View PDB file in Pymol (old forum post comments not available)

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hezhaobin
Posts: 3
Joined: Fri May 14, 2021 8:52 pm

View PDB file in Pymol (old forum post comments not available)

Post by hezhaobin »

I'm pretty new to structural biology and encountered a couple of related issues that seem to all have to do with secondary structure information not included in the model pdb files. From the FAQ page, I found the old forum post but it seems like the comments associated with old posts are not viewable anymore (like here: https://zhanglab.ccmb.med.umich.edu/bbs/?q=node/4096). I wonder if it's just me or something related to the forum.

Here are my several questions/issues, which I believe are all related:
  1. the Index.html file viewed from the I-TASSER website has the Jmol app loaded and thus the results are easily viewable. But after I download and extract the tar ball, and open the index.html file from my computer, the apps are not loaded. I guess this is by design?
  2. the static gif files are zero kb in the downloaded tar ball.
  3. As commented by several users on the old forum, the model viewed in Pymol with the pdb file in the tar ball looks different from the one rendered by jmol on the website. Specifically, several beta-sheets are missing.
Any suggestions would be greatly appreciated!
robpearc
Posts: 40
Joined: Sun May 02, 2021 5:49 pm

Re: View PDB file in Pymol (old forum post comments not available)

Post by robpearc »

Hello,

Yes, unfortunately we experienced a hardware failure, which made our old forum unrecoverable. However, we have moved to our new forum.

1. Yes, this depends on how you are trying to view the html file, which would require that you have the appropriate apps installed in the correct location as coded in the html file.

2. If the static gif files are zero kb, there may have been an error in generating the files. Are the model1-5.pdb files also 0 kb, as the gif files are created from these?

3. The secondary structures displayed by different programs will look different. In general, Pymol is stricter than other programs, and assigns less helical/sheet residues. You may refer to https://pymolwiki.org/index.php/Dss on how to alter the secondary structure assignment.
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