Re: [ccp4bb] EDS server

[Yuri Pompeu]

A simple way to validate real space density fit is to look at it under 
validate--->density fit anlysis in COOT.
I think even the GUI of phenix.refine at the end of a run the results give a 
list of all residues that are under the user-definied RSCCoeficient.
With those two tools you should be able to see what you need to see

[ccp4bb] Asset stripping the Uppsala Software Factory...

[Gerard DVD Kleywegt]

Hi all,

Unfortunately, I am no longer able to support or maintain (let alone develop 
or port to new OS versions) any of my old USF programs. For this reason, Mark 
Harris (http://xray.bmc.uu.se/markh/email.html) has made a distribution kit 
with source code (yes, Fortran77...) and compilation scripts and instructions 
for about three dozen of the USF programs (mostly from the RAVE and X-UTIL 
packages, but also including LSQMAN).


If you want to keep (some of) the USF programs running on future hardware or 
OS versions, or if you want to modify or re-use some of the code, feel free to 
download the whole caboodle. (If you should want to publish or redistribute 
modified versions that use substantial chunks of my code, I would appreciate 
it if you talked to me first though.)


The download site is:

  http://xray.bmc.uu.se/markh/usf/

You can also download sets of ready-made binaries for a few OSes (but these 
will not be kept up-to-date in the future).


Send any comments, bug reports, questions, suggestions, requests, feedback, 
experiences with new OS versions, etc. to Mark - not to me! Mark will do his 
best to provide basic support for a few months - after that, you're on your 
own.


--Gerard

PS: Little known gastromathematical curiosity: let "z" be the radius and "a" 
the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! 
(Hmmm - I'm getting hungry.)


**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

Re: [ccp4bb] scalepack--scale data in .sca format with original index

[Ethan Merritt]

On Friday, September 02, 2011 08:56:03 am Jerry McCully wrote:
> 
> Dear ALL;
> 
>I am sorry for this "HKL2000 scalepack" question.
> 
>To confirm the scape group using Pointless, I processed the images 
> using HKL2000
>but kept the original index using "No merge original index".
> 
>Now Pointless gave the right space group, and I want to merge my 
> data 
>from the existing ".sca" file with the original index to report 
> the scaling
>statistics.

Since you have already processed the data in pointless, it seems to me that
the simplest and most logical thing to do is simply to continue with the output
from pointless by feeding it to scala.   In the CCP4i GUI, the path is
  Data Reduction
  -> Scale and Merge Intensities
 
  

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

Re: [ccp4bb] EDS server

[Pavel Afonine]

> You have those tools at hand, but you need to script them or type whatever
> you like.
> The RSR fit e.g. can be found in MAPMAN with the command RS_fit-real-space
> blabla
> All plots generated on the EDS server site should have a USF tool which
> produces some numbers which you then convert via R or any other plotting
> program into a visual representation.
> Of which particular tool were you thinking ? The RSR is sort of the density
> fit plot in Coot.
>

FYI:

phenix.model_vs_data model.pdb data.hkl

will give you all this in one go: RSRs (for all atoms/residues), model stats
(including all MolProbity scores), data statistics (including twinning
analysis), R-factors, etc...

Pavel.

[ccp4bb] scalepack--scale data in .sca format with original index

[Jerry McCully]

Dear ALL;

   I am sorry for this "HKL2000 scalepack" question.

   To confirm the scape group using Pointless, I processed the images 
using HKL2000 but kept the original index using "No merge original index".

   Now Pointless gave the right space group, and I want to merge my 
data from the existing ".sca" file with the original index to report the 
scaling statistics.

  Can anyone help me to correct the following scripts? By the way, the 
orignal index format in Scalepack is (6i4, i6, 2i2, i3, 2f8.1).

Thanks a lot and have a nice weekend,

Jerry



Format scalepack 


FILE 1 'no-merge-original-index.sca'

@reject

resolution 40 1.8


number of zones 20

estimated error

0.06 0.07 0.07 0.07 0.08

0.07 0.08 0.07 0.07 0.04

0.03 0.03 0.03 0.03 0.02

0.02 0.02 0.02 0.02 0.02

error scale factor 1.3

default scale 10

rejection probability 0.0001

scale restrain 0.01

B restrain 0.02

space group P2221

unit cell 70.19188.586   158.41690.000   
90.00090.000

output file 'merge.sca'

postrefine 20

merge


  

Re: [ccp4bb] EDS server

[Bernhard Rupp (Hofkristallrat a.D.)]

> it will be before we all travel to work with jetpacks or flying cars

http://www.popularmechanics.com/science/4247253

" Thunderbolt Aerosystems, based in California, plans to start selling its
ThunderPack TP-R2G2 rocket belt to customers this summer."

http://www.popularmechanics.com/technology/aviation/news/terrafugias-flying-
car-clears-regulatory-hurdles

" The Terrafugia company now plans to fly the production prototypes next
March.."

:-)

BR


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard
DVD Kleywegt
Sent: Friday, September 02, 2011 7:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] EDS server

Hi all,

> Simple question, is there a way I can upload my own data into the EDS 
> server? I see only place for it to take from data already published in 
> the PDB.

First of all, if you deposit at PDBe, EDS will be run on your deposition and
you can access the results after annotation. Second, RCSB operates a
validation server that carries out similar calculations and which you can
use prior to deposition.

Having said that, yes, there is actually an *unsupported* version of EDS to
which you can upload your model and structure factors (MTZ or CIF file).
Note that it is unsupported, unofficial, unmaintained, buyer beware and your
mileage may vary.

In the future, there will of course be a shiny new wwPDB X-ray validation
server which will include EDS-style calculations. (I won't make any promises
as to when, but it will be before we all travel to work with jetpacks or
flying cars.)

--Gerard

PS: If you want to try out the *unsupported* etc. PRedeposition EDS server
(PREDS), throw your browser at http://eds.bmc.uu.se/eds/preds.php (but read
http://eds.bmc.uu.se/eds/preds_help.html first).

**
Gerard J.  Kleywegt

 http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
**
The opinions in this message are fictional.  Any similarity
to actual opinions, living or dead, is purely coincidental.
**

Re: [ccp4bb] No Cl- or S Anomalous Signal

[Gerard Bricogne]

Dear Jacob,

 ... or you could use the "anomalous residual map" in SHARP, the first
program to offer this kind of calculation 15 years ago or so: see 

   La Fortelle, E. de & Bricogne, G. (1997). Methods Enzymol. 276, 472–494.

and/or the SHARP manual at 

   http://www.globalphasing.com/sharp/manual/chapter5.html#RESIDMAPS

We have routinely observed since the inception of these maps that their
signal-to-noise ratio is significantly greater than that of the ordinary
anomalous difference Fourier maps. The same holds for the isomorphous or
dispersive residual maps vs. ordinary difference Fourier maps.

 If you do not find the expected signal, it could just be that your data
collection protocol gave rise to too much differential radiation damage on
average between the measurement of Bijvoet pairs. This would tend to happen
especially if your crystal has low symmetry.


 Good luck!
 
   Gerard.
 
--
On Fri, Sep 02, 2011 at 02:08:23PM +0100, Randy Read wrote:
> Dear Jacob,
> 
> The signal for weak anomalous sites can be stronger in Phaser SAD LLG maps 
> than in model-phased anomalous difference Fouriers, especially if the 
> substructure already contains the stronger sites, so that you're just looking 
> for what is still left to be explained in the SAD data.  You could try 
> running Phaser in MR-SAD mode, giving the current protein model as a partial 
> structure, providing the substructure of the Se sites, and looking for 
> purely-imaginary scatterers ("LLGCOMPLETE SCATTERER AX" in a script, or check 
> the box labelled "Complete with purely anomalous scatterer" in the ccp4i 
> GUI).  In this situation you don't want to look for S or Cl atoms as such, 
> because the real part of their scattering is already accounted for well in 
> the protein model.
> 
> Best wishes,
> 
> Randy Read
> 
> On 1 Sep 2011, at 23:29, Jacob Keller wrote:
> 
> > Update:
> > 
> > I tried more anomalous maps, this time with the originally-deposited
> > data at 1.8 Ang (mine were similar, substrate-soaked crystals) and
> > phases from the refined model, and the Se sites are now ~40-50 sigma,
> > and there is still totally nothing at the Cl and S sites, even though
> > in 2Fo-Fc the Cl is ~9 sigma, and the S is 8 sigma (the Se is ~15
> > sigma). If it has reasonably-high electron density, shouldn't it have
> > at least some anomalous scattering? I am wondering whether somehow the
> > model phases are biasing the map, but I can't really imagine how that
> > would be...
> > 
> > JPK
> > 
> > 
> > On Thu, Sep 1, 2011 at 3:15 PM, Bosch, Juergen  wrote:
> >> Where in refinement of your model are you ?
> >> At an early stage I wouldn't be surprised to only see SeMets but once 
> >> you've
> >> refined your structure and go back to calculate an anomalous map with the
> >> improved phases you might double your signal for SeMet and start seeing
> >> sulfurs.
> >> An alternative explanation, you've blasted your crystals at the synchrotron
> >> and the remaining anomalous signal is too weak to show the sulfurs.
> >> Just two thoughts,
> >> Jürgen
> >> On Sep 1, 2011, at 4:03 PM, Jacob Keller wrote:
> >> 
> >> Dear Crystallographers,
> >> 
> >> I recently have been working with a 2.5 Ang SeMet peak wavelength
> >> dataset which contains 2 cys's and also a couple of bona fide Cl ions
> >> (reasonable b-factor/site is semi-buried/water does not work). In the
> >> FFT anomalous difference map using PhiC from the refined model and
> >> Dano, I can see the MSE's at ~10 sigma, but no Cl ions, even though Cl
> >> should have f" = ~0.3 versus Se's f" = ~4, and no S's in the cys,
> >> despite f" = 0.23e. There is really no anomalous peak at all--is it
> >> just the smallness of the signal, or are the Se's somehow "swamping
> >> out" the other signal? Perhaps the phases are tainted by the presence
> >> of semet in the model?
> >> 
> >> Looking for suggestions,
> >> 
> >> Jacob Keller
> >> 
> >> ***
> >> Jacob Pearson Keller
> >> Northwestern University
> >> Medical Scientist Training Program
> >> cel: 773.608.9185
> >> email: j-kell...@northwestern.edu
> >> ***
> >> 
> >> ..
> >> 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://web.mac.com/bosch_lab/
> >> 
> >> 
> >> 
> >> 
> >> 
> > 
> > 
> > 
> > -- 
> > ***
> > Jacob Pearson Keller
> > Northwestern University
> > Medical Scientist Training Program
> > cel: 773.608.9185
> > email: j-kell...@northwestern.edu
> > ***
> 
> --
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Instit

Re: [ccp4bb] EDS server

[Gerard DVD Kleywegt]

Hi all,

Simple question, is there a way I can upload my own data into the EDS 
server? I see only place for it to take from data already published in the 
PDB.


First of all, if you deposit at PDBe, EDS will be run on your deposition and 
you can access the results after annotation. Second, RCSB operates a 
validation server that carries out similar calculations and which you can use 
prior to deposition.


Having said that, yes, there is actually an *unsupported* version of EDS to 
which you can upload your model and structure factors (MTZ or CIF file). Note 
that it is unsupported, unofficial, unmaintained, buyer beware and your 
mileage may vary.


In the future, there will of course be a shiny new wwPDB X-ray validation 
server which will include EDS-style calculations. (I won't make any promises 
as to when, but it will be before we all travel to work with jetpacks or 
flying cars.)


--Gerard

PS: If you want to try out the *unsupported* etc. PRedeposition EDS server 
(PREDS), throw your browser at http://eds.bmc.uu.se/eds/preds.php (but read 
http://eds.bmc.uu.se/eds/preds_help.html first).


**
   Gerard J.  Kleywegt

http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

Re: [ccp4bb] No Cl- or S Anomalous Signal

[James Holton]

It is quite possible that the S- and Cl- signal is being lost under that 
from the Se sites.  Could be:

1) simply noise that would swamp the S-SAD signal anyway
2) you just aren't contouring your map low enough ("sigma" is not on an 
absolute scale)
3)  trigonometry.  Remember, with SAD you are not looking at the heavy 
atom contribution (FH) directly, you are looking at the projection of FH 
that is orthogonal to FP (the protein contribution). Hence the weaker 
atom positions have less and less influence on DANO as the Se signal 
becomes stronger.


One way to test the last hypothesis is to calculate anomalous 
differences from your model and see what that anomalous-difference map 
looks like.  You can get DANOcalc for a given PDB file and wavelength 
using the CCP4 Suite and my script:

http://bl831.als.lbl.gov/~jamesh/mlfsom/ano_sfall.com

or you can do it with phenix.fmodel after you look up the f', f" for all 
your elements at the wavelength of interest.


It is interesting to see what happens if you set f" = 100 electrons or 
more.  If f" is too big, then it swamps FP, and you can no longer get 
phases by SAD.


-James Holton
MAD Scientist

On 9/1/2011 3:29 PM, Jacob Keller wrote:

Update:

I tried more anomalous maps, this time with the originally-deposited
data at 1.8 Ang (mine were similar, substrate-soaked crystals) and
phases from the refined model, and the Se sites are now ~40-50 sigma,
and there is still totally nothing at the Cl and S sites, even though
in 2Fo-Fc the Cl is ~9 sigma, and the S is 8 sigma (the Se is ~15
sigma). If it has reasonably-high electron density, shouldn't it have
at least some anomalous scattering? I am wondering whether somehow the
model phases are biasing the map, but I can't really imagine how that
would be...

JPK


On Thu, Sep 1, 2011 at 3:15 PM, Bosch, Juergen  wrote:

Where in refinement of your model are you ?
At an early stage I wouldn't be surprised to only see SeMets but once you've
refined your structure and go back to calculate an anomalous map with the
improved phases you might double your signal for SeMet and start seeing
sulfurs.
An alternative explanation, you've blasted your crystals at the synchrotron
and the remaining anomalous signal is too weak to show the sulfurs.
Just two thoughts,
Jürgen
On Sep 1, 2011, at 4:03 PM, Jacob Keller wrote:

Dear Crystallographers,

I recently have been working with a 2.5 Ang SeMet peak wavelength
dataset which contains 2 cys's and also a couple of bona fide Cl ions
(reasonable b-factor/site is semi-buried/water does not work). In the
FFT anomalous difference map using PhiC from the refined model and
Dano, I can see the MSE's at ~10 sigma, but no Cl ions, even though Cl
should have f" = ~0.3 versus Se's f" = ~4, and no S's in the cys,
despite f" = 0.23e. There is really no anomalous peak at all--is it
just the smallness of the signal, or are the Se's somehow "swamping
out" the other signal? Perhaps the phases are tainted by the presence
of semet in the model?

Looking for suggestions,

Jacob Keller

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

..
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://web.mac.com/bosch_lab/

Re: [ccp4bb] Coot problem

[Paul Emsley]

Dear all,

I am using coot 0.6.2 on MacBook. It was working nicely when I was 
using previous version. With this new coot I am problem as I can not 
do anything except visualisation. If I try to build or refine always 
show the message "refinement setup failure, Failed to find 
restraints" or "missing dictionary". I reinstall the coot but still 
have the same problem. I was not able to locate the dictionary. Can 
please anybody suggest me something, how to solve the problem.




It is not clear if you are using a Bill Scott binary or not (I believe 
those binaries run the test suite before distribution).


Coot 0.6.2 is synched to CCP4 6.2 for the dictionary.  If you are 
experiencing problems, that may be due to a version mis-match.


You should read the console - it might provide some insight.

You may wish to contact me (off-list) to pursue this.

Paul.

Re: [ccp4bb] No Cl- or S Anomalous Signal

[Randy Read]

Dear Jacob,

The signal for weak anomalous sites can be stronger in Phaser SAD LLG maps than 
in model-phased anomalous difference Fouriers, especially if the substructure 
already contains the stronger sites, so that you're just looking for what is 
still left to be explained in the SAD data.  You could try running Phaser in 
MR-SAD mode, giving the current protein model as a partial structure, providing 
the substructure of the Se sites, and looking for purely-imaginary scatterers 
("LLGCOMPLETE SCATTERER AX" in a script, or check the box labelled "Complete 
with purely anomalous scatterer" in the ccp4i GUI).  In this situation you 
don't want to look for S or Cl atoms as such, because the real part of their 
scattering is already accounted for well in the protein model.

Best wishes,

Randy Read

On 1 Sep 2011, at 23:29, Jacob Keller wrote:

> Update:
> 
> I tried more anomalous maps, this time with the originally-deposited
> data at 1.8 Ang (mine were similar, substrate-soaked crystals) and
> phases from the refined model, and the Se sites are now ~40-50 sigma,
> and there is still totally nothing at the Cl and S sites, even though
> in 2Fo-Fc the Cl is ~9 sigma, and the S is 8 sigma (the Se is ~15
> sigma). If it has reasonably-high electron density, shouldn't it have
> at least some anomalous scattering? I am wondering whether somehow the
> model phases are biasing the map, but I can't really imagine how that
> would be...
> 
> JPK
> 
> 
> On Thu, Sep 1, 2011 at 3:15 PM, Bosch, Juergen  wrote:
>> Where in refinement of your model are you ?
>> At an early stage I wouldn't be surprised to only see SeMets but once you've
>> refined your structure and go back to calculate an anomalous map with the
>> improved phases you might double your signal for SeMet and start seeing
>> sulfurs.
>> An alternative explanation, you've blasted your crystals at the synchrotron
>> and the remaining anomalous signal is too weak to show the sulfurs.
>> Just two thoughts,
>> Jürgen
>> On Sep 1, 2011, at 4:03 PM, Jacob Keller wrote:
>> 
>> Dear Crystallographers,
>> 
>> I recently have been working with a 2.5 Ang SeMet peak wavelength
>> dataset which contains 2 cys's and also a couple of bona fide Cl ions
>> (reasonable b-factor/site is semi-buried/water does not work). In the
>> FFT anomalous difference map using PhiC from the refined model and
>> Dano, I can see the MSE's at ~10 sigma, but no Cl ions, even though Cl
>> should have f" = ~0.3 versus Se's f" = ~4, and no S's in the cys,
>> despite f" = 0.23e. There is really no anomalous peak at all--is it
>> just the smallness of the signal, or are the Se's somehow "swamping
>> out" the other signal? Perhaps the phases are tainted by the presence
>> of semet in the model?
>> 
>> Looking for suggestions,
>> 
>> Jacob Keller
>> 
>> ***
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> cel: 773.608.9185
>> email: j-kell...@northwestern.edu
>> ***
>> 
>> ..
>> 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://web.mac.com/bosch_lab/
>> 
>> 
>> 
>> 
>> 
> 
> 
> 
> -- 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
> ***

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] Low resolution structure determination advice

[Tanner, John J.]

Did you try density modification starting with the sad phases with phase 
extension to 2.7 A followed by auto-tracing?  The model should be better than 
the one built from the 3.7 A sad map.



Sent from Jack's iPad

On Sep 1, 2011, at 11:24 PM, "Kianoush Sadre-Bazzaz" 
mailto:ksad...@yahoo.com>> wrote:

Hi Basu,

You mentioned molecular replacement was not successful for this project. Which 
model was used for this procedure? Have you tried your partially built 
structure as a model to obtain preliminary phases for your native (2.7A) data 
set? If there is  any luck with that, you might be able to combine phases from 
this procedure with the Selenium SAD phases, as already suggested.

Kianoush

--- On Thu, 9/1/11, Basudeb Bhattacharyya 
mailto:bbhattach...@wisc.edu>> wrote:

From: Basudeb Bhattacharyya 
mailto:bbhattach...@wisc.edu>>
Subject: [ccp4bb] Low resolution structure determination advice
To:  
CCP4BB@JISCMAIL.AC.UK
Date: Thursday, September 1, 2011, 9:31 AM

Dear all,

We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 750 amino acids and naturally binds zinc.  We have 
a SeMet data set that goes down to 3.7 angstroms.  4 of 8 selenium sites are 
ordered and visible in addition to our zincs and we've modeled about 450 
residues of C-alpha backbone off a pure SAD density map
(we've tried other phasing experiments such as Zn SAD, MAD, etc. and the best 
maps--clear density and visible secondary structures--we get are off Se SAD).  
We have one monomer per AU (and we have secondary structure coverage over our 
entire protein based on looking at conserved domains of our 
protein--unfortunately, MR is not working for this project).
R/Rfree hits a minimum of 37/41 respectively in spacegroup P32 (we've tried P3 
and P31, which haven't worked).  We also have a native set down to 2.7 
angstroms.  We are able to place our working model into the native data set, 
but we are unable to further refine the structure in Refmac (density doesn’t 
improve and the stats creep up).  Addition of side chains only makes our stats 
worse.  The data sets are clean (no twinning, etc.).  While we understand that 
we may need more phasing information (i.e. our initial model may still be quite 
inaccurate given resolution and size of the protein among other things--we are 
trying to improve this), we're wondering if anyone might have some other 
suggestions or insights about how we can move forward given the data that we 
currently have. Thanks in advance for any advice.

Sincerely,

Basu

[ccp4bb] Coot problem

[Md Shaik]

Dear all, 

I am using coot 0.6.2 on MacBook. It was working nicely when I was using 
previous version. With this new coot I am problem as I can not do anything 
except visualisation. If I try to build or refine always show the message 
"refinement setup failure, Failed to find restraints" or "missing dictionary". 
I reinstall the coot but still have the same problem. I was not able to locate 
the dictionary. Can please anybody suggest me something, how to solve the 
problem.  


Thanks in advance

Md. Munan Shaik

Department of Biological Chemistry
School of Bioscience and Biotechnology
via G. Colombo 03
University of Padova
Padova 35131, Italy
Mobile: 00393275671896
E-mail: munanbt2...@yahoo.com
 munan.sh...@unipd.it

Re: [ccp4bb] EDS server

[Careina Edgooms]

Yes I would like to use it as part of validation ie to see RSCC maps and other 
validation based on density. If EDS cannot do this, is there another program 
that does something similar? I am aware of overlapmap in ccp4 but it is not as 
thorough.




From: Tim Gruene 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, September 2, 2011 1:29 PM
Subject: Re: [ccp4bb] EDS server

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


Dear Boaz,

On 09/02/2011 01:19 PM, Boaz Shaanan wrote:
> Hi,
> 
> I could be missing something, but why would you want to do this? Once (or 
Obviously because one would like to see the analyses before submitting
the structure to the PDB, as part of the validation process.

Tim

> shortly after) your coordinates (and SF's!) are in the PDB database, your 
> structure will be available through the EDS website to whoever is interested.
> 
> Cheers,
> 
> Boaz
> 
> /Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> 
> E-mail: bshaa...@bgu.ac.il 
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710 /
> //
> //
> /
> 
> /
> 
> *From:*CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] 
>  on behalf of Careina Edgooms 
> [careinaedgo...@yahoo.com] 
> *Sent:* Friday, September 02, 2011 11:41 AM
> *To:*CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] EDS server
> 
> Dear all
> 
> Simple question, is there a way I can upload my own data into the EDS server? 
> I 
> see only place for it to take from data already published in the PDB.
> 
> Apologies for non ccp4 based question
> Careina

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

GPG Key ID = A46BEE1A

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Re: [ccp4bb] EDS server

[Tim Gruene]

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Dear Boaz,

On 09/02/2011 01:19 PM, Boaz Shaanan wrote:
> Hi,
> 
> I could be missing something, but why would you want to do this? Once (or 
Obviously because one would like to see the analyses before submitting
the structure to the PDB, as part of the validation process.

Tim

> shortly after) your coordinates (and SF's!) are in the PDB database, your 
> structure will be available through the EDS website to whoever is interested.
> 
> Cheers,
> 
> Boaz
> 
> /Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> 
> E-mail: bshaa...@bgu.ac.il 
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710 /
> //
> //
> /
> 
> /
> 
> *From:*CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] 
>  on behalf of Careina Edgooms 
> [careinaedgo...@yahoo.com] 
> *Sent:* Friday, September 02, 2011 11:41 AM
> *To:*CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] EDS server
> 
> Dear all
> 
> Simple question, is there a way I can upload my own data into the EDS server? 
> I 
> see only place for it to take from data already published in the PDB.
> 
> Apologies for non ccp4 based question
> Careina

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

GPG Key ID = A46BEE1A

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Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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iVu3Ty1lwyv6qR2KLtgb9I4=
=Vx/X
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[ccp4bb] EDS server

[Careina Edgooms]

Dear all

Simple question, is there a way I can upload my own data into the EDS server? I 
see only place for it to take from data already published in the PDB.

Apologies for non ccp4 based question
Careina

Re: [ccp4bb] 64-bit CCP4

[Tom Oldfield]

 Some important reason for using 64bit is due to the following.

The "effective" precision of a float (32bit) is about 5 dp
The "effective" precision of a double/real*8 (64 bit) is about 10 dp

The number of dp is only approximate since we are encoding this using 
binary.

The max/min value of a float (32bit) is e37, and for 8bit number if e128

Using a 64 bit number to store coordinates makes no sence of course 
since experiements don't provide this, but when doing complex 
calculations such as matrix manipulation (in graphics programs), or 
non-linear fitting (refinement) then we must store intermediate results 
with 64bit number or interesting distorsions will propogate in your 
structure.   Error due to data precision propogates very fast !


In machine code a 64 bit number can be fetched with a single instruction 
on a 64 bit OS, whereas a 32bit OS requires a double memory fetch.  It 
does depend on how the hardware vendor designed the underlying 
micro-code of the drivers - sometimes these will use 64bit firm-ware 
fetches on 32bit OS for forward compatibility, but in general a 64bit OS 
will allow the hard computation with 64bit numbers to run faster as the 
machine code has less memory fetches.


Ie programs with complex manipulation will run faster on a 64 bit machine.

Another issue is that the heap and stack limitations in computer 
languages limit the size of contigious regions of memory that can be 
address by a single "offset" address machine code instruction.  An array 
defined in  machine code uses a start point + offset - and sometimes 
this offset is only 16bit (ah!) or 32bit-signed.  So not only is the 
maximum size of memory available to a program 4G on a 32bit computer, 
the single contigious memory chunk is less on a 32bit machine.  This 
causes problems with 2D or ND arrays, and it was typical that a 
4000x4000 matrix was the limit on 32bit computers (as it used 16bit 
offsetting) - and certainly on all machines I used in my past.   
Contigious memory sizes are much larger on 64bit OS - the effective size 
of an array is now unlimited (almost).


It is just easier to write more complex programs on computers so we 
(devlopers) can make these more powerful computers run slower than the 
old computers we had before.


Regards
Tom


On Thu, Sep 01, 2011 at 11:36:21AM -0700, Ethan Merritt wrote:

On Thursday, September 01, 2011 11:02:50 am Ed Pozharski wrote:

I am almost sure this has been addressed before, so you can go after me
for insufficient googling.  However,

1.  Is there any *significant* advantage in using 64-bit CCP4 binaries
(primarily speed)?
2.  IIUC, the standard CCP4 download results in 32-bit binaries being
run on a 64-bit system.  Works for me (except for the weird iMosflm
issue), but given that 64-bit OS is becoming more and more common, isn't
it time for 64-bit binaries option?  The answer, of course, is no if you
answered no to 1 above.

The generic answer is that there is no intrinsic speed advantage to running
a 64-bit binary rather than a 32-bit binary.  In fact it may run slower
due to larger pointer sizes and hence poorer cache performance.
However, 32-bit binaries cannot access more than 4GB of address space.

But the x64 architecture provides more registers and faster instructions
than x86.  So a 32-bit binary using the x64 instruction set can run faster
than a 32-bit binary using only x86 instructions.  Therefore you need to
choose the right compiler options in order to get the benefit of the faster
architecture.

I do not know if there are specific CCP4 programs that fall outside of
the generic case described above.

Ethan

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

[ccp4bb] X-ray protein crystallography course at the Department of Biochemistry, University of Oulu, Oulu, Finland

[Rik Wierenga]

This is the first announcement of an X-ray protein crystallography  
course in Oulu, Finland, from January, 30 till February 3, 2012.  
Further details of the outline of the program are given on the  
WWW-site, as listed below. The topic of the course focuses on data  
collection, data processing, data tracking and phasing. The course is  
sponsored by Biocenter Oulu, Biocenter Finland and BioStruct-X.


The following teachers have agreed to contribute:
-Manfred Weiss (Berlin, Germany) (General Introduction)
-Rik Wierenga (Oulu, Finland) (General Introduction)
-Harry Powell (Cambridge, UK) (MOSFLM/SCALA)
-Marianna Biadene (Karlsruhe, Germany) (PROTEUM)
-Kay Diederichs (Constanz, Germany) (XDS)
-George Sheldrick (Göttingen, Germany) (SHELXC/D/E)
-Martin Walsh (Diamond, UK) (on-site and remote data collection at the  
Diamond synchrotron)

-Chris Morris  (Daresbury, UK) (PiMS/xtalPiMS)
-Stuart McNicholas (York, UK) (CCP4MG)

It will be possible to collect in-house data. More details are also  
available on our WWW-site. Participants are encouraged to bring their  
own data and/or their own crystals.


Please contact Vanja Kapetaniou for registration, as documented on the  
WWW-site; please include in the registration a cv and a brief  
statement on your motivation why this course will be beneficial for you.


Rik Wierenga, Vanja Kapetaniou, Kristian Koski  
http://www.biochem.oulu.fi/struct/xraycourse/