User talk:Eran Hodis

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News from Greece

Hi Eran, actually I was on vacation after the summer school of Erice! The last days I'm back in the lab and try to find the rythm of the experiments ;) I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc. We'll be in contact..you'll see the progress of my page!

best wishes Maria


Hi Eran, Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep. best regards Trevor

Hi Eran. How are you? I'm Maria Ambrazi..do you remember from Erice? Can you send me your e-mail...I would like to ask you something on proteopedia!

Bad green link

Eran, I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?

Karl

After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.

Karl


PDBsum site

Eran, After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.

By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.

Karl

Eran, I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.

Karl

Proteopedia for teaching

Hi Eran

I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:

1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)

2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.

cheers!

Shaun

What to do with my students contributions

Hi Eran,

I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?

Tom

Surfaces

Hi Eran,

I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.

Tom

more on surfaces

Hi

Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.
my best
Tom
PS. So, what is the Israeli greetings/salutation during Hannukah?

Cheers Eran!

Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific.


BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --Dan Bolser 10:58, 5 January 2009 (IST)

RE:

Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST)

With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --Dan Bolser 15:24, 5 January 2009 (IST)
After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --Dan Bolser 16:00, 5 January 2009 (IST)

RE: Models

Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!

-Mark

Moving scenes from one page to another

Hi Eran,

I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <scene>...<scene/> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.

Tom

Other Media in Proteopedia?

Hi Eran,

I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the <img src="www.filename.jpg"> code you can use for linking to images)?

-Mark

tilman

Eran, you are right. That page Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10 is obsolete. I've saved the content to the proper Sandbox_10.

You can delete it. Thanks, Tilman

References

Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.

-Mark

good enough?

Would you say, this is good enough to replace 2a7g? What more does it need for a page 'Thermolysin'? --Ralf Stephan 16:57, 7 February 2009 (IST)

It's certainly enough to replace 2a7g, and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making "metalloprotease" as a interwiki link. We have a not-so-well developed page on Matrix_metalloproteinases, but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says "calcium atoms (yellow)" but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools.
A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new 2a7g page as well as elaborate more -- especially if there are other structures. --Eran Hodis 02:34, 8 February 2009 (IST)
  • There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).
Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.
  • So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?
That's the current mode of thinking. Of course better ideas will be adopted.
  • Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.
Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be.
  • /Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.
Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.
  • Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too.
Ok good.
Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --Ralf Stephan 10:16, 8 February 2009 (IST)
Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --Eran Hodis 12:27, 8 February 2009 (IST)

java.io.File not found

Do you understand why the applet can't find the PDB file in Helix-turn-helix motif? --Ralf Stephan 17:57, 8 February 2009 (IST)

Never mind, I found it out myself: I forgot to provide a scene. --Ralf Stephan 18:14, 8 February 2009 (IST)

Image Issue

Hi Eran, I got your message and will take care of it. I think modified images were okay. Thanks! Leah

ditto leah. thanks! becca

Scrambled Eggs

Any chance you are referring to egg cells and fertilization ? :)

Applet Behavior

Eran, the applets in Z-DNA page seem to be behaving erratically. At times there is no display and at times they are not in the frame. There is also a problem with the sugar puckering option in DNA page. The applet freezes when this is selected. Could you please verify if you are facing the same problems?

Adithya Sagar 21:06, 22 October 2009 (IST)

Image license

Originally from {Molecular cell biology. Lodish, Harvey 5 ed: - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3. Libris: 8926100.}

Original uploader was Roadnottaken at en.wikipedia 2007-03-22

The image was found from Wikipedia and was a modified image that is a "GNU Free Documentation License" I changed the properties of my image file and it should give the proper acknowledgments.

-Matt

Restriction endonucleases complexes with DNA - PspGI (3bm3) case

Hi, Eran!

It is nice to see such quick assistance with tech bug. It is pity I found proteopedia after we published article on two protein-DNA structures. I will try in my Ph.D. thesis to visualise review of REase-DNA complexes with proteopedia.

greatings from Vilne, Dima

Now I see it was not bug but database case.

molscript2Jmol

Hi,

Is it possible simple coversion or implementation of molscript input and/or .mols files to Jmol script?

Request for categories adding

Could I add in "Categories" chapter my own specific markups? For example, I would like to classify restriction endonucleases complexes with DNA in respect of what native methyltranferases are: 6-methyl adenine, 5- or 4- methyl cytosine?

Dima

Thanks

Eran-

Wow, I randomly checked in on Proteopedia today after being away for a while and saw your message. That's great that you were able to make a un-do button. It will be a good tool, especially for those who are new to Proteopedia and experimenting with how things work.

PS. I just tried it out and I'm excited there's also a re-do button. It's even better than I expected.

Emily Forschler 22:48, 18 March 2010 (IST)

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