Re: [ccp4bb] qtrview command line options

[Andrey Lebedev]

After ccp4 update No 19, Log–files can be opened with qtrview from the command 
line:

logview name.log

This also works for log-files generated with "quick scale" and "quick symmetry" 
from imosflm.

If ccp4 database entries do not exist, input and output files will not be shown 
in the viewer
(except for "quick scale" and "quick symmetry" files).

Regards

Andrey



On 11 Mar 2013, at 20:06, Lebedev, Andrey (STFC,RAL,SC) wrote:

> 
> Hi Ed
> 
> Thank you for the suggestion.
> We are looking into this and hopefully will provide a solution soon.
> 
> Regards
> 
> Andrey
> 
> 
> On 11 Mar 2013, at 14:26, Ed Pozharski wrote:
> 
>> Is there some way of opening a log file (specifically, the
>> pointandscale.log that imosflm bridge to scala generates) with qtrview
>> from command line?
>> 
>> I tried, of course, this
>> 
>> qtrview pointandscale.log
>> 
>> but it opens empty, no log-file. I tried qtrview -h and qtrview --help
>> and man qtrview but there is seemingly no documentation.
>> 
>> I found the source code (yes, I can google) and can deduce that
>> available options at startup are 
>> 
>> --log-file
>> --report-xml
>> --report-xrt
>> --inp-file
>> 
>> The only thing that works is 
>> 
>> qrtview --log-file pointandscale.log
>> 
>> but that only shows me the log-file itself, i.e. no graphs etc.  I
>> understand that the program was designed primarily for ccp4 gui and I
>> know loggraph (and it works).
>> 
>> By the way, checkout instructions for the qtrview repository at
>> 
>> https://fg.oisin.rc-harwell.ac.uk/projects/qtrview/
>> 
>> don't work throwing this error
>> 
>> bzr: ERROR: Connection error: curl connection error (server certificate
>> verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile:
>> none)
>> on https://fg.oisin.rc-harwell.ac.uk/anonscm/bzr/qtrview/.bzr/smart 
>> 
>> Cheers,
>> 
>> Ed.
>> 
>> -- 
>> "Hurry up before we all come back to our senses!"
>>  Julian, King of Lemurs
> 


-- 
Scanned by iCritical.

Re: [ccp4bb] first use of synchrotron radiation in PX

[Ethan Merritt]

On Saturday, 16 March 2013, James Holton wrote:
> The first report of shooting a protein crystal at a synchrotron (I 
> think) was in 1976:
> http://www.pnas.org/content/73/1/128.full.pdf
> that was rubredoxin
> 
> The first PDB file that contains a "SYNCHROTRON=Y" entry is 1tld 
> (trypsin), which was deposited in 1989:
> http://dx.doi.org/10.1016/0022-2836(89)90110-1
> But the structure of trypsin was arguably already "solved" at that time.
> 
> Anomalous diffraction was first demonstrated by Coster, Knoll and Prins 
> in 1930
> http://dx.doi.org/10.1007/BF01339610
> this was 20 years before Bijvoet.  But not with a synchrotron and 
> definitely not with a protein
> 
> The first protein to be solved using anomalous was crambin in 1981:
> http://dx.doi.org/10.1038/290107a0
> but this was not using a synchrotron
> 
> The first demonstration of MAD on a protein at a synchrotron was a Tb 
> soak of parvalbumin in 1985
> http://dx.doi.org/10.1016/0014-5793(85)80207-6
> but one could argue that several parvalbumins were already known at that 
> time.
> 
> The first MAD structure from native metals was cucumber blue copper 
> protein (2cbp) in 1989
> http://dx.doi.org/10.1126%2Fscience.3406739

The original CBP MAD structure (1CBP) was published in 1988.

Also 1988:
  Lamprey hemoglobin (Fe MAD) DOI: 10.1002/prot.340040202

1989:
  Streptavidin (Se MAD): PNAS 1989 86 (7) 2190-2194

> The first "new" structure using MAD, as well as the first SeMet was 
> ribonuclease H (1rnh) in 1990
> http://dx.doi.org/10.1126/science.2169648
> 
> If anyone knows of earlier cases, I'd like to hear about it!

Ethan

> 
> -James Holton
> MAD Scientist
> 
> On 3/13/2013 7:38 AM, Alan Cheung wrote:
> > Hi all - i'm sure this many will know this : when and what was the 
> > first protein structure solved on a synchrotron?
> >
> > Thanks in advance
> > Alan
> >
> >
> 

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

[James Holton]

Well, when it comes to observations/parameters, it is important to 
remember that not all observations are created equal.  10,000 
"observations" with I/sigma = 1 are definitely not as desirable as 
10,000 observations with I/sigma = 10.  Not all parameters are created 
equal either.  Yes, you may have 3,000 atoms, but there are bonds 
between them and that means you don't REALLY have 3,000*3 degrees of 
freedom.  How many "parameters" are removed by each bond, of course, 
depends on how tight your geometry weight is.  So, although the 
observations/parameters rule of thumb is useful for knowing roughly just 
how much you are asking of your fitting program, it is a qualitative 
assessment only.  Not quantitative.


It is instructive to consider the 1-dimensional case.  Say you have 100 
data points, evenly spaced, and you are fitting a curve to them.  If you 
fit a 100th-order polynomial to these points, then you can always get 
your curve to pass straight through every single point.  But do you want 
to do that?  What if the error bars are huge and you can see that the 
points follow a much smoother curve?  In that case, you definitely want 
to reduce the number of "parameters" so that you are not 
"over-fitting".  But how can you tell if your simplified model is 
plausible?  Well, one way to do it is leave out some of the observations 
from the fit and see if a curve fit to the other ones predicts those 
points reasonable well.  This is called a "cross check" (aka, Rfree).


The equivalent of "resolution" in this case is the scale on the x-axis.  
Yes, a scale factor.  100 points along the x-axis with a unit cell 
length of 200 is equivalent to "2A data", but if you change the unit 
cell to 300 A and you still have 100 "samples", then that is equivalent 
to 3A data with the same number of "observations".  But wait!  Shouldn't 
2A data always be "better" than 3A data if everything else is equal?  
Well, the difference comes from knowing the "scale" of what you are 
trying to measure. If you're trying to assign an atom-atom distance to 
either a hydrogen bond or a van der Waals bump, then you need to tell 
~2.0 A from ~3.5 A, so now suddenly the scale of the x-axis (200A vs 300 
A) matters.  The problem becomes one of propagating the error bars of 
the data (on the y axis) into error bars on the parameters of the fit 
(on the x-axis).  For my 1-D case of 100 points, this is equivalent to 
"knowing" how smooth your fitted function should be.  Yes, having more 
data points can be "better", but it is the size of your error bars 
relative to what you are trying to measure that is actually important.


So, one way of thinking about the difference between 3A data with 50% 
solvent vs 3.6A data with 80% solvent is to "scale" the 3.0A unit cell 
so that it has the same volume as the 3.6A crystal's unit cell.  Then 
you effectively have two structures with different 
observations/parameters and the SAME resolution (because you have 
changed the scale of space for one of them).  The re-scaling is 
mathematically equivalent to stretching the 3.0 A electron density map, 
so all you have done is "inflate" the protein so that the atoms are now 
farther apart.  Does this make them easier to distinguish?  No, because 
although they are farther apart, they are also "fatter".  Stretching the 
map changes both the peak widths and the distance between them 
proportionally.  The width of atomic peaks is actually very closely 
related to the resolution (especially at ~3A), so after stretching the 
map the peak widths in both thte 3A/50% and 3.6A/80% cases will be about 
the same, but the distances between the peaks will be larger in the map 
that came from the 3A/50% data.  So, relatively speaking 
(delta-bond/bond_length), you still have more "accuracy" with the 3A 
case, no matter what the observations/parameters ratio is.


Of course, all this is assuming that all you are interested in is bond 
lengths.  If you happen to know your bond lengths already (such as 
covalent bonds) then that changes the relationship between the errors in 
your data and the parameter you are trying to measure.  To put things 
another way, a 60 nm resolution 3D reconstruction of a 5-micron wide 
cell represents about as many "observations" as a 1.2A crystal structure 
of a 100 A unit cell. Which is "more accurate"?  Depends on the question 
you are trying to ask.


So, to answer the OP's question, I still think 3.0A is better than 
3.6A.  Yes, higher solvent content gives you better phases, and phase 
accuracy IS important for placing atoms (30 degrees of phase error at 3 
A means that the spatial waves at that resolution are "off" by an 
average of ~0.25 A).  But, that advantage is really only in the initial 
stages of phasing, and it fades as soon as the experimental phases start 
holding your refinement back more than they help (which actually happens 
rather quickly).  Remember, the 'bulk solvent' model, as far as the 
phases are concerned, i

Re: [ccp4bb] first use of synchrotron radiation in PX

[Bosch, Juergen]

Thank you James, you should write a History book about the modern x-ray times.
Or better make one of those movies you are famous for.

Jürgen

On Mar 16, 2013, at 10:46 AM, James Holton wrote:

The first report of shooting a protein crystal at a synchrotron (I
think) was in 1976:
http://www.pnas.org/content/73/1/128.full.pdf
that was rubredoxin

The first PDB file that contains a "SYNCHROTRON=Y" entry is 1tld
(trypsin), which was deposited in 1989:
http://dx.doi.org/10.1016/0022-2836(89)90110-1
But the structure of trypsin was arguably already "solved" at that time.

Anomalous diffraction was first demonstrated by Coster, Knoll and Prins
in 1930
http://dx.doi.org/10.1007/BF01339610
this was 20 years before Bijvoet.  But not with a synchrotron and
definitely not with a protein

The first protein to be solved using anomalous was crambin in 1981:
http://dx.doi.org/10.1038/290107a0
but this was not using a synchrotron

The first demonstration of MAD on a protein at a synchrotron was a Tb
soak of parvalbumin in 1985
http://dx.doi.org/10.1016/0014-5793(85)80207-6
but one could argue that several parvalbumins were already known at that
time.

The first MAD structure from native metals was cucumber blue copper
protein (2cbp) in 1989
http://dx.doi.org/10.1126%2Fscience.3406739

The first "new" structure using MAD, as well as the first SeMet was
ribonuclease H (1rnh) in 1990
http://dx.doi.org/10.1126/science.2169648

If anyone knows of earlier cases, I'd like to hear about it!

-James Holton
MAD Scientist

On 3/13/2013 7:38 AM, Alan Cheung wrote:
Hi all - i'm sure this many will know this : when and what was the
first protein structure solved on a synchrotron?

Thanks in advance
Alan



..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] first use of synchrotron radiation in PX

[James Holton]

The first report of shooting a protein crystal at a synchrotron (I 
think) was in 1976:

http://www.pnas.org/content/73/1/128.full.pdf
that was rubredoxin

The first PDB file that contains a "SYNCHROTRON=Y" entry is 1tld 
(trypsin), which was deposited in 1989:

http://dx.doi.org/10.1016/0022-2836(89)90110-1
But the structure of trypsin was arguably already "solved" at that time.

Anomalous diffraction was first demonstrated by Coster, Knoll and Prins 
in 1930

http://dx.doi.org/10.1007/BF01339610
this was 20 years before Bijvoet.  But not with a synchrotron and 
definitely not with a protein


The first protein to be solved using anomalous was crambin in 1981:
http://dx.doi.org/10.1038/290107a0
but this was not using a synchrotron

The first demonstration of MAD on a protein at a synchrotron was a Tb 
soak of parvalbumin in 1985

http://dx.doi.org/10.1016/0014-5793(85)80207-6
but one could argue that several parvalbumins were already known at that 
time.


The first MAD structure from native metals was cucumber blue copper 
protein (2cbp) in 1989

http://dx.doi.org/10.1126%2Fscience.3406739

The first "new" structure using MAD, as well as the first SeMet was 
ribonuclease H (1rnh) in 1990

http://dx.doi.org/10.1126/science.2169648

If anyone knows of earlier cases, I'd like to hear about it!

-James Holton
MAD Scientist

On 3/13/2013 7:38 AM, Alan Cheung wrote:
Hi all - i'm sure this many will know this : when and what was the 
first protein structure solved on a synchrotron?


Thanks in advance
Alan

[ccp4bb] Fwd: [ccp4bb] CCP4 Update 019

[eugene . krissinel]

Apologies for everybody, the previous message was sent to BB by mistake, please 
disregard.

Eugene Krissinel

Begin forwarded message:

Date: 16 March 2013 11:25:08 GMT
To: mailto:andrey.lebe...@stfc.ac.uk>>
Cc: mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] CCP4 Update 019

Spasibo Andrey,

Ne znayu poka kak na Linuxe i vse ostal'noe, no na Mac superpose ne 
proupdeitirovalas', matritsy ne pechataet. Poka ne znayu chto sluchilos'

Eugene

On 15 Mar 2013, at 23:51, Andrey Lebedev wrote:

Dear CCP4 Users

A CCP4 update has just been released, consisting of the following changes.

* Aimless: Task interface fixed in part of input customisation section
* Molrep: Improvements to scoring system and bug fixes
* Logview: Command-prompt routine for viewing individual log files with QtRView
  Simply call it with path to the log file as the only parameter
* QtRView: Cosmetic improvements and changes for Logview
* Gesamt: Now prints superposition matrices also in fractional coordinates
* Superpose: Now prints superposition matrices also in fractional coordinates

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


--
Scanned by iCritical.




-- 
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Re: [ccp4bb] CCP4 Update 019

[eugene . krissinel]

Spasibo Andrey,

Ne znayu poka kak na Linuxe i vse ostal'noe, no na Mac superpose ne 
proupdeitirovalas', matritsy ne pechataet. Poka ne znayu chto sluchilos'

Eugene

On 15 Mar 2013, at 23:51, Andrey Lebedev wrote:

> Dear CCP4 Users
> 
> A CCP4 update has just been released, consisting of the following changes.
> 
> * Aimless: Task interface fixed in part of input customisation section
> * Molrep: Improvements to scoring system and bug fixes
> * Logview: Command-prompt routine for viewing individual log files with 
> QtRView
>Simply call it with path to the log file as the only parameter
> * QtRView: Cosmetic improvements and changes for Logview
> * Gesamt: Now prints superposition matrices also in fractional coordinates
> * Superpose: Now prints superposition matrices also in fractional coordinates
> 
> If you do not currently receive updates, consider re-installing your
> CCP4 setup using the latest binary packages, which now have the CCP4 Update 
> Manager (ccp4um) integrated.
> 
> Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
> therefore upgrade if necessary. Please report any bugs to 
> c...@stfc.ac.uk
> 
> Many thanks for using CCP4
> 
> Andrey Lebedev
> 
> 
> -- 
> Scanned by iCritical.
> 


-- 
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Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

[dusan turk]

Dear Guangyu Zhu,

if this is not a hypothetical case you can refine both structures in each 
crystal form separately using whatever software and compare them later.
The structure can be refined also in both crystal forms simultaneously using 
the multi crystal NCS refinement as implemented in MAIN http://www-bmb.ijs.si/ 
and thereby double the data to parameter ratio when compared to the one crystal 
form data set refinement.

best regards,
dusan

On Mar 16, 2013, at 1:00 AM, CCP4BB automatic digest system 
 wrote:

> Date:Thu, 14 Mar 2013 20:27:44 -0400
> From:Guangyu Zhu 
> Subject: Resolution and data/parameter ratio, which one is more important?
> 
> I have this question. For exmaple, a protein could be crystallized in two 
> crystal forms. Two crystal form have same space group, and 1 molecule/asymm. 
> One crystal form diffracts to 3A with 50% solvent; and the other diffracts to 
> 3.6A with 80% solvent. The cell volume of 3.6A crystal must be 5/2=2.5 times 
> larger because of higher solvent content. If both data collecte to same 
> completeness (say 100%), 3.6A data actually have higher data/parameter ratio, 
> 5/2/(3.6/3)**3= 1.45 times to 3A data. For refinement, better data/parameter 
> should give more accurate structure, ie. 3.6A data is better. But higher 
> resolution should give a better resolved electron density map. So which 
> crystal form really give a better (more reliable and accurate) protein 
> structure?

Re: [ccp4bb] anti-His6 Ab

[Juha Vahokoski]

http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27397.html

Since the discussion, we tried qiagen ab, and I was quite happy with it. I
did not do extensive performance tests, but it was better than the previous
ab.

Regards,
Juha

On Friday, 15 March 2013, Elias Fernandez wrote:

> Dear All, would you be able to recommend a primary anti-His6 Ab for
> western blotting? Thus far, the ones we’ve used are not very specific to
> the N-terminal hexahistidines and we pick up lots of background. Also,
> there’s one (others?) from Sigma that is conjugated to HRP, but costs
> ~$650. Thanks! Elias
>


-- 
"Genius may have its limitations, but stupidity is not thus handicapped."
-Elbert Hubbard

Juha Vahokoski
Kalliotie 16 as. 10
90500 Oulu
Finland
mobile:+358 40 5286 778