Org Prep Daily

September 21, 2006

My Struggle

Filed under: Uncategorized — milkshake @ 11:22 pm

WordPress, the software behind this blog (and also the company running the hosting service) is not very friendly to structures of organic molecules. It mangles them. I have been trying to fight the problem desperately, by importing high-pixel images – but this only bogged down this blog. So I would like to apologize to everybody who arrived here, just to see a bunch of closed icons. Reading Org Prep Daily must have been like swimming in cold porridge and I am sorry for the aggravation. 

I think I finally figured out a tolerable way of putting up the structures. (200-400% enlarged ChemDraw structures exported as gif-files). This alternative is more gentle to the Worpress servers, producing only 8-10k gif files per scheme. The resulting pictures are still bit fuzzy around the edges – and I have to put up structures in large size to avoid disappearing atoms and jagged bonds.

I will try to improve graphical quality of this blog. Meanwhile, you should be able to open a new window with picture-perfect structures when klicking on fuzzy mangled ones throughout the blogtext. 

Also, I compared Firefox with IE and Org Prep Daily does not seem to be much slower in Firefox now. Please, let me know about any further nuisance experienced here.  

Update: It looks like one can get a decent upload of Chemdraw structures if they were scaled in Chemdraw (Object-Scale) from the original ACS-document settings (0.20 in) to exactly 0.30in bond median. (“Scale selected object to 0.3in median bond”). The document is then saved as gif file. The gif file is uploaded to WordPress (as full size) and the size is set using the picture editor in WordPress compose menu to exactly match the gif original size. This technique works well also for the 0.40in bond median size but the produced reaction schemes are too big to properly display in the blog on 17-inch monitor and would not fit page on printout.   


  1. I can give you some room on our FTP, it’ll allow you to have higher quality images and its on a good size pipe. Just send over an e-mail and I’ll set one up for you.


    Comment by Mitch — September 22, 2006 @ 2:04 am

  2. Mitch: thank you for the offer, I will give WordPress some more chance, for the next few weeks. I think the graphics are OK now (if one can tolerate their gargantuan size), I just have to figure things out. Also, did you have any problems with accessing the Org Prep Daily tonight – after I put up the new gif-picture files in place of the previous big PNGs?

    Comment by milkshake — September 22, 2006 @ 2:13 am

  3. Yes, it is pretty amamzing how poorly Chemdraw mates with other programs (like say, WordPress or Powerpoint)- go Cambridgesoft!!

    Milkshake- well done, this is a slick concept for a blog. Are you interested in good preps submitted by readers? Obviously, that cuts down on the “totally hand-on” nature, but, a la Woodward, I think it is great to highlight research that works exactly as published.

    Comment by Jose — September 22, 2006 @ 10:54 am

  4. First, good to see you writing stuff… I like reading these.

    You know, I have had great luck with blogger. It is free. True, it does not play nice with wrod press, but the interface is really intuitive.

    Comment by Milo — September 22, 2006 @ 1:34 pm

  5. Milo, it is not real blogging what I do, it is more like a poster section here…

    Jose: I will put up procedures from people in the future. Here is what I wrote to HOMO-LUMO: Send me what you have – The procedures do not need to be original. The requirement is that the procedures are easy to do, reliable (you tried it couple times and it always worked), scalable, interesting and useful. Purification details, NMR spectra should be included. (Like a write-up to a contract lab: you would not want anybody to get stuck making the stuff for you.) OrgSyn is a good example.

    If you are working on a total synthesis project, the most suitable procedures would probably entail the reagents, the building blocks and the initial 2-3 steps that are necessarily run in multigram quantities, to push the material through. You should not publish anything that would put you and your project in jeopardy. Academic groups and companies alike are furious when scooped by competition (because details of work in progress were leaked). Use common sense.

    Comment by milkshake — September 22, 2006 @ 1:46 pm

  6. The size of the structures is a little odd at first, but not too bad. The only exception is the most recent posts – the right side of the equations are getting covered up by the navigation bar.

    Comment by Come back, zinc! — September 22, 2006 @ 11:02 pm

  7. Zinc: I have forgotten that my monitor is quite big. I tried to fix the drawing. Did the sidebar overlap problem go away, with the benzodioxole acid?

    Comment by milkshake — September 23, 2006 @ 4:59 pm

  8. Yeah, it looks much better now.

    Comment by Come back, zinc! — September 23, 2006 @ 7:58 pm

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