<p>in PyMol use, from menu :</p>
<p><strong>File</strong> ---&gt; <strong>Export Molecule...</strong> ---&gt; and before hitting Save</p>
<p>select the molecules you want to save toghether (in the same .pdb file)</p>
<p>with the <strong>Selection</strong> drop down list either <strong>all</strong> (all the loaded mols are saved) or <strong>enabled</strong> (you can enable the ones you want to be saved toghether)</p>
<p>Examples of Save menu :</p>
<p><a href="https://i.sstatic.net/HzXndsOy.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/HzXndsOy.png" alt="enter image description here" /></a></p>
<p><a href="https://i.sstatic.net/1KGNaeg3.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/1KGNaeg3.png" alt="enter image description here" /></a></p>
<p>For command line see <a href="https://sourceforge.net/p/pymol/mailman/pymol-users/thread/6344E6FB-5129-4053-9654-EBBDD5A41B1D%40systemsbiology.org/#msg20094707" rel="nofollow noreferrer">Thread: [PyMOL] independent positioning of two proteins, in preparation for RosettaDock? </a></p>

CC BY-SA 4.0
2024-12-12T17:56:09.043Z
Thank you. This can save the 4 structures in one PDB file, but I wanted to first connect them together, to assemble the final structure, then save into one PDB file. Alignment is not the way to do it, as far as I understand. Is it possible in PyMol or other softwares?
Alpha
CC BY-SA 4.0
2024-12-12T18:14:28.603Z
what do you mean by "Is it possible to connect and merge 4 different PDB files together," please clarify and produce an example of actual input and desidered output – 
pippo1980
pippo1980
CC BY-SA 4.0
2024-12-11T19:47:44.517Z
2024-12-11T19:58:23.353Z
2024-12-11T19:58:23.353Z
pippo1980
<p>I have an optimized design for the corn RNA aptamer, <a href="https://files.rcsb.org/view/5BJO.pdb" rel="nofollow noreferrer">PDB: 5BJO</a>. I generated the 3D structures for the parts that I plan to add on trRosettaRNA. I want to connect them with the 5BJO PDB fiIe in PyMol, then perform Molecular dynamics. Is this possible?</p>
<p>This is the final design that I am trying to get. I have the 3D structure for each part separately. I was looking for a way to connect them together to build this model. Is it possible to assemble them in PyMol or other softwares? Thank you.</p>
<p><a href="https://i.sstatic.net/yjUNmM0w.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/yjUNmM0w.png" alt="enter image description here" /></a></p>

CC BY-SA 4.0
2024-12-12T18:13:59.870Z
what do you mean by "Is it possible to connect and merge 4 different PDB files together," please clarify and produce an example of actual input and desidered output
pippo1980
CC BY-SA 4.0
2024-12-12T20:07:04.090Z
@alpha do consider signing pippo1980's answer as accepted. Its good to do this all round.
M__
CC BY-SA 4.0
2024-12-13T04:44:01.163Z
@pippo1980 
Thank you, I updated the description.
Alpha
CC BY-SA 4.0
2024-12-13T13:56:08.353Z
I see. Think you'll have to add manually the CONECT record between protein chains and RNA polymer. See [Creating "stable" bond with PYMOL](https://stackoverflow.com/questions/25905660/creating-stable-bond-with-pymol) and the PDB file for [1ZR2:
Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently Linked to two Cleaved DNAs](https://files.rcsb.org/view/1ZR2.pdb)
pippo1980
CC BY-SA 4.0
2024-12-13T14:06:50.550Z
about pymol, when saving ALL (or ENABLED) objects in a .pdb file toghether it does keep atom numbering and remember that other Ligands (HETATM) are saved next to the chain they belong to
pippo1980
CC BY-SA 4.0
2024-12-13T14:34:28.253Z
[Pdb use ter records](https://pymolwiki.org/index.php/Pdb_use_ter_records)  this is something new to me too, try to use it before saving if you wish to create single chains out of multiple
pippo1980
CC BY-SA 4.0
2024-12-13T14:58:44.327Z
@alpha do consider signing pippo1980's answer as accepted. Its good to do this all round and its a comprehensive answer including the points in the discussion.
M__
<pymol><rna-structure><molecular-dynamics><chimera>
Connecting and merging multiple RNA 3D structures in PyMol/Chimera
# Connecting and merging multiple RNA 3D structures in PyMol/Chimera

(Asked by: username_0 on 2024-12-11)

I have an optimized design for the corn RNA aptamer, [PDB: 5BJO](https://files.rcsb.org/view/5BJO.pdb). I generated the 3D structures for the parts that I plan to add on trRosettaRNA. I want to connect them with the 5BJO PDB fiIe in PyMol, then perform Molecular dynamics. Is this possible?

This is the final design that I am trying to get. I have the 3D structure for each part separately. I was looking for a way to connect them together to build this model. Is it possible to assemble them in PyMol or other softwares? Thank you.

[![enter image description here](https://i.sstatic.net/yjUNmM0w.png)](https://i.sstatic.net/yjUNmM0w.png)

**Tags:** pymol, rna-structure, molecular-dynamics, chimera
> **Comments:**
> **username_1**: what do you mean by "Is it possible to connect and merge 4 different PDB files together," please clarify and produce an example of actual input and desidered output  
> **username_2**: @alpha do consider signing pippo1980's answer as accepted. Its good to do this all round.  
> **username_0**: @pippo1980  Thank you, I updated the description.  
> **username_1**: I see. Think you'll have to add manually the CONECT record between protein chains and RNA polymer. See [Creating "stable" bond with PYMOL](https://stackoverflow.com/questions/25905660/creating-stable-bond-with-pymol) and the PDB file for [1ZR2: Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently Linked to two Cleaved DNAs](https://files.rcsb.org/view/1ZR2.pdb)  
> **username_1**: about pymol, when saving ALL (or ENABLED) objects in a .pdb file toghether it does keep atom numbering and remember that other Ligands (HETATM) are saved next to the chain they belong to  
> **username_1**: [Pdb use ter records](https://pymolwiki.org/index.php/Pdb_use_ter_records)  this is something new to me too, try to use it before saving if you wish to create single chains out of multiple  
> **username_2**: @alpha do consider signing pippo1980's answer as accepted. Its good to do this all round and its a comprehensive answer including the points in the discussion.  

---

## 1 answers

### Answer by username_1 on 2024-12-11. Score: 1 | Accepted answer

in PyMol use, from menu :

**File** ---> **Export Molecule...** ---> and before hitting Save

select the molecules you want to save toghether (in the same .pdb file)

with the **Selection** drop down list either **all** (all the loaded mols are saved) or **enabled** (you can enable the ones you want to be saved toghether)

Examples of Save menu :

[![enter image description here](https://i.sstatic.net/HzXndsOy.png)](https://i.sstatic.net/HzXndsOy.png)

[![enter image description here](https://i.sstatic.net/1KGNaeg3.png)](https://i.sstatic.net/1KGNaeg3.png)

For command line see [Thread: [PyMOL] independent positioning of two proteins, in preparation for RosettaDock?](https://sourceforge.net/p/pymol/mailman/pymol-users/thread/6344E6FB-5129-4053-9654-EBBDD5A41B1D%40systemsbiology.org/#msg20094707)

> **Comments:**
> **username_0**: Thank you. This can save the 4 structures in one PDB file, but I wanted to first connect them together, to assemble the final structure, then save into one PDB file. Alignment is not the way to do it, as far as I understand. Is it possible in PyMol or other softwares?  
> **username_1**: what do you mean by "Is it possible to connect and merge 4 different PDB files together," please clarify and produce an example of actual input and desidered output –  pippo1980  

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