[Proteopedia] NMR format, bot tasks
Eran Hodis
eran.hodis at weizmann.ac.il
Mon Feb 9 05:11:12 EST 2009
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
More information about the Proteopedialist-for-users
mailing list