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

<p><a href="https://i.sstatic.net/cfCVA.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cfCVA.png" alt="ccp4MG screenshot"></a></p>

<p>(this is a Find dialog from ccp4MG)</p>

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

CC BY-SA 4.0
2020-04-29T00:48:43.763Z
Thank you, I need to understand the format in CIF so as to create my own CIF file
lanselibai
CC BY-SA 4.0
2020-04-29T07:54:38.877Z
@lanselibai do you want to create an mmCIF file in a text editor? why?
marcin
CC BY-SA 4.0
2020-04-30T02:54:49.957Z
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.
lanselibai
CC BY-SA 4.0
2020-04-30T09:53:54.207Z
@lanselibai to understand assemblies you may start with [Introduction to Biological Assemblies and the PDB Archive](https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies) at RCSB's PDB101.
marcin
CC BY-SA 4.0
2020-04-30T13:25:05.543Z
Sure, I will read it! Thank you!
lanselibai
CC BY-SA 4.0
2020-04-28T16:07:00.403Z
2020-04-28T16:07:00.403Z
marcin
<p>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.</p>

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

<p>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.</p>

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

<p><a href="https://i.sstatic.net/akVRW.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/akVRW.png" alt="enter image description here"></a></p>

CC BY-SA 4.0
2020-04-29T09:48:37.727Z
You could try opening the PDBXML version of the file in an XML viewer that lets you collapse sections.
jgreener
CC BY-SA 4.0
2020-04-30T03:09:45.777Z
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?
lanselibai
<pdb><text-processing>
Protein PDB/CIF text file reader that can fold a same section into one line
# Protein PDB/CIF text file reader that can fold a same section into one line

(Asked by: username_0 on 2020-04-28)

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](https://i.sstatic.net/akVRW.png)](https://i.sstatic.net/akVRW.png)

**Tags:** pdb, text-processing
> **Comments:**
> **username_1**: You could try opening the PDBXML version of the file in an XML viewer that lets you collapse sections.  
> **username_0**: 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?  

---

## 1 answers

### Answer by username_2 on 2020-04-28. Score: 1

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

[![ccp4MG screenshot](https://i.sstatic.net/cfCVA.png)](https://i.sstatic.net/cfCVA.png)

(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.

> **Comments:**
> **username_0**: Thank you, I need to understand the format in CIF so as to create my own CIF file  
> **username_2**: @lanselibai do you want to create an mmCIF file in a text editor? why?  
> **username_0**: 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.  
> **username_2**: @lanselibai to understand assemblies you may start with [Introduction to Biological Assemblies and the PDB Archive](https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies) at RCSB's PDB101.  
> **username_0**: Sure, I will read it! Thank you!  

---

