EDS server

From: Careina Edgooms
Date: 2 September 2011 09:41

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

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From: Boaz Shaanan

Hi,

I could  be missing something, but why would you want to do this? Once (or 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                                                     

                

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From: Tim Gruene
Dear Boaz,
Obviously because one would like to see the analyses before submitting
the structure to the PDB, as part of the validation process.

Tim

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


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From: 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.

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From: Boaz Shaanan

Does EDS have validation tools that are not available to us prior to submission to wPDB or as part of the submission process? Just wondering.

         Boaz

             

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From: Careina Edgooms

as far as I can see you can only use it on a PDB file so that is post submission. It gives a lot of information about the structure that would be useful prior to submission.

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From: Bosch, Juergen

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.

Jürgen

...

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From: Gerard DVD Kleywegt

Hi all, 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/ 
******************************************************************
  The opinions in this message are fictional.  Any similarity
  to actual opinions, living or dead, is purely coincidental.
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http://www.popularmechanics.com/science/4247253

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:-)

BR

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From: Pavel Afonine

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.  

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From: 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