0
$\begingroup$

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

$\endgroup$
2
  • $\begingroup$ You could try opening the PDBXML version of the file in an XML viewer that lets you collapse sections. $\endgroup$
    – jgreener
    Apr 29, 2020 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, 2020 at 3:09

1 Answer 1

1
$\begingroup$

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.

$\endgroup$
5
  • $\begingroup$ Thank you, I need to understand the format in CIF so as to create my own CIF file $\endgroup$
    – lanselibai
    Apr 29, 2020 at 0:48
  • 2
    $\begingroup$ @lanselibai do you want to create an mmCIF file in a text editor? why? $\endgroup$
    – marcin
    Apr 29, 2020 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, 2020 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, 2020 at 9:53
  • $\begingroup$ Sure, I will read it! Thank you! $\endgroup$
    – lanselibai
    Apr 30, 2020 at 13:25

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.