Is there a software that can recognise the protein PDB/CIF files, and fold multiple lines of a same section into one line, so that it is easier to handle? I need to understand the format in CIF so as to create my own CIF file.

For example, when Notepad++ is used to read a .py file, it can fold the same section into one line.

So for a PDB/CIF file, e.g. all the atom lines for a same chain can be folded into one line, and I can expand it if needed.

Like this picture, assuming "This PC" is the whole protein, while the other objects are the different chains.

enter image description here

  • $\begingroup$ You could try opening the PDBXML version of the file in an XML viewer that lets you collapse sections. $\endgroup$
    – jgreener
    Apr 29 '20 at 9:48
  • $\begingroup$ Thank you, the PDBXML file is 10 times the size of a CIF file. The 5TX1 has 100 MB. Can you recommend a software that is good for PDBXML? $\endgroup$
    – lanselibai
    Apr 30 '20 at 3:09

Programs that work with PDB and mmCIF files may present the structure as a tree, for example:

ccp4MG screenshot

(this is a Find dialog from ccp4MG)

but I'd be surprised if a text editor had such a feature. Normally, you don't edit PDB files in a text editor.

  • $\begingroup$ Thank you, I need to understand the format in CIF so as to create my own CIF file $\endgroup$
    – lanselibai
    Apr 29 '20 at 0:48
  • 2
    $\begingroup$ @lanselibai do you want to create an mmCIF file in a text editor? why? $\endgroup$
    – marcin
    Apr 29 '20 at 7:54
  • $\begingroup$ I am trying to do homology modelling for a virus capsid based on an existing CIF (5TX1, as the template) in the PDB database. The CIF template contains the assembly information, which I want to understand. But the CIF file is too long, which is very easy to get lost. $\endgroup$
    – lanselibai
    Apr 30 '20 at 2:54
  • $\begingroup$ @lanselibai to understand assemblies you may start with Introduction to Biological Assemblies and the PDB Archive at RCSB's PDB101. $\endgroup$
    – marcin
    Apr 30 '20 at 9:53
  • $\begingroup$ Sure, I will read it! Thank you! $\endgroup$
    – lanselibai
    Apr 30 '20 at 13:25

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