00   0.20  0.00

Truncate says the data is twinned, with a twinning fraction of 0.25.
That is consistent with the bad-but-not-awful Rmerge in P422, right?

I have a promising initial MR solution in P4(2) with four monomers
in the a.s.u. It refines to R/Rfree = 0.36/0.38 in refmac but only  
if I

enable the twinned data option. Twinning fraction refines to
  Twin fractions=0.4322   0.5678

My thought was to use the 4-fold NCS and solvent flattening in  
resolve to

clean up and ideally auto-trace into the initial mediocre maps.
The resolution is not great, but the 4-fold NCS should help a lot.
Unfortunately, so far as I can figure out resolve ignores the twinning
and is stuck dealing with R > 0.60 and extremely poor maps.

I tried de-twinning the data, but this was not a great success.
Should I believe the truncate estimate of 25% twinning fraction
or the refmac estimate of 43%?  Neither?  In any case, feeding the
supposedly detwinned data to either refmac or resolve produces
worse results that I was getting before attempted detwinning.

Any advice?

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] YATQ (yet another twinning question) - may involve pirates

[Garib Murshudov]

I hope Kevin will respond soon. I think he has done (or is planning to  
do) to twinning and ncs in his pipeline of model building.
I think something like that may already be in new ARP/wARP (Victor and  
Tasos will correct me if I am wrong)


regards
Garib

On 23 Apr 2010, at 23:16, Ethan Merritt wrote:


In a nutshell
=
  Is there a way to make solve/resolve behave reasonably if the data
  is twinned?  Is there a recommended alternative path to clean up and
  maybe even auto-trace a map with 4-fold NCS but twinned data?
  Maybe Pirate/Buccaneer?

In detail
=
I'm fighting with a structure that is probably/maybe in P4(2).

  2.6A data 98% complete
  Rmerge = 0.07 in P4
  Rmerge = 0.16 in P422(note the disturbingly low value)

Pointless is 88% confident it's P4(2).

  Laue GroupLklhd   NetZc  Zc+   Zc-CCCC-  Rmeas   R-

= 1  P 4/m  ***  0.916   4.68  9.36  4.67   0.94  0.47   0.09   
0.30

10  P 4/m m m   0.000   6.83  6.83  0.00   0.68  0.00   0.20  0.00

Truncate says the data is twinned, with a twinning fraction of 0.25.
That is consistent with the bad-but-not-awful Rmerge in P422, right?

I have a promising initial MR solution in P4(2) with four monomers
in the a.s.u. It refines to R/Rfree = 0.36/0.38 in refmac but only  
if I

enable the twinned data option. Twinning fraction refines to
  Twin fractions=0.4322   0.5678

My thought was to use the 4-fold NCS and solvent flattening in  
resolve to

clean up and ideally auto-trace into the initial mediocre maps.
The resolution is not great, but the 4-fold NCS should help a lot.
Unfortunately, so far as I can figure out resolve ignores the twinning
and is stuck dealing with R > 0.60 and extremely poor maps.

I tried de-twinning the data, but this was not a great success.
Should I believe the truncate estimate of 25% twinning fraction
or the refmac estimate of 43%?  Neither?  In any case, feeding the
supposedly detwinned data to either refmac or resolve produces
worse results that I was getting before attempted detwinning.

Any advice?

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

[ccp4bb] YATQ (yet another twinning question) - may involve pirates

[Ethan Merritt]

In a nutshell
=
   Is there a way to make solve/resolve behave reasonably if the data
   is twinned?  Is there a recommended alternative path to clean up and
   maybe even auto-trace a map with 4-fold NCS but twinned data?
   Maybe Pirate/Buccaneer?

In detail
=
I'm fighting with a structure that is probably/maybe in P4(2).

   2.6A data 98% complete
   Rmerge = 0.07 in P4
   Rmerge = 0.16 in P422(note the disturbingly low value)

Pointless is 88% confident it's P4(2).

   Laue GroupLklhd   NetZc  Zc+   Zc-CCCC-  Rmeas   R-  

= 1  P 4/m  ***  0.916   4.68  9.36  4.67   0.94  0.47   0.09  0.30 
 10  P 4/m m m   0.000   6.83  6.83  0.00   0.68  0.00   0.20  0.00 

Truncate says the data is twinned, with a twinning fraction of 0.25.
That is consistent with the bad-but-not-awful Rmerge in P422, right?

I have a promising initial MR solution in P4(2) with four monomers
in the a.s.u. It refines to R/Rfree = 0.36/0.38 in refmac but only if I
enable the twinned data option. Twinning fraction refines to
   Twin fractions=0.4322   0.5678

My thought was to use the 4-fold NCS and solvent flattening in resolve to
clean up and ideally auto-trace into the initial mediocre maps.
The resolution is not great, but the 4-fold NCS should help a lot.
Unfortunately, so far as I can figure out resolve ignores the twinning
and is stuck dealing with R > 0.60 and extremely poor maps.

I tried de-twinning the data, but this was not a great success.
Should I believe the truncate estimate of 25% twinning fraction
or the refmac estimate of 43%?  Neither?  In any case, feeding the
supposedly detwinned data to either refmac or resolve produces 
worse results that I was getting before attempted detwinning.

Any advice?

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

[Jon Schuermann]

Hari,

What twin tests have you run? Results? If your data really is 
P43212 and you drop to P212121 you will still have the additional 
two-fold operator in your data. An operator is a mathematical operator, 
which could be crystallographic or twin.


I never refine a structure with twin refinement from the beginning 
(even if I suspect it is twinned). I do iterative rounds of model 
building and conventional refinement until I cannot get the R-factor any 
lower. Depending on many factors (resolution, twin fraction, etc.), I 
usually get stuck in the mid-30's. At this point I will investigate twin 
refinement or other possible SG's.


If you start using twin refinement too early in the model building 
process, I have seen programs report much too low R-factors and 
exaggerated twin fractions. Probably, a programmer like Garib or Peter 
could comment on why.


Jon



On 04/23/2010 04:28 PM, hari jayaram wrote:
I am refining a twinned dataset in possible spacegroup P212121 . 
Pointless thinks it is P43212 , but based on reading this posting 
(http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html) 
I think it is P212121.


The starting R/Rfree after molecular replacement  ( single site 
mutant)  was 34/38 to 2.2 A


After an initial round of restrained refinement ( without twin 
refinement) and minimal rebuilding I got the R/Rfree to 30/34


Then I did an amplitude based twin refinement - The twin fraction was 
0.48 k,h,-l and 0.52 h,k,l and The r/rfree became 24/29


After a little more rebuilding ( a few residues out of 800 residues in 
ASU) and another twin refinement I got an r/rfree of 22/27 . Now the 
twin fraction was 0.87 (h,k,l) and 0.13 (k,h,-1)


The maps looked a little better allowing me to fix a few more residues

Finally the same twin refinement gives me no twin operators and the 
R/Rfree is 22/26



All the twinning tests indicate a serious twinning in my crystal.  Any 
ideas why I am seeing this


Hari






--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439

email: schue...@anl.gov
Tel: (630) 252-0682
Fax: (630) 252-0687

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

[Garib Murshudov]

And another (not so) minor point: Defferences between R/Rfree with  
twin on and off suggest that there is strong correlation between twin  
and NCS. For this cases better dealt with if you use twin refinement  
with sufficiently strong NCS restraints. In new refmac (www.ysbl.york.ac.uk/refmac/ 
  site: look for the experimental version) and in phenix (as far as I  
know) you can do NCS automatically.


Even after twin refinement with ncs I would check if higher space  
group is possible. You can try to do it using for example zanuda (from  
the webserver www.ysbl.york.ac.uk/YSBLPrograms/index.jsp). I think  
phenix.triage may be able to do similar things.


regards
Garib

On 23 Apr 2010, at 22:28, hari jayaram wrote:

I am refining a twinned dataset in possible spacegroup P212121 .  
Pointless thinks it is P43212 , but based on reading this posting (http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html 
) I think it is P212121.


The starting R/Rfree after molecular replacement  ( single site  
mutant)  was 34/38 to 2.2 A


After an initial round of restrained refinement ( without twin  
refinement) and minimal rebuilding I got the R/Rfree to 30/34


Then I did an amplitude based twin refinement - The twin fraction  
was 0.48 k,h,-l and 0.52 h,k,l and The r/rfree became 24/29


After a little more rebuilding ( a few residues out of 800 residues  
in ASU) and another twin refinement I got an r/rfree of 22/27 . Now  
the twin fraction was 0.87 (h,k,l) and 0.13 (k,h,-1)


The maps looked a little better allowing me to fix a few more residues

Finally the same twin refinement gives me no twin operators and the  
R/Rfree is 22/26



All the twinning tests indicate a serious twinning in my crystal.   
Any ideas why I am seeing this


Hari

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

[Garib Murshudov]

You may be using output reflection data  from the previous cycle of  
refinement for the next session. After twin refinement output Fobs  
(confusingly) may be detwinned. You can try to use original reflection  
data file (e.g. after scala/truncate/freerflag) and  for refinement  
and it may clarify things a bit. If you are using original reflection  
data file for refinement then I do not knwo the reason of such  
peculiar behaviour.


I have seen that twin fraction during refinement goes down but I am  
not sure that it would happen  substatioally if your R/Rfree were as  
you stated before twin refinement.


regards
Garib

On 23 Apr 2010, at 22:28, hari jayaram wrote:

I am refining a twinned dataset in possible spacegroup P212121 .  
Pointless thinks it is P43212 , but based on reading this posting (http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html 
) I think it is P212121.


The starting R/Rfree after molecular replacement  ( single site  
mutant)  was 34/38 to 2.2 A


After an initial round of restrained refinement ( without twin  
refinement) and minimal rebuilding I got the R/Rfree to 30/34


Then I did an amplitude based twin refinement - The twin fraction  
was 0.48 k,h,-l and 0.52 h,k,l and The r/rfree became 24/29


After a little more rebuilding ( a few residues out of 800 residues  
in ASU) and another twin refinement I got an r/rfree of 22/27 . Now  
the twin fraction was 0.87 (h,k,l) and 0.13 (k,h,-1)


The maps looked a little better allowing me to fix a few more residues

Finally the same twin refinement gives me no twin operators and the  
R/Rfree is 22/26



All the twinning tests indicate a serious twinning in my crystal.   
Any ideas why I am seeing this


Hari

[ccp4bb] Shifting twin fraction with refinement - finally zero

[hari jayaram]

I am refining a twinned dataset in possible spacegroup P212121 . Pointless
thinks it is P43212 , but based on reading this posting (
http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html)
I think it is P212121.

The starting R/Rfree after molecular replacement  ( single site mutant)  was
34/38 to 2.2 A

After an initial round of restrained refinement ( without twin refinement)
and minimal rebuilding I got the R/Rfree to 30/34

Then I did an amplitude based twin refinement - The twin fraction was 0.48
k,h,-l and 0.52 h,k,l and The r/rfree became 24/29

After a little more rebuilding ( a few residues out of 800 residues in ASU)
and another twin refinement I got an r/rfree of 22/27 . Now the twin
fraction was 0.87 (h,k,l) and 0.13 (k,h,-1)

The maps looked a little better allowing me to fix a few more residues

Finally the same twin refinement gives me no twin operators and the R/Rfree
is 22/26


All the twinning tests indicate a serious twinning in my crystal.  Any ideas
why I am seeing this

Hari

Re: [ccp4bb] Adding TER card in PDB file

[Tim Gruene]

You can do it with any text editor. From 
$CCP4/html/pdbformat.html#part1ter:
Cols.  1-3Record name "TER"
  7-11Serial number
  18-20   Residue name
  21-27   Sequence identifier

So you copy the serial number, residue name and sequence identifier from the
very line which precedes the "TER"-line.

Tim

On Fri, Apr 23, 2010 at 11:55:21PM +0530, Mike England wrote:
> Hi all,
> 
> I will greatly appreciate your help for the following:
> 
> I am getting an error of not having TER card at the end of chain
> during precheck of PDB deposition. Hence, I would like to add TER card
> at the end of  chain in my PDB file. Adding TER card manually is not
> problem but how to add "Atom serial number" ? Can it be done by some
> kind of PDB edit ?
> 
> Thank you very much.
> 
> Mike

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

GPG Key ID = A46BEE1A



signature.asc
Description: Digital signature

Re: [ccp4bb] Substitute for Lithium Sulfate

[Jim Pflugrath]

I would test several hypotheses.  You have a multitude of salts to choose
from.  Test them all.
Let me ask you this:  What anions can you test?   What's already on your
shelf of chemicals?  What did you test already?
 
Jim

  _  

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Yi-Liang Liu
Sent: Friday, April 23, 2010 12:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Substitute for Lithium Sulfate


Hi Everyone,


I have a question about the crystallization condition. Currently the
condition I use contains 0.2M lithium sulfate. However, the ligand there
seems to compete the site where sulfate binds in the active site. Are there
any good substitute to replace the Lithium sulfate in my crystallization
buffer?

Best,

Lucas

[ccp4bb] Adding TER card in PDB file

[Mike England]

Hi all,

I will greatly appreciate your help for the following:

I am getting an error of not having TER card at the end of chain
during precheck of PDB deposition. Hence, I would like to add TER card
at the end of  chain in my PDB file. Adding TER card manually is not
problem but how to add "Atom serial number" ? Can it be done by some
kind of PDB edit ?

Thank you very much.

Mike

[ccp4bb] Substitute for Lithium Sulfate

[Yi-Liang Liu]

Hi Everyone,

I have a question about the crystallization condition. Currently the  
condition I use contains 0.2M lithium sulfate. However, the ligand  
there seems to compete the site where sulfate binds in the active  
site. Are there any good substitute to replace the Lithium sulfate in  
my crystallization buffer?


Best,

Lucas

Re: [ccp4bb] phenix error message

[Tim Gruene]

On Fri, Apr 23, 2010 at 08:23:30AM -0700, Pavel Afonine wrote:
>
>
> On 4/23/10 8:14 AM, Tim Gruene wrote:
>> On Fri, Apr 23, 2010 at 07:20:15AM -0700, Nathaniel Echols wrote:
>>   
>>> On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene  
>>> wrote:
>>>
>>> 
 we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
 Testing. After starting a refinement job, the following error message shows
 up:

   
>>> Tim: please report these errors to either b...@phenix-online.org, or the
>>> phenixbb.  Most of the Phenix developers don't read CCP4BB and I'm trying to
>>> avoid filling it with Phenix-related chatter.
>>> 
>> So be it.
>
> I read (as interactive as phenixbb). And post... -:)

I am not surprised. From the list of authors of the reference of phenix you are
certainly not the only one!
>
> Pavel.

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

GPG Key ID = A46BEE1A



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Re: [ccp4bb] MacBookPro problems

[Jürgen Bosch]

Yeah, send your Zalman vendor a nice email and let them exchange your DVI 
adapter. Had that problem too - alternatively you can scavenge one DVI adapter 
from another computer and test it. I wouldn't be surprised if it works, that's 
how I figured it out.

Jürgen

On Apr 23, 2010, at 9:37 AM, Joachim Reichelt wrote:

> Dear all,
> 
> I just got a MacBookPro.
> I have two questions:
> How to get the keyboard shortcuts in coot or pymol up, e.g. F to
> open the file dialog.
> 
> and
> 
> whenever I connect a zalman 220 (stereo ready) monitor to the mac using
> a miniDisplayPort to DVI
> adapter, the monitor is not recognized and so it is completely dark. The
> Mac does not show the monitor in the dialogues but an error message.
> 
> -- 
> Joachim

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

Re: [ccp4bb] phenix error message

[Pavel Afonine]

On 4/23/10 8:14 AM, Tim Gruene wrote:

On Fri, Apr 23, 2010 at 07:20:15AM -0700, Nathaniel Echols wrote:
  

On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene  wrote:



we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
Testing. After starting a refinement job, the following error message shows
up:

  

Tim: please report these errors to either b...@phenix-online.org, or the
phenixbb.  Most of the Phenix developers don't read CCP4BB and I'm trying to
avoid filling it with Phenix-related chatter.


So be it.


I read (as interactive as phenixbb). And post... -:)

Pavel.

Re: [ccp4bb] phenix error message

[Tim Gruene]

On Fri, Apr 23, 2010 at 07:20:15AM -0700, Nathaniel Echols wrote:
> On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene  wrote:
> 
> > we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
> > Testing. After starting a refinement job, the following error message shows
> > up:
> >
> 
> Tim: please report these errors to either b...@phenix-online.org, or the
> phenixbb.  Most of the Phenix developers don't read CCP4BB and I'm trying to
> avoid filling it with Phenix-related chatter.
So be it.
> 
> 
> >  File
> > "/xtal/Suites/64bit/phenix-1.6.1-357/build/intel-linux-2.6-x86_64/base/lib/python2.6/copy_reg.py",
> > line 84, in _reduce_ex
> >dict = getstate()
> > TypeError: 'NoneType' object is not callable
> > < snap >8
> >
> > Does anyone know what the error messages mean and how we can overcome them?
> >
> 
> No, it is one of the less well-thought-out features of Python which I made
> the mistake of using, and it is extremely difficult to debug.  The problem
> is some sort of corruption in the project database, but it isn't clear how
> it happens or how to fix it.  Did you try closing and restarting the GUI?
>  Also, this error apparently only happens when there is an error in the
> refinement.  Unfortunately, the original message is being suppressed by this
> one.  The next nightly build should report the original error; I would
> recommend downloading that and trying it.  (Hopefully tomorrow, but some
> unrelated problems are preventing us from releasing any installers right
> now.)
> 
> You can also try running the same refinement from the command line - it will
> almost certainly fail, but it will at least tell you what to fix in your
> inputs (or what to report as a bug - could be either).
> 

We are going to try the nightly build and also the command line.
I'll post the results to the bugs-address.

Thanks for the recmmendations. Tim
> thanks,
> Nat

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

GPG Key ID = A46BEE1A



signature.asc
Description: Digital signature

Re: [ccp4bb] Biobar 2.0.1

[Jayashankar]

Very much appreciable.
thanks

S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.


On Fri, Apr 23, 2010 at 4:50 PM, Jawahar Swaminathan wrote:

>  Biobar version 2.0.1 is now available.
>
> Biobar is a powerful browsing and searching toolbar developed at EMBL-EBI's
> Protein Data Bank in Europe (PDBe; pdbe.org).
>
> Biobar works inside Firefox browsers on all supported operating systems.
> Biobar provides easy access to over 40 biological data sources, including
> Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and
> Animal-specific databases. In addition to facilitating search and retrieval,
> Biobar also provides static links to important bioinformatics sites and
> services including those at the European Bioinformatics Institute (EBI), the
> National Center for Biotechnology Information (NCBI) and the DNA Data Bank
> of Japan (DDBJ). Biobar further provides one-stop access to major
> data-deposition sites for nucleotide, protein and 3D-structure data and
> links to many sequence and structure alignment and analysis tools.
>
> For more information please see:
>
> http://www.ebi.ac.uk/pdbe/docs/biobar.html
>
> For installation, please go to:
>
> https://addons.mozilla.org/en-US/firefox/addon/169
>
> You may also be interested in simple search plugins for IE7/8, Google
> Chrome or Firefox to query the EBI EB-eye service or the PDBe. Get these
> from:
>
> PDBe: http://mycroft.mozdev.org/search-engines.html?name=pdbe
> EBI EB-eye: http://mycroft.mozdev.org/search-engines.html?name=eb-eye
>
> Please send any questions, queries to jawa...@ebi.ac.uk
>
> regards -
>
> Jawahar Swaminathan
> http://www.pdbe.org/
>

[ccp4bb] Biobar 2.0.1

[Jawahar Swaminathan]

 Biobar version 2.0.1 is now available.

Biobar is a powerful browsing and searching toolbar developed at 
EMBL-EBI's Protein Data Bank in Europe (PDBe; pdbe.org).


Biobar works inside Firefox browsers on all supported operating systems. 
Biobar provides easy access to over 40 biological data sources, 
including Genomic, Proteomic, Functional, Literature, Taxonomic, 
Structural, Plant and Animal-specific databases. In addition to 
facilitating search and retrieval, Biobar also provides static links to 
important bioinformatics sites and services including those at the 
European Bioinformatics Institute (EBI), the National Center for 
Biotechnology Information (NCBI) and the DNA Data Bank of Japan (DDBJ). 
Biobar further provides one-stop access to major data-deposition sites 
for nucleotide, protein and 3D-structure data and links to many sequence 
and structure alignment and analysis tools.


For more information please see:

http://www.ebi.ac.uk/pdbe/docs/biobar.html

For installation, please go to:

https://addons.mozilla.org/en-US/firefox/addon/169

You may also be interested in simple search plugins for IE7/8, Google 
Chrome or Firefox to query the EBI EB-eye service or the PDBe. Get these 
from:


PDBe: http://mycroft.mozdev.org/search-engines.html?name=pdbe
EBI EB-eye: http://mycroft.mozdev.org/search-engines.html?name=eb-eye

Please send any questions, queries to jawa...@ebi.ac.uk

regards -

Jawahar Swaminathan
http://www.pdbe.org/

Re: [ccp4bb] phenix error message

[Nathaniel Echols]

On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene  wrote:

> we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
> Testing. After starting a refinement job, the following error message shows
> up:
>

Tim: please report these errors to either b...@phenix-online.org, or the
phenixbb.  Most of the Phenix developers don't read CCP4BB and I'm trying to
avoid filling it with Phenix-related chatter.


>  File
> "/xtal/Suites/64bit/phenix-1.6.1-357/build/intel-linux-2.6-x86_64/base/lib/python2.6/copy_reg.py",
> line 84, in _reduce_ex
>dict = getstate()
> TypeError: 'NoneType' object is not callable
> < snap >8
>
> Does anyone know what the error messages mean and how we can overcome them?
>

No, it is one of the less well-thought-out features of Python which I made
the mistake of using, and it is extremely difficult to debug.  The problem
is some sort of corruption in the project database, but it isn't clear how
it happens or how to fix it.  Did you try closing and restarting the GUI?
 Also, this error apparently only happens when there is an error in the
refinement.  Unfortunately, the original message is being suppressed by this
one.  The next nightly build should report the original error; I would
recommend downloading that and trying it.  (Hopefully tomorrow, but some
unrelated problems are preventing us from releasing any installers right
now.)

You can also try running the same refinement from the command line - it will
almost certainly fail, but it will at least tell you what to fix in your
inputs (or what to report as a bug - could be either).

thanks,
Nat

Re: [ccp4bb] MacBookPro problems

[Phil Evans]

I'm using a MacbookPro with a Zalman monitor with a DVI to DVI connector (an 
older MBP with a DVI port), and it works fine with no problems - not much help 
to you though

and altF works for me

Phil

On 23 Apr 2010, at 14:37, Joachim Reichelt wrote:

> Dear all,
> 
> I just got a MacBookPro.
> I have two questions:
> How to get the keyboard shortcuts in coot or pymol up, e.g. F to
> open the file dialog.
> 
> and
> 
> whenever I connect a zalman 220 (stereo ready) monitor to the mac using
> a miniDisplayPort to DVI
> adapter, the monitor is not recognized and so it is completely dark. The
> Mac does not show the monitor in the dialogues but an error message.
> 
> -- 
> Joachim

Re: [ccp4bb] Protein/DNA complex in Buccaneer

[Kevin Cowtan]

Yes, this can be done, but you need buccaneer 1.4, which I haven't 
released yet. We've seen significant benefits to preserving the heavy 
atoms through to the refinement, although the code has been written so 
that it can preserve DNA or any other know structure features as well.


I'll try and put together a release next week so you can try it out.

Kyle Dolan wrote:

Hello,

I am trying to use Buccaneer to improve the model of a protein/DNA 
complex which I solved recently. However, my initial attempt failed 
because the program deleted the DNA chains and rebuilt protein chains in 
their density. Is there a way to specify that the expected outcome 
should contain a DNA ligand--either in the input model pdb or the input 
sequence file--and to instruct the program to only work on the protein 
during building?


Thanks,
Kyle

Kyle T. Dolan
Department of Biochemistry and Molecular Biology
The University of Chicago
k...@uchicago.edu 

[ccp4bb] Protein/DNA complex in Buccaneer

[Kyle Dolan]

Hello,

I am trying to use Buccaneer to improve the model of a protein/DNA complex
which I solved recently. However, my initial attempt failed because the
program deleted the DNA chains and rebuilt protein chains in their density.
Is there a way to specify that the expected outcome should contain a DNA
ligand--either in the input model pdb or the input sequence file--and to
instruct the program to only work on the protein during building?

Thanks,
Kyle

Kyle T. Dolan
Department of Biochemistry and Molecular Biology
The University of Chicago
k...@uchicago.edu

[ccp4bb] MacBookPro problems

[Joachim Reichelt]

Dear all,

I just got a MacBookPro.
I have two questions:
How to get the keyboard shortcuts in coot or pymol up, e.g. F to
open the file dialog.

and

whenever I connect a zalman 220 (stereo ready) monitor to the mac using
a miniDisplayPort to DVI
adapter, the monitor is not recognized and so it is completely dark. The
Mac does not show the monitor in the dialogues but an error message.

-- 
Joachim

Re: [ccp4bb] how to make cholesterol solution

[Jose Antonio Cuesta Seijo]

An alternative could be to disolve your cholesterol in methanol or maybe in
50% methanol, then add it directly to the drop. Does your protein tolerate
10-20% methanol? Then you can add the methanol-cholesterol solution you
your hanging drops directly and mix fast. The methanol is volatile and will
end up mostly in the reservoir leaving onlt traces in the drop, while the
cholesterol will stay in the water. It might precipitate at first, but
should redissolve or not precipitate at all if it binds your protein.

Jose Antonio Cuesta-Seijo.



"Jerry McCully"  wrote:
> 
> Dear ALL:
> 
>  Sorry for this kind of off-topic question.
> 
> I am going to co-crystallize one protein with cholesterol. I read
some
> papers saying that
> their protein can be pre-incubated with 1mM cholesterol in the presence
of 5%
> (v/v) ethanol.
> 
>TO do so, I first dissolved cholesterol in 100% ethanol at a
concentration of
> 10mM. However, it is very difficult to make the dilution into 5% ethanol
either
> just in water or some buffers.
> 
>Does anyone have such experience to make cholesterol solution in
normal
> buffers plus some ethanol?
> 
>Thanks a lot,
> 
> Jerry McCully
>
> _
> The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with
> Hotmail. 
>
http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5


--
***
Jose Antonio Cuesta-Seijo

Biophysical
Chemistry Group
Department of Chemistry
University of Copenhagen 
Tlf:
+45-35320261
Universitetsparken 5 
DK-2100 Copenhagen,
Denmark
***

Re: [ccp4bb] phenix error message

[Tim Gruene]

On Fri, Apr 23, 2010 at 01:12:36PM +0200, Tim Gruene wrote:
> Hello,
> 
> we are using the latex phenix version (1.6.1) on PCs with Debain Stable or

Sorry, I meant 'latest' version, in case this causes confusion... 

> Testing. After starting a refinement job, the following error message shows 
> up:
> 
> 
> snip 8< -->
> A Python error was detected.  This is probably a bug; click "OK" to send a 
> bug report to the PHENIX developers.
> 
> 
> TypeError : 'NoneType' object is not callable
> 
> Traceback (most recent call last):
>   File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Runtime.py", line 
> 132, in OnExcept
> self.current_job.error()
>   File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
> 107, in error
> self._clean_up(*args, **kwds)
>   File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
> 65, in _clean_up
> wxGUI2.project_manager.update_project_and_save(self.project_id)
>   File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
> 823, in update_project_and_save
> self.update_project_timestamp(project_id, job.time_finished)
>   File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
> 838, in update_project_timestamp
> project.save()
>   File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
> 276, in save
> easy_pickle.dump(self.save_file, self)
>   File 
> "/xtal/Suites/64bit/phenix-1.6.1-357/cctbx_project/libtbx/easy_pickle.py", 
> line 14, in dump
> return cPickle.dump(obj, _open(file_name, "wb"), 1)
>   File 
> "/xtal/Suites/64bit/phenix-1.6.1-357/build/intel-linux-2.6-x86_64/base/lib/python2.6/copy_reg.py",
>  line 84, in _reduce_ex
> dict = getstate()
> TypeError: 'NoneType' object is not callable
> < snap >8
> 
> (We cannot click 'OK' because our computers are not connected to the internet.
> 
> Does anyone know what the error messages mean and how we can overcome them?
> 
> Thanks a lot, Tim
> 
> 
> 
> -- 
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 



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

GPG Key ID = A46BEE1A



signature.asc
Description: Digital signature

[ccp4bb] phenix error message

[Tim Gruene]

Hello,

we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
Testing. After starting a refinement job, the following error message shows up:


snip 8< -->
A Python error was detected.  This is probably a bug; click "OK" to send a bug 
report to the PHENIX developers.


TypeError : 'NoneType' object is not callable

Traceback (most recent call last):
  File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Runtime.py", line 
132, in OnExcept
self.current_job.error()
  File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
107, in error
self._clean_up(*args, **kwds)
  File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
65, in _clean_up
wxGUI2.project_manager.update_project_and_save(self.project_id)
  File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
823, in update_project_and_save
self.update_project_timestamp(project_id, job.time_finished)
  File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
838, in update_project_timestamp
project.save()
  File "/xtal/Suites/64bit/phenix-1.6.1-357/phenix/wxGUI2/Tracking.py", line 
276, in save
easy_pickle.dump(self.save_file, self)
  File 
"/xtal/Suites/64bit/phenix-1.6.1-357/cctbx_project/libtbx/easy_pickle.py", line 
14, in dump
return cPickle.dump(obj, _open(file_name, "wb"), 1)
  File 
"/xtal/Suites/64bit/phenix-1.6.1-357/build/intel-linux-2.6-x86_64/base/lib/python2.6/copy_reg.py",
 line 84, in _reduce_ex
dict = getstate()
TypeError: 'NoneType' object is not callable
< snap >8

(We cannot click 'OK' because our computers are not connected to the internet.

Does anyone know what the error messages mean and how we can overcome them?

Thanks a lot, Tim



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

GPG Key ID = A46BEE1A



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Description: Digital signature

[ccp4bb] Fw: [ccp4bb] degradation of protein durring freez thaw

[MARTYN SYMMONS]

Sounds like good advice - I suppose that since pure water un-freezes last, you 
could have protein concentration inhomogeneities? So in areas where the protein 
concentration is raised it could start to feel like crashing out.


All the best
Martyn

Martyn Symmons
Cambridge



- Original Message 
From: Frank Niesen 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, 23 April, 2010 10:40:59
Subject: Re: [ccp4bb] degradation of protein durring freez thaw

An aspect that is sometimes overlooked is that the need to avoid mini 
freeze-thaw cycles does not only call for a quick, snap-freeze process for 
samples (in thin-walled PCR tube and not too large volume; 50-100 ul I'd 
recommend), but - in turn - also for quick thawing: I prefer holding the PCR 
tube under running cold water straight after removal from the freezer, and 
stick into the ice bucket only after I see that all of the sample is thawed.
Best,
Frank

Re: [ccp4bb] degradation of protein durring freez thaw

[Frank Niesen]

An aspect that is sometimes overlooked is that the need to avoid mini 
freeze-thaw cycles does not only call for a quick, snap-freeze process for 
samples (in thin-walled PCR tube and not too large volume; 50-100 ul I'd 
recommend), but - in turn - also for quick thawing: I prefer holding the PCR 
tube under running cold water straight after removal from the freezer, and 
stick into the ice bucket only after I see that all of the sample is thawed.
Best,
Frank

[ccp4bb] scala and xds data

[Ingo P. Korndoerfer]

dear colleagues,

i convert xds_ascii.hkl with pointless to .mtz.

but recently (possibly since the latest xds release, not sure) scala
then exits my attempts to reduce the data :

  Reflection rotation value outside range in Batch header 
 Reflection2   1   6 Isym =3 Batch  73
 Rotation 46.8000 should be in range  46.8000 47.4500


  Reflection rotation value outside range in Batch header 
 Reflection3   0   1 Isym =5 Batch  76
 Rotation 48.7500 should be in range  48.7500 49.4000


  Reflection rotation value outside range in Batch header 
 Reflection3   1  -1 Isym =5 Batch  76
 Rotation 48.7500 should be in range  48.7500 49.4000


  Reflection rotation value outside range in Batch header 
 Reflection3   1   0 Isym =5 Batch  81
 Rotation 52. should be in range  52. 52.6500


  Reflection rotation value outside range in Batch header 
 Reflection3   1   5 Isym =   12 Batch  74
 Rotation 47.4500 should be in range  47.4500 48.1000


  Reflection rotation value outside range in Batch header 
 Reflection3   1   6 Isym =3 Batch  83
 Rotation 53.3000 should be in range  53.3000 53.9500

has anybody seen this or would anybody have an idea what i have been
overlooking ?

ingo

-- 
CRELUX GmbH
 
Dr. Ingo Korndoerfer
Head of Crystallography

Am Klopferspitz 19a
82152 Martinsried
Germany

Phone: +49 89 700760210
Fax: +49 89 700760222 
korndoer...@crelux.com
www.crelux.com

Amtsgericht München HRB 165552 - Managing Directors: Dr. Michael Schäffer, Dr. 
Ismail Moarefi

This e-mail may contain confidential and/or privileged information. If you are 
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Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Informationen. 
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haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. 
Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht 
gestattet.



<>

Re: [ccp4bb] Setting Microbatch trays !!

[Emmanuel Saridakis]

Dear Rashmi,

The original standard for microbatch crystallisation is paraffin oil (from 
Sigma or elsewhere). Drops set under paraffin oil lose almost no water, so it 
works like a well-sealed batch experiment, in other words you need to have your 
conditions right and you do get crystals. Paraffin oil is the only case where 
the reported conditions are the true ones.

Al's oil allows slow water evaporation through the oil, so the drops get slowly 
concentrated, something like a vapour diffusion, except that you don't have a 
well-defined end-point, i.e. a reservoir solution. Douglas Instruments I think 
sell some microbatch plates with a channel around them which can be used as a 
reservoir for such cases. Al's oil may thus give you more hits, since the 
supersaturation of the drops gets progressively higher. Of course, you don't 
know what the true crystallisation conditions are.

Silicone oil allows a great deal of evaporation through it, so it may actually 
give you even more hits but you also may end up with drops drying out before 
having the chance to produce any crystals, unless you use the plates I talked 
about before, in which case it works a lot like a vapour diffusion experiment.

Have a look at Douglas Instruments' web page: there is a lot of relevant info 
in there.

Cheers,

Emmanuel Saridakis


  - Original Message - 
  From: rashmi panigrahi 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Friday, April 23, 2010 5:35 AM
  Subject: [ccp4bb] Setting Microbatch trays !!


  Hi,
  While setting up microbatch trays  (under oil crystallization),
  1.  Has anybody used mineral oil (sigma M8410) and obtained some crystal hits?
  2.  Has anybody used anything other than Al's oil from Hampton, as Parafin 
oil from sigma or silicone oil from sigma and obtained some crystal hits?
  Thanks

  -- 
  rashmi

Re: [ccp4bb] Rsym problems...maybe???

[Peter Artymiuk]

I'd worry a bit. If the data are strong and the R factor is that bad you may 
have got your space group wrong (pseudo, not crystallographic 4 fold?)

Pete Artymiuk


On 22 Apr 2010, at 18:22, Frank von Delft wrote:

> Yeah, stop worrying!  Your I/sdI is all that matters.
> phx
> 
> 
> On 22/04/2010 18:06, Daniel Bonsor wrote:
>> Hello again.
>> 
>> At first I was not worry but maybe now I am. I have completed a structure 
>> and submitted to the PDB. They queried my Rsym value in the highest 
>> resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the 
>> time as I had:
>> 
>> 99.4% completeness
>> Mean(I/sdI) of 2.5
>> and a redundancy of 11 (which would explain the high Rsym)
>> Space group I422
>> 
>> My Rpim in this shell is 30%.
>> 
>> Should I reduce the resolution and start from scratch again or is everything 
>> fine and dandy and I should stop worrying?
>>