MichaelsSNoteBook/2008-3-12

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(New page: ===Wednesday, 03/12/08=== Yay, my own online lab notebook (second tryout ^^). After several tryouts to keep a notebook by (handwritten or typed), it turned out that I wasn`t able to mak...)
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# I've continued the stuff with the PSVS quality scores. It turned out (like expected) that our X-ray structures hat better Z-scores  ( (calibrated with Hi-res X-ray structures!!!) for PROCHECK (all dihedral) and Molprobity (only "ordered" residues for NMR case used) than the corresponding NMR members. It's a bit argueable whether that is a good metric, I should talk to Amy about that. I also should carefully read the discussion section of the paper to avoid missunderstandings or missapplications.  
# I've continued the stuff with the PSVS quality scores. It turned out (like expected) that our X-ray structures hat better Z-scores  ( (calibrated with Hi-res X-ray structures!!!) for PROCHECK (all dihedral) and Molprobity (only "ordered" residues for NMR case used) than the corresponding NMR members. It's a bit argueable whether that is a good metric, I should talk to Amy about that. I also should carefully read the discussion section of the paper to avoid missunderstandings or missapplications.  
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# Fixed the 1KF5_2AAS. Turned out that the X-ray structure had lots of alternative residues and something weird (ANISOU ?! what is that actually?!) too. Something made them act weird, but after checking that again it should work now. I should survey for this anormalities in pdb structures (maybe script?). However, the computations are running.  
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## Fixed the 1KF5_2AAS. Turned out that the X-ray structure had lots of alternative residues and something weird (ANISOU ?! what is that actually?!) too. Something made them act weird, but after checking that again it should work now. I should survey for this anormalities in pdb structures (maybe script?). However, the computations are running.  
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# I double checked all structures for anormalities. It looks like, that at least the nomin and E2_100 backbones are complete and the same, so the input structures work propertly. I'am looking carefully for bugs in the code, but so far I couldn't detect any. It's questionable, whether looking for bugs is useful (maybe no bugs exist anymore...). Anyways, I SHOULD BE AWARE OF ARTIFACTS, maybe "carefully" DOUBLECHECK ALL "EXCEPTIONS" IN DATA.  
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### I double checked all structures for anormalities. It looks like, that at least the nomin and E2_100 backbones are complete and the same, so the input structures work propertly. I'am looking carefully for bugs in the code, but so far I couldn't detect any. It's questionable, whether looking for bugs is useful (maybe no bugs exist anymore...). Anyways, I SHOULD BE AWARE OF ARTIFACTS, maybe "carefully" DOUBLECHECK ALL "EXCEPTIONS" IN DATA.  
-===Things to do===-
-===Things to do===-

Revision as of 18:47, 12 March 2008

Wednesday, 03/12/08

Yay, my own online lab notebook (second tryout ^^).

After several tryouts to keep a notebook by (handwritten or typed), it turned out that I wasn`t able to make something that I keep up updating most of the time ^^. Sooo this is my new notebook, which I'am (hopefully) keep up to date from now.

Things that I did today:

  1. I've continued the stuff with the PSVS quality scores. It turned out (like expected) that our X-ray structures hat better Z-scores ( (calibrated with Hi-res X-ray structures!!!) for PROCHECK (all dihedral) and Molprobity (only "ordered" residues for NMR case used) than the corresponding NMR members. It's a bit argueable whether that is a good metric, I should talk to Amy about that. I also should carefully read the discussion section of the paper to avoid missunderstandings or missapplications.
    1. Fixed the 1KF5_2AAS. Turned out that the X-ray structure had lots of alternative residues and something weird (ANISOU ?! what is that actually?!) too. Something made them act weird, but after checking that again it should work now. I should survey for this anormalities in pdb structures (maybe script?). However, the computations are running.
      1. I double checked all structures for anormalities. It looks like, that at least the nomin and E2_100 backbones are complete and the same, so the input structures work propertly. I'am looking carefully for bugs in the code, but so far I couldn't detect any. It's questionable, whether looking for bugs is useful (maybe no bugs exist anymore...). Anyways, I SHOULD BE AWARE OF ARTIFACTS, maybe "carefully" DOUBLECHECK ALL "EXCEPTIONS" IN DATA.

-===Things to do===-

  1. Data collection. Since my calculations are done, I can again gather ALL results and plott them and summarize. Once that is done, I can look at them for analyzation. Maybe I should formulate some questions, for what I'am acually looking for ...
  1. Move to Xiaorans desk. Finally out of the hallway *yay*
  1. Write essays for Hölderlin and Medizintechnik
  1. Start writing paper ^^. A little bid more than just methods ...
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