[Proteopedia] NMR format, bot tasks

Karl Oberholser oberhols at messiah.edu
Mon Feb 9 09:04:35 EST 2009


Eran,
I would like my name added to the list of recipients.
 
Karl
 
 
Karl M. Oberholser 
Professor Chemistry
Chemistry & Biochemistry Dept.    
Messiah College 
Grantham, PA  US 
Molecular Science Lab:
http://www.messiah.edu/molscilab/ 
Proteopedia user page: 
http://proteopedia.org/wiki/index.php/User:Karl_Oberholser                 
    


>>> Eran Hodis <eran.hodis at weizmann.ac.il> 2/9/2009 5:11 AM >>>
Ralf,

Jaime has a script that sends a daily list of pages that have been  
changed or are new.  Would you (and would anyone else on this list)  
like him to add you to the list of recipients? Here is the output  
since the script began running:


  Feb  9 09:45:02 2009
8 new/updated Proteopedia pages

Alexander Berchansky      1gqr
Eran Hodis                Functional_annotation
James D Watson            James_D_Watson/Structural_Templates
James D Watson            James_D_Watson/Using_Jmol
Ralf Stephan              2a7g
Ralf Stephan              Matrix_metalloproteinases
Ralf Stephan              Acetylcholine
Ralf Stephan              Helix-turn-helix_motif

Sun Feb  8 09:45:02 2009
3 new/updated Proteopedia pages

Eran Hodis                Site
Jaime Prilusky            1ea5
Jaime Prilusky            Functional_annotation

Sat Feb  7 09:45:03 2009
6 new/updated Proteopedia pages

Angel Herraez             1w4l
Angel Herraez             1w6r
Eran Hodis                Biological_Unit
Eran Hodis                PISA
Eran Hodis                1ea5
Eran Hodis                1ea5_test

Fri Feb  6 09:45:02 2009
2 new/updated Proteopedia pages

Lindsey Butler            1j8r
Lindsey Butler            1j8s


Sat Jan 31 09:45:04 2009
2 new/updated Proteopedia pages

Lindsey Butler            1inl
Lindsey Butler            1jq3


Fri Jan 30 09:45:04 2009
3 new/updated Proteopedia pages

Eran Hodis                Human_RecQ-Like_protein_1
Jaime Prilusky            Complex_III_of_Electron_Transport_Chain
Ramiro Barrantes          1tdh

Wed Jan 28 09:45:17 2009
2 new/updated Proteopedia pages

Eran Hodis                Human_RecQ-Like_protein_1
Ramiro Barrantes          1r2y

Wed Jan 28 09:45:04 2009
2 new/updated Proteopedia pages

Alexander Berchansky      1acl
Marc Gillespie            Hemoglobin


Tue Jan 27 09:45:04 2009
3 new/updated Proteopedia pages

Jaime Prilusky            AChE_bivalent_inhibitors
Lindsey Butler            1ml0
Lindsey Butler            1mkf



Sun Jan 25 09:45:03 2009
2 new/updated Proteopedia pages

Alexander Berchansky      AChE_bivalent_inhibitors_(Part_II)
Jaime Prilusky            AChE_bivalent_inhibitors

Sat Jan 24 09:45:02 2009
2 new/updated Proteopedia pages

Lindsey Butler            1ks2
Lindsey Butler            1o8b


Wed Jan 21 09:45:04 2009
2 new/updated Proteopedia pages

Lindsey Butler            1m6y
Lindsey Butler            1n2x

Mon Jan 19 09:45:04 2009
4 new/updated Proteopedia pages

Eran Hodis                2tmv
Eran Hodis                2p1q
Eran Hodis                2p1n
Tom Gluick                Tom_Gluick/Human_Glutamine_Synthetase/ 
Quaternary_Structure


Sat Jan 17 09:45:03 2009
3 new/updated Proteopedia pages

Eran Hodis                Complex_III_of_Electron_Transport_Chain
Tom Gluick                Large_Image_Showing_Signature_with_labels
Tom Gluick                Tom_Gluick/Human_Glutamine_Synthetase/ 
Large_Image_Showing_Signature_with_labels

Fri Jan 16 09:45:02 2009
4 new/updated Proteopedia pages

David S. Goodsell         2p1n
David S. Goodsell         2p1q
Mark Hoelzer              SMART_Teams
Mark Hoelzer              2rh1

Thu Jan 15 09:45:03 2009
2 new/updated Proteopedia pages

Karl Oberholser           Complex_III_of_Electron_Transport_Chain
Savannah Anderson         Lactose_Permease


Tue Jan 13 09:45:02 2009
3 new/updated Proteopedia pages

Lindsey Butler            1s99
Lindsey Butler            1sbr
Tilman Schirmer           C-di-GMP


Mon Jan 12 09:45:04 2009
3 new/updated Proteopedia pages

Alexander Berchansky      1dx6
Alexander Berchansky      1e3q
Jaime Prilusky            Main_Page

Sat Jan 10 09:45:02 2009
3 new/updated Proteopedia pages

Karl Oberholser           Karl_oberholser/PPDK_large
Karl Oberholser           Karl_Oberholser/ 
Phosphoenolpyruvate:Sugar_Phosphotransferase
Tom Gluick                Tom_Gluick/Human_Glutamine_Synthetase


Thu Jan  8 09:45:04 2009
10 new/updated Proteopedia pages

Karl Oberholser           Karl_Oberholser/Ramachandran_Plots
Tilman Schirmer           1w25
Tilman Schirmer           2rde
Tilman Schirmer           2v0n
Tilman Schirmer           3bre
Tilman Schirmer           1ywu
Tilman Schirmer           2bas
Tilman Schirmer           2r6o
Tilman Schirmer           2gjg
Tilman Schirmer           1yln

Sat Jan  3 09:45:03 2009
3 new/updated Proteopedia pages

Eric Martz                Eric_Martz's_Favorites
Eric Martz                Resolution
Joel L. Sussman           Personal_favorites

Fri Jan  2 09:45:03 2009
2 new/updated Proteopedia pages

Alexander Berchansky      AChE_bivalent_inhibitors
Joel L. Sussman           Joel_Sussman's_Favorites

Thu Jan  1 09:45:03 2009
5 new/updated Proteopedia pages

Alexander Berchansky      AChE_inhibitors_and_substrates
Alexander Berchansky      1vot
Eran Hodis                2g5x
Eric Martz                Conservation,_Evolutionary
Joel L. Sussman           1v04

Wed Dec 31 09:45:04 2008
4 new/updated Proteopedia pages

Alexander Berchansky      2ace
Jaime Prilusky            2g5x
Wayne Decatur             2g5x
Wayne Decatur             Isoelectric_point

Tue Dec 30 09:45:02 2008
7 new/updated Proteopedia pages

Eric Martz                Structure_of_E._coli_DnaC_helicase_loader
Joel L. Sussman           1zgb
Wayne Decatur             Standard_Residues
Wayne Decatur             Getting_Unremediated_PDB_Files
Wayne Decatur             Non-Standard_Residue
Wayne Decatur             Wayne_Decatur/ 
Editing_Getting_Unremediated_PDB_Files
Wayne Decatur             Wayne_Decatur/I-Ppo_Morph_Methods

Sat Dec 27 09:45:02 2008
3 new/updated Proteopedia pages

Claudio Garutti           Prion_protein
Tom Gluick                Tom_Gluick/glutamine_synthetase/Assignment_8
Tom Gluick                Tom_Gluick/glutamine_synthetase/Assignment_1

Thu Dec 25 09:45:02 2008
2 new/updated Proteopedia pages

Joel L. Sussman           Main_Page
Tom Gluick                Tom_Gluick/glutamine_synthetase/Assignment_3

Tue Dec 16 09:45:02 2008
4 new/updated Proteopedia pages

Eran Hodis                Doppel
Eran Hodis                Prion_protein
Eran Hodis                Wanted_pages
Eran Hodis                 
Teaching_Scenes,_Tutorials,_and_Educators'_Pages

Mon Dec 15 09:45:02 2008
2 new/updated Proteopedia pages

Jaime Prilusky            Prion_protein
Kurt Giles                Doppel

Thu Dec 11 09:45:04 2008
2 new/updated Proteopedia pages

Eran Hodis                Personal_favorites
Eran Hodis                Favorites

Wed Dec 10 09:45:03 2008
2 new/updated Proteopedia pages

Kurt Giles                Prion_protein
Shiela M. Jones           Kinesin-5


Sat Dec  6 09:45:04 2008
3 new/updated Proteopedia pages

Adrian Aldrich            Adrian_Aldrich/ 
Prokaryotic_Glutamine_Synthetase_Pfam_Domains_Outline
Adrian Aldrich            AdrainOutline
Lindsey Butler            1pc6

Fri Dec  5 09:45:03 2008
2 new/updated Proteopedia pages

Lawrence Sheringham Borketey Lawrence_Sheringham_Borketey/ 
ATP_Phosphoribosyl_Transferase_(HisG)
Lawrence Sheringham Borketey ATP_Phosphoribosyl_Transferase

Wed Dec  3 09:45:02 2008
4 new/updated Proteopedia pages

Alexander Berchansky      DNA- 
binding_protein_VirE2_from_Agrobacterium_tumefaciens_complexed_with_chaperone_VirE1
Alexander Berchansky      Insecticidal_delta- 
endotoxin_Cyt2Ba_from_Bacillus_thuringiensis
Jamie LaFrance            Dronpa
Max Lein                  1gpa

Tue Dec  2 09:45:03 2008
8 new/updated Proteopedia pages

Alexander Berchansky      1u65
Alexander Berchansky      1xxm
Alexander Berchansky      2b5r
Alexander Berchansky      2b83
Alexander Berchansky      2rkx
Alexander Berchansky      2v9d
Alexander Berchansky      Antizyme_Inhibitor
Daniel Seeman             Alpha-1-antitrypsin

Wed Nov 26 09:45:04 2008
11 new/updated Proteopedia pages

Aparna Gorthi             Phosphoglucose_isomerase
Daniel Seeman             Daniel_Seeman/Alpha-1-antitrypsin
David Bruhn               OhrR
Eran Hodis                1b1h
Eric Martz                Student_Projects
Jaime Prilusky            Pyruvate_phosphate_dikinase
Jaime Prilusky             
Enzyme_I_of_the_Phosphoenolpyruvate:Sugar_Phosphotransferase_System
Luis E Ramirez-Tapia      1pjr
Mangai Periasamy          Isochorismate_pyruvate_lyase
Wayne Decatur             Wayne_Decatur/Sanbox0
Yash Patankar             Yash_Patankar//_Class_tutorial

Tue Nov 25 09:45:05 2008
4 new/updated Proteopedia pages

Dan Bolser                Hydrogen_in_macromolecular_models
Eran Hodis                Proteopedia_Page_Contributors_and_Editors
Lindsey Butler            1sqe
Lindsey Butler            1xbw

Sun Nov 23 09:45:02 2008
4 new/updated Proteopedia pages

Eran Hodis                Main_Page
Eric Martz                Water_in_macromolecular_models
Eric Martz                Hydrogen_in_macromolecular_models
Eric Martz                Quality_assessment_for_molecular_models

Sat Nov 22 09:45:02 2008
4 new/updated Proteopedia pages

Eric Martz                Transcription_Termination_Factor_Rho
Eric Martz                Asymmetric_Unit
Eric Martz                2oar
Wayne Decatur              
Teaching_Scenes,_Tutorials,_and_Educators'_Pages


Fri Nov 21 09:45:04 2008
5 new/updated Proteopedia pages

Edwin Kim                 Cytochrome
Eric Martz                Teaching_Strategies_Using_Proteopedia
Wayne Decatur             Wayne_Decatur/Chem791A_Work_Session
Wayne Decatur             Wayne_Decatur/Teaching_Proteopedia
Wayne Decatur             Green_Fluorescent_Protein

Thu Nov 20 09:45:04 2008
2 new/updated Proteopedia pages

Marc Boudvillain          Transcription_Termination_Factor_Rho
Wayne Decatur             Teaching_Strategies_Using_Proteopedia


Wed Nov 19 09:45:03 2008
3 new/updated Proteopedia pages

Eran Hodis                Rainbow
Raymond Hui               2npm
Raymond Hui               2p1i

Mon Nov 17 09:45:04 2008
6 new/updated Proteopedia pages

Alexander Berchansky      2f1o
Steven Tuyishime          Ezekwe/Lakkur/Tuyishime
Yongmin Kim               Youngdae
Yongmin Kim               Glu_Binding_Site
Youngsen Jeng             Scene_authoring_tools
Youngsen Jeng             Rainbow

Sat Nov 15 09:45:02 2008
2 new/updated Proteopedia pages

Lindsey Butler            2f96
Lindsey Butler            2is3


Tue Nov 11 09:45:03 2008
3 new/updated Proteopedia pages

Azeem Bhatti              Practice_Page
Lindsey Butler            2fgc
Warren DeLano             Hydrogen_bonds


Mon Nov 10 09:45:02 2008
2 new/updated Proteopedia pages

Alexander Berchansky      1y7w
Eran Hodis                2oar

Fri Nov  7 09:45:03 2008
2 new/updated Proteopedia pages

Alexander Berchansky      1zgc
Lindsey Butler            2i5r


Wed Nov  5 09:45:04 2008
5 new/updated Proteopedia pages

Eric Martz                FirstGlance_in_Jmol
Eric Martz                Protein_Explorer
Eric Martz                Swiss-PDBViewer_=_DeepView
Eric Martz                About_Macromolecular_Structure
Eric Martz                 
Teaching_Scenes,_Tutorials,_and_Educators'_Pages


Tue Nov  4 09:45:02 2008
8 new/updated Proteopedia pages

Eric Martz                Peptide
Eric Martz                Chime
Eric Martz                Molecular_modeling_and_visualization_software
Eric Martz                RasMol
Eric Martz                Jmol
Eric Martz                PyMOL
Lindsey Butler            2qh1
Lindsey Butler            1pvm

Fri Oct 31 09:45:02 2008
2 new/updated Proteopedia pages

Eric Martz                Structure_Gallery_Generator
Jaime Prilusky            Structure_Gallery_Generator

Wed Oct 29 11:48:22 2008
18 new/updated Proteopedia pages

Alexander Berchansky      2oui
Alexander Berchansky      2nvb
Alexander Berchansky      1s0w
Alexander Berchansky      1zgb
Eric Martz                Lac_repressor
Eric Martz                 
Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza
Eric Martz                Structures_Gallery_Generator
Jaime Prilusky            Related_structure
Lindsey Butler            2paq
Lindsey Butler            2par
Lindsey Butler            2pau
Lindsey Butler            2qmx
Lindsey Butler            2qmw
Tom Gluick                Tom_Gluick/glutamine_synthetase
Wayne Decatur             Wayne_Decatur/ 
Plant_Viral_Protein_p19_Suppression_of_RNA_Silencing
Wayne Decatur             Wayne_Decatur/ 
Suppression_of_RNA_Silencing_by_Viruses
Wayne Decatur             Wayne_Decatur/ 
Flock_house_virus_B2_protein_Suppression_of_RNA_Silencing
Wayne Decatur             Wayne_Decatur/ 
Tomato_aspermy_virus_protein_2b_Suppression_of_RNA_Silencing
On Feb 9, 2009, at 10:51 AM, Ralf Stephan wrote:

> Dan wrote
>>>> The question, however, that's bothering me is that IMHO there  
>>>> should
>>>> be a link from any structure page to that topic pages where the
>>>> structure is used. It could be text like 'See also the topics:' at
>>>> the top or a row in the info box 'Topic pages:' or a paragraph in
>>>> the section 'About this structure' reading e.g. 'This structure is
>>>> also used in the pages ...'
>>>>
>>>> Since it can't be relied on that authors do such backlinks, and  
>>>> this
>>>> can be automatized, it should be automatized at some time.
>>>
>>> That's a really great idea if it can be done well. How would you  
>>> suggest
>>> doing this (of course automatically)?  Let's say you're on the  
>>> page for
>>> 1ea5, do you want to list, on the page for 1ea5, all other pages  
>>> that link
>>> to 1ea5?  Or all other pages that link to 1ea5 but are not PDB- 
>>> entry pages?
>>> I'm just worried that such an automatically generated list might,  
>>> in some
>>> instances, be long and irrelevant.  Of course as you've said, the  
>>> person who
>>> created the Topic page should link from the topic page to the PDB  
>>> entry page
>>> and vice versa, but they will sometimes neglect to do this.
>>>
>>>>
>>>>
>>>> On another note, I would like to see a list of all structure pages
>>>> that have been enhanced by other authors than OCA. This should be
>>>> automatized, too.
>>>
>>> Eric, at one point you were interested in such a list -- what did  
>>> you do?
>>
>> We do something similar over on PDBWiki using an extension known as  
>> DPL.
>>
>> http://www.mediawiki.org/wiki/Extension:DynamicPageList 
>
> Thanks for that link. Indeed, it should be possible to implement
> something approximating my ideas using DPL.
>
> 1) What appears possible: having a link on each structure page
>   'List topics where this structure is used in a scene'.
>   Pages are selected according to the title matching a regexp AND
>   the content matching a regexp (titleregexp, includematch)
> 2) What appears possible: a link somewhere that lists all structure
>   pages in a specific category (like Single protein) or all structure
>   pages in general (pages starting with digit) where the last
>   change was not done by OCA (notlastmodifiedby).
>
> As this is more or less what I intended, and writing and running a bot
> is so much more hassle, I'm all for installing DPL on the server.
>
>
> ralf
>
> _______________________________________________
> Proteopedialist-for-users mailing list
> Proteopedialist-for-users at bioinformatics.org 
> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users


Eran Hodis
eran.hodis at weizmann.ac.il 




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