User talk:Ralf Stephan

From Proteopedia

Welcome to Proteopedia! We hope you will contribute much and well. You will probably want to watch the narrated video guide and use the help pages for later reference. Again, welcome and have fun! Eran Hodis 14:14, 6 February 2009 (IST)

Morphs

Hi Ralf,

Eventually you might want to consider adding morphs to give the idea of the conformational changes in the transport proteins between their open and closed states. An example can be found on the Proton Channels page that Eric Martz created. The morph itself does not represent the actual motion between the two states -- open and closed -- but rather is a linear interpolation (in most morphs) between the starting structure and the ending structure.

Best, Eran Hodis 18:37, 6 February 2009 (IST)

Yes, actually, I chose my first protein after I had a good look at the Yale gallery what they had. I'm aware of the scarcity of structures. Thanks. --Ralf Stephan 18:41, 6 February 2009 (IST)

Reponse

Hi Ralf, I responded on my user talk page. Best, --Eran Hodis 02:35, 8 February 2009 (IST)

Wikipedia link to Metalloproteases

In regards to a Wikipedia link to the page on metalloproteases, please see Proteopedia:Policy#Links_to_Wikipedia. You're welcome to help shape this policy, but our current thinking is that if the link is to a page that could benefit from 3D images, then we should link to the page in Proteopedia (even if it doesn't exist, to encourage creation), and that page can then link to Wikipedia. --Eran Hodis 12:34, 8 February 2009 (IST)

No, you're right, the german language entry is much better. I'll translate it for Proteopedia. --Ralf Stephan 12:36, 8 February 2009 (IST)

Gzipped PDBS

You should now be able to upload gzipped PDBs --Eran Hodis 19:08, 17 February 2009 (IST)

Great, many thanks! --Ralf Stephan 20:55, 17 February 2009 (IST)

Internal links in Applet captions

Hi Ralf, Fixed this problem. Thanks for pointing out bugs that are simple to fix! --Eran Hodis 19:20, 18 February 2009 (IST)

Thanks for fixing, anyway! --Ralf Stephan 20:03, 18 February 2009 (IST)

odd changes in scenes

Regarding this problem you brought up:

problems with scenes changing unexpectedly appear in the first applet on the aconitase (older version) page. There are 3 green links, and if you click 1,2,1,2,1... the two scenes will stay as they show the first time clicked, but as soon as you click 3, 2 will appear different (the three yellow amino side chains around the cluster lack several atoms/bonds then). I have a problem with 3, too, as it doesn't show as it was saved, but this is more elusive at the moment. --Ralf Stephan 18:37, 21 February 2009 (IST)

I confirm that I see the problem too. Are you using the SAT to create your scenes or do you right click on the Jmol, open up the console and type commands into Jmol by hand? --Eran Hodis 00:42, 7 March 2009 (IST)

Scene 3 was built using the console. Is it not recommended? Not everything is possible with SAT. --Ralf Stephan 10:09, 7 March 2009 (IST)

You should be able to build your scenes using any method you wish (SAT or console). I just wanted to know because it would give me a hint as to the type of problem we're facing. Thanks --Eran Hodis 13:20, 7 March 2009 (IST)

References/Applet bug

The references/applet bug should now be fixed. Let us know if you notice any side-effects to the fix. Thanks for reporting it. --Eran Hodis 18:59, 7 March 2009 (IST)