<div dir="ltr"><div dir="ltr"><div>I am sorry, but the above links did not help me.</div>Yes they are together in one model. But if suppose a receptor has NAD in it , it shows in the residue region. But after docking the ligand name becomes the same as the receptor. So it is difficult for me to show which ligand I have used to dock.<div><br></div><div>I have attached an example pdb file.</div><div>Here both the ligand and receptor are in chain A and have the same name : dock.pdb</div><div>and under "residue" my docked ligand is not coming. How to save a pdb file (docked file) which considers the receptor and ligand separately in the same PDB, like for example in the 3U31 file which I have attached (PDB file downloaded from PDB) has NAD, gol, etc under residues. and when I am using another software to check the interaction, it is showing the interactions with all the residues. But this "dock" PDB file which I made (after docking) there is difficult to understand the interaction as it is showing no ligand bound, since both of them are saved under the same name.<br><br><br><br><div id="mt-signature">
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<span style="color:transparent;font-size:0">08/07/20, 09:56:05 PM</span>
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</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 7, 2020 at 9:48 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Shinjini,<br>
It is unclear what name you are talking about. There is a "model name", maybe the ligand and receptor are together in one model. There is a "file name" of the saved PDB file. There are "residue names," many different amino acids in the receptor, each one with its own name, and probably the ligand also has another different residue name. Each atom also has an "atom name."<br>
<br>
If you want separate files, just select the atoms you want in one file, use menu: File ... Save PDB and choose the option to "save selected atoms only". Then select the atoms you want in the other file, and use the same process to save another PDB file. You can name each file whatever you want.<br>
<br>
Selecting atoms:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html</a>><br>
<br>
Saving PDB files:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb</a>><br>
<br>
If you want to change residue names or atom names, maybe you just want to text-edit the PDB file directly (not using Chimera). Here is some explanation of PDB file format so you can understand how to edit the text.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Aug 7, 2020, at 7:37 AM, Shinjini Ghosh <<a href="mailto:shinjinighosh2014@gmail.com" target="_blank">shinjinighosh2014@gmail.com</a>> wrote:<br>
> <br>
> For analysis, I want to have a PDB file of let's say with the first docked ligand in chimera which I did with autodock vina. I was able to save and open it in chimera. But the receptor and the ligand are both having the same name which I am using to save my PDB file. How can I change the names of receptor and ligand in the PDB file so that it is considered as different molecules in that particular PDB file. I want to give two different names to the receptor and the ligand in that particluar PDB file. This I need for my project.<br>
> Please help me with this.<br>
> Thank you.<br>
<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr">Shinjini Ghosh.<div>Student of Master of Science,</div><div>Biophysics and Molecular Biology'<br><div>Rajabazar Science College,</div><div>University of Calcutta.</div></div></div></div><img width="0" height="0" class="mailtrack-img" alt="" style="display:flex" src="https://mailtrack.io/trace/mail/b384a851ccd868279cf88e25de8dd35e19fe7efe.png?u=4751225"></div><div id="DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2"><br>
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