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<DIV>Eran,</DIV>
<DIV>I would like my name added to the list of recipients.</DIV>
<DIV> </DIV>
<DIV>Karl</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>
<DIV>Karl M. Oberholser </DIV>
<DIV>Professor Chemistry</DIV>
<DIV>Chemistry & Biochemistry Dept. <BR>Messiah College </DIV>
<DIV>Grantham, PA US </DIV>
<DIV>Molecular Science Lab:</DIV>
<DIV><A href="http://www.messiah.edu/molscilab/">http://www.messiah.edu/molscilab/</A><BR><EM>Proteopedia</EM> user page: </DIV>
<DIV><A href="http://proteopedia.org/wiki/index.php/User:Karl_Oberholser">http://proteopedia.org/wiki/index.php/User:Karl_Oberholser</A> <BR></DIV><BR><BR>>>> Eran Hodis <eran.hodis@weizmann.ac.il> 2/9/2009 5:11 AM >>><BR>Ralf,<BR><BR>Jaime has a script that sends a daily list of pages that have been <BR>changed or are new. Would you (and would anyone else on this list) <BR>like him to add you to the list of recipients? Here is the output <BR>since the script began running:<BR><BR><BR> Feb 9 09:45:02 2009<BR>8 new/updated Proteopedia pages<BR><BR>Alexander Berchansky 1gqr<BR>Eran Hodis Functional_annotation<BR>James D Watson &nbs
p; James_D_Watson/Structural_Templates<BR>James D Watson James_D_Watson/Using_Jmol<BR>Ralf Stephan 2a7g<BR>Ralf Stephan Matrix_metalloproteinases<BR>Ralf Stephan Acetylcholine<BR>Ralf Stephan Helix-turn-helix_motif<BR><BR>Sun Feb 8 09:45:02 2009<BR>3 new/updated Proteopedia pages<BR><BR>Eran Hodis Site<BR>Jaime Prilusky 1ea5<BR>Jaime Prilusky Functional_annotation<BR><
BR>Sat Feb 7 09:45:03 2009<BR>6 new/updated Proteopedia pages<BR><BR>Angel Herraez 1w4l<BR>Angel Herraez 1w6r<BR>Eran Hodis Biological_Unit<BR>Eran Hodis PISA<BR>Eran Hodis 1ea5<BR>Eran Hodis 1ea5_test<BR><BR>Fri Feb 6 09:45:02 2009<BR>2 new/updated Proteopedia pages<BR><BR>Lindsey Butler 1j8r<BR>Lindsey Butler 1j8s<BR><BR><BR>Sat Jan 31 0
9:45:04 2009<BR>2 new/updated Proteopedia pages<BR><BR>Lindsey Butler 1inl<BR>Lindsey Butler 1jq3<BR><BR><BR>Fri Jan 30 09:45:04 2009<BR>3 new/updated Proteopedia pages<BR><BR>Eran Hodis Human_RecQ-Like_protein_1<BR>Jaime Prilusky Complex_III_of_Electron_Transport_Chain<BR>Ramiro Barrantes 1tdh<BR><BR>Wed Jan 28 09:45:17 2009<BR>2 new/updated Proteopedia pages<BR><BR>Eran Hodis Human_RecQ-Like_protein_1<BR>Ramiro Barrantes 1r2y<BR><BR>Wed Jan 28 09:45:04 2009<BR>2 new/updated Proteopedia pages<BR><
BR>Alexander Berchansky 1acl<BR>Marc Gillespie Hemoglobin<BR><BR><BR>Tue Jan 27 09:45:04 2009<BR>3 new/updated Proteopedia pages<BR><BR>Jaime Prilusky AChE_bivalent_inhibitors<BR>Lindsey Butler 1ml0<BR>Lindsey Butler 1mkf<BR><BR><BR><BR>Sun Jan 25 09:45:03 2009<BR>2 new/updated Proteopedia pages<BR><BR>Alexander Berchansky AChE_bivalent_inhibitors_(Part_II)<BR>Jaime Prilusky AChE_bivalent_inhibitors<BR><BR>Sat Jan 24 09:45:02 2009<BR>2 new/updated Proteopedia pages<BR><BR>Lindsey Butler 1ks2<BR>Lindsey Butler &
nbsp; 1o8b<BR><BR><BR>Wed Jan 21 09:45:04 2009<BR>2 new/updated Proteopedia pages<BR><BR>Lindsey Butler 1m6y<BR>Lindsey Butler 1n2x<BR><BR>Mon Jan 19 09:45:04 2009<BR>4 new/updated Proteopedia pages<BR><BR>Eran Hodis 2tmv<BR>Eran Hodis 2p1q<BR>Eran Hodis 2p1n<BR>Tom Gluick Tom_Gluick/Human_Glutamine_Synthetase/ <BR>Quaternary_Structure<BR><BR><BR>Sat Jan 17 09:45:03 2009<BR>3 new/updated Proteopedia pages<BR><BR>Eran Hodis  
; Complex_III_of_Electron_Transport_Chain<BR>Tom Gluick Large_Image_Showing_Signature_with_labels<BR>Tom Gluick Tom_Gluick/Human_Glutamine_Synthetase/ <BR>Large_Image_Showing_Signature_with_labels<BR><BR>Fri Jan 16 09:45:02 2009<BR>4 new/updated Proteopedia pages<BR><BR>David S. Goodsell 2p1n<BR>David S. Goodsell 2p1q<BR>Mark Hoelzer SMART_Teams<BR>Mark Hoelzer 2rh1<BR><BR>Thu Jan 15 09:45:03 2009<BR>2 new/updated Proteopedia pages<BR><BR>Karl Oberholser &nb
sp; Complex_III_of_Electron_Transport_Chain<BR>Savannah Anderson Lactose_Permease<BR><BR><BR>Tue Jan 13 09:45:02 2009<BR>3 new/updated Proteopedia pages<BR><BR>Lindsey Butler 1s99<BR>Lindsey Butler 1sbr<BR>Tilman Schirmer C-di-GMP<BR><BR><BR>Mon Jan 12 09:45:04 2009<BR>3 new/updated Proteopedia pages<BR><BR>Alexander Berchansky 1dx6<BR>Alexander Berchansky 1e3q<BR>Jaime Prilusky Main_Page<BR><BR>Sat Jan 10 09:45:02 2009<BR>3 new/updated Proteopedia pages<BR><BR>Karl Oberholser Karl_oberholser/PPDK_large<BR>Karl Oberholser
Karl_Oberholser/ <BR>Phosphoenolpyruvate:Sugar_Phosphotransferase<BR>Tom Gluick Tom_Gluick/Human_Glutamine_Synthetase<BR><BR><BR>Thu Jan 8 09:45:04 2009<BR>10 new/updated Proteopedia pages<BR><BR>Karl Oberholser Karl_Oberholser/Ramachandran_Plots<BR>Tilman Schirmer 1w25<BR>Tilman Schirmer 2rde<BR>Tilman Schirmer 2v0n<BR>Tilman Schirmer 3bre<BR>Tilman Schirmer 1ywu<BR>Tilman Schirmer 2bas<BR>Tilman Schirmer &nb
sp; 2r6o<BR>Tilman Schirmer 2gjg<BR>Tilman Schirmer 1yln<BR><BR>Sat Jan 3 09:45:03 2009<BR>3 new/updated Proteopedia pages<BR><BR>Eric Martz Eric_Martz's_Favorites<BR>Eric Martz Resolution<BR>Joel L. Sussman Personal_favorites<BR><BR>Fri Jan 2 09:45:03 2009<BR>2 new/updated Proteopedia pages<BR><BR>Alexander Berchansky AChE_bivalent_inhibitors<BR>Joel L. Sussman Joel_Sussman's_Favorites<BR><BR>Thu Jan 1 09:45:03 2009<BR>5 new/updated Proteopedia pages<BR><BR>Alexander Berchansky&n
bsp; AChE_inhibitors_and_substrates<BR>Alexander Berchansky 1vot<BR>Eran Hodis 2g5x<BR>Eric Martz Conservation,_Evolutionary<BR>Joel L. Sussman 1v04<BR><BR>Wed Dec 31 09:45:04 2008<BR>4 new/updated Proteopedia pages<BR><BR>Alexander Berchansky 2ace<BR>Jaime Prilusky 2g5x<BR>Wayne Decatur 2g5x<BR>Wayne Decatur Isoelectric_point<BR><BR>Tue Dec 30 09:45:02 2008<BR>7 new/updated Proteopedia pages<BR><BR>Eric Martz
Structure_of_E._coli_DnaC_helicase_loader<BR>Joel L. Sussman 1zgb<BR>Wayne Decatur Standard_Residues<BR>Wayne Decatur Getting_Unremediated_PDB_Files<BR>Wayne Decatur Non-Standard_Residue<BR>Wayne Decatur Wayne_Decatur/ <BR>Editing_Getting_Unremediated_PDB_Files<BR>Wayne Decatur Wayne_Decatur/I-Ppo_Morph_Methods<BR><BR>Sat Dec 27 09:45:02 2008<BR>3 new/updated Proteopedia pages<BR><BR>Claudio Garutti Prion_protein<BR>Tom Gluick
Tom_Gluick/glutamine_synthetase/Assignment_8<BR>Tom Gluick Tom_Gluick/glutamine_synthetase/Assignment_1<BR><BR>Thu Dec 25 09:45:02 2008<BR>2 new/updated Proteopedia pages<BR><BR>Joel L. Sussman Main_Page<BR>Tom Gluick Tom_Gluick/glutamine_synthetase/Assignment_3<BR><BR>Tue Dec 16 09:45:02 2008<BR>4 new/updated Proteopedia pages<BR><BR>Eran Hodis Doppel<BR>Eran Hodis Prion_protein<BR>Eran Hodis Wanted_pages<BR>Eran
Hodis <BR>Teaching_Scenes,_Tutorials,_and_Educators'_Pages<BR><BR>Mon Dec 15 09:45:02 2008<BR>2 new/updated Proteopedia pages<BR><BR>Jaime Prilusky Prion_protein<BR>Kurt Giles Doppel<BR><BR>Thu Dec 11 09:45:04 2008<BR>2 new/updated Proteopedia pages<BR><BR>Eran Hodis Personal_favorites<BR>Eran Hodis Favorites<BR><BR>Wed Dec 10 09:45:03 2008<BR>2 new/updated Proteopedia pages<BR><BR>Kurt Giles Prion_protein<BR>Shiela M. Jones &nb
sp; Kinesin-5<BR><BR><BR>Sat Dec 6 09:45:04 2008<BR>3 new/updated Proteopedia pages<BR><BR>Adrian Aldrich Adrian_Aldrich/ <BR>Prokaryotic_Glutamine_Synthetase_Pfam_Domains_Outline<BR>Adrian Aldrich AdrainOutline<BR>Lindsey Butler 1pc6<BR><BR>Fri Dec 5 09:45:03 2008<BR>2 new/updated Proteopedia pages<BR><BR>Lawrence Sheringham Borketey Lawrence_Sheringham_Borketey/ <BR>ATP_Phosphoribosyl_Transferase_(HisG)<BR>Lawrence Sheringham Borketey ATP_Phosphoribosyl_Transferase<BR><BR>Wed Dec 3 09:45:02 2008<BR>4 new/updated Proteopedia pages<BR><BR>Alexander Berchansky DNA- <BR>binding_protein_VirE2_from_Agrobacterium_tumefaciens_complexed_with_chaperone_VirE1<BR>Alexander Berchansky Insecticidal
_delta- <BR>endotoxin_Cyt2Ba_from_Bacillus_thuringiensis<BR>Jamie LaFrance Dronpa<BR>Max Lein 1gpa<BR><BR>Tue Dec 2 09:45:03 2008<BR>8 new/updated Proteopedia pages<BR><BR>Alexander Berchansky 1u65<BR>Alexander Berchansky 1xxm<BR>Alexander Berchansky 2b5r<BR>Alexander Berchansky 2b83<BR>Alexander Berchansky 2rkx<BR>Alexander Berchansky 2v9d<BR>Alexander Berchansky Antizyme_Inhibitor<BR>Daniel Seeman Alpha-1-antitrypsin<BR><BR>Wed Nov 26 09:45:04 2008<BR>11 new/updated Proteopedia pages<BR><BR>Aparna Gorthi &nbs
p; Phosphoglucose_isomerase<BR>Daniel Seeman Daniel_Seeman/Alpha-1-antitrypsin<BR>David Bruhn OhrR<BR>Eran Hodis 1b1h<BR>Eric Martz Student_Projects<BR>Jaime Prilusky Pyruvate_phosphate_dikinase<BR>Jaime Prilusky <BR>Enzyme_I_of_the_Phosphoenolpyruvate:Sugar_Phosphotransferase_System<BR>Luis E Ramirez-Tapia 1pjr<BR>Mangai Periasamy Isochorismate_pyruvate_lyase<BR>Wayne Decatur&nbs
p; Wayne_Decatur/Sanbox0<BR>Yash Patankar Yash_Patankar//_Class_tutorial<BR><BR>Tue Nov 25 09:45:05 2008<BR>4 new/updated Proteopedia pages<BR><BR>Dan Bolser Hydrogen_in_macromolecular_models<BR>Eran Hodis Proteopedia_Page_Contributors_and_Editors<BR>Lindsey Butler 1sqe<BR>Lindsey Butler 1xbw<BR><BR>Sun Nov 23 09:45:02 2008<BR>4 new/updated Proteopedia pages<BR><BR>Eran Hodis Main_Page<BR>Eric Martz  
; Water_in_macromolecular_models<BR>Eric Martz Hydrogen_in_macromolecular_models<BR>Eric Martz Quality_assessment_for_molecular_models<BR><BR>Sat Nov 22 09:45:02 2008<BR>4 new/updated Proteopedia pages<BR><BR>Eric Martz Transcription_Termination_Factor_Rho<BR>Eric Martz Asymmetric_Unit<BR>Eric Martz 2oar<BR>Wayne Decatur <BR>Teaching_Scenes,_Tutorials,_and_Educators'_Pages<BR><BR><BR>Fri Nov 21 09:45:04 2008<BR>5 ne
w/updated Proteopedia pages<BR><BR>Edwin Kim Cytochrome<BR>Eric Martz Teaching_Strategies_Using_Proteopedia<BR>Wayne Decatur Wayne_Decatur/Chem791A_Work_Session<BR>Wayne Decatur Wayne_Decatur/Teaching_Proteopedia<BR>Wayne Decatur Green_Fluorescent_Protein<BR><BR>Thu Nov 20 09:45:04 2008<BR>2 new/updated Proteopedia pages<BR><BR>Marc Boudvillain Transcription_Termination_Factor_Rho<BR>Wayne Decatur Teaching_Strategies_Using_Proteopedia<BR><BR><BR>Wed Nov 19
09:45:03 2008<BR>3 new/updated Proteopedia pages<BR><BR>Eran Hodis Rainbow<BR>Raymond Hui 2npm<BR>Raymond Hui 2p1i<BR><BR>Mon Nov 17 09:45:04 2008<BR>6 new/updated Proteopedia pages<BR><BR>Alexander Berchansky 2f1o<BR>Steven Tuyishime Ezekwe/Lakkur/Tuyishime<BR>Yongmin Kim Youngdae<BR>Yongmin Kim Glu_Binding_Site<BR>Youngsen Jeng Scene_authoring_tools<BR>Youngsen Jeng &
nbsp; Rainbow<BR><BR>Sat Nov 15 09:45:02 2008<BR>2 new/updated Proteopedia pages<BR><BR>Lindsey Butler 2f96<BR>Lindsey Butler 2is3<BR><BR><BR>Tue Nov 11 09:45:03 2008<BR>3 new/updated Proteopedia pages<BR><BR>Azeem Bhatti Practice_Page<BR>Lindsey Butler 2fgc<BR>Warren DeLano Hydrogen_bonds<BR><BR><BR>Mon Nov 10 09:45:02 2008<BR>2 new/updated Proteopedia pages<BR><BR>Alexander Berchansky 1y7w<BR>Eran Hodis 2oar<BR><BR>Fri Nov 7 09:45:03 2008<BR>2 new/updated Proteopedia pages<BR><B
R>Alexander Berchansky 1zgc<BR>Lindsey Butler 2i5r<BR><BR><BR>Wed Nov 5 09:45:04 2008<BR>5 new/updated Proteopedia pages<BR><BR>Eric Martz FirstGlance_in_Jmol<BR>Eric Martz Protein_Explorer<BR>Eric Martz Swiss-PDBViewer_=_DeepView<BR>Eric Martz About_Macromolecular_Structure<BR>Eric Martz <BR>Teaching_Scenes,_Tutorials,_and_Educators'_Pages<BR><BR><BR>Tue Nov 4 09:45:02 2008<BR>8 new/updated Proteopedia pages<BR><BR>Eric
Martz Peptide<BR>Eric Martz Chime<BR>Eric Martz Molecular_modeling_and_visualization_software<BR>Eric Martz RasMol<BR>Eric Martz Jmol<BR>Eric Martz PyMOL<BR>Lindsey Butler 2qh1<BR>Lindsey Butler 1pvm<BR><BR>Fri Oct 31 09:45:02 2008<BR>2 new/updated Proteopedia pages<BR><BR>Eric Martz &nb
sp; Structure_Gallery_Generator<BR>Jaime Prilusky Structure_Gallery_Generator<BR><BR>Wed Oct 29 11:48:22 2008<BR>18 new/updated Proteopedia pages<BR><BR>Alexander Berchansky 2oui<BR>Alexander Berchansky 2nvb<BR>Alexander Berchansky 1s0w<BR>Alexander Berchansky 1zgb<BR>Eric Martz Lac_repressor<BR>Eric Martz <BR>Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza<BR>Eric Martz Structures_Gallery_Generator<BR>Jaime Prilusky &n
bsp; Related_structure<BR>Lindsey Butler 2paq<BR>Lindsey Butler 2par<BR>Lindsey Butler 2pau<BR>Lindsey Butler 2qmx<BR>Lindsey Butler 2qmw<BR>Tom Gluick Tom_Gluick/glutamine_synthetase<BR>Wayne Decatur Wayne_Decatur/ <BR>Plant_Viral_Protein_p19_Suppression_of_RNA_Silencing<BR>Wayne Decatur Wayne_Decatur/ <BR>Suppression_of_RNA_Silencing_by_Viruses<BR>Wayne Decatur
Wayne_Decatur/ <BR>Flock_house_virus_B2_protein_Suppression_of_RNA_Silencing<BR>Wayne Decatur Wayne_Decatur/ <BR>Tomato_aspermy_virus_protein_2b_Suppression_of_RNA_Silencing<BR>On Feb 9, 2009, at 10:51 AM, Ralf Stephan wrote:<BR><BR>> Dan wrote<BR>>>>> The question, however, that's bothering me is that IMHO there <BR>>>>> should<BR>>>>> be a link from any structure page to that topic pages where the<BR>>>>> structure is used. It could be text like 'See also the topics:' at<BR>>>>> the top or a row in the info box 'Topic pages:' or a paragraph in<BR>>>>> the section 'About this structure' reading e.g. 'This structure is<BR>>>>> also used in the pages ...'<BR>>>>><BR>>>>> Since it can't be relied on that authors do such backlinks, and <BR>>>>> this<
BR>>>>> can be automatized, it should be automatized at some time.<BR>>>><BR>>>> That's a really great idea if it can be done well. How would you <BR>>>> suggest<BR>>>> doing this (of course automatically)? Let's say you're on the <BR>>>> page for<BR>>>> 1ea5, do you want to list, on the page for 1ea5, all other pages <BR>>>> that link<BR>>>> to 1ea5? Or all other pages that link to 1ea5 but are not PDB- <BR>>>> entry pages?<BR>>>> I'm just worried that such an automatically generated list might, <BR>>>> in some<BR>>>> instances, be long and irrelevant. Of course as you've said, the <BR>>>> person who<BR>>>> created the Topic page should link from the topic page to the PDB <BR>>>> entry page<BR>>>> and vice versa, but they will sometimes neglect to do this.<BR>>>
><BR>>>>><BR>>>>><BR>>>>> On another note, I would like to see a list of all structure pages<BR>>>>> that have been enhanced by other authors than OCA. This should be<BR>>>>> automatized, too.<BR>>>><BR>>>> Eric, at one point you were interested in such a list -- what did <BR>>>> you do?<BR>>><BR>>> We do something similar over on PDBWiki using an extension known as <BR>>> DPL.<BR>>><BR>>> <A href="http://www.mediawiki.org/wiki/Extension:DynamicPageList">http://www.mediawiki.org/wiki/Extension:DynamicPageList</A><BR>><BR>> Thanks for that link. Indeed, it should be possible to implement<BR>> something approximating my ideas using DPL.<BR>><BR>> 1) What appears possible: having a link on each structure page<BR>> 'List topics where this structure is used in a scene'.<BR>> Pages are selected according to
the title matching a regexp AND<BR>> the content matching a regexp (titleregexp, includematch)<BR>> 2) What appears possible: a link somewhere that lists all structure<BR>> pages in a specific category (like Single protein) or all structure<BR>> pages in general (pages starting with digit) where the last<BR>> change was not done by OCA (notlastmodifiedby).<BR>><BR>> As this is more or less what I intended, and writing and running a bot<BR>> is so much more hassle, I'm all for installing DPL on the server.<BR>><BR>><BR>> ralf<BR>><BR>> _______________________________________________<BR>> Proteopedialist-for-users mailing list<BR>> Proteopedialist-for-users@bioinformatics.org<BR>> <A href="http://www.bioinformatics.org/mailman/listinfo/proteopedialist">http://www.bioinformatics.org/mailman/listinfo/proteopedialist</A>-for-users<BR><BR>Eran Hodis<BR>eran.hodis@weizmann.ac.il<BR><BR>
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