[Proteopedia] NMR format, bot tasks

Dan Bolser dan.bolser at gmail.com
Mon Feb 9 07:04:01 EST 2009


Why not send this to the list once a month?

Its interesting to get a regular update of who has been doing what.



2009/2/9 Eran Hodis <eran.hodis at weizmann.ac.il>:
> 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
>>
>> _______________________________________________
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>> 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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> Proteopedialist-for-users at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users
>



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