<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
Elaine<br>
<br>
Ran into a problem.<br>
<br>
I need to combine a Ligand and a Protein n in order to use LigPlot+
to characterize the bound ligand in the active site of the protein.
Both pdb files are attached.<br>
<br>
Following the steps in the URL you referenced:<br>
<br>
Open Chimera<br>
Open Ligand<br>
Open Protein<br>
Open favorites --> Model Pane<br>
��� at this point the only active choice is 'activate all'<br>
Click on Ligand<br>
��� copy/combine is now active<br>
Right click Protein <br>
Copy/Combine<br>
��� 2 combination is now aticve<br>
Save 2.pdb<br>
<br>
Edit 2.pdb to conform with LigPlus+ pdb file format (2edited.pdb)<br>
<br>
Open 2.pdb in� LigPlot+<br>
<img alt="" src="cid:part1.09030803.05010501@sbcglobal.net"
height="598" width="802"><br>
Oops - and other not printable comments. Not exactly the expected
result.� Just what is the problem?<br>
<br>
HETATM�� 25� H� UNLD���� 1���� -25.457� -6.079 183.671� 0.00�
0.00���������� H<br>
MDL<br>
ATOM����� 1� N�� SER A� 13���� -59.051� 40.339 226.398� 0.00�
0.00����� AS1� N<br>
�������������������������������
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ �� <br>
Misaligned fields! (Unfortunately, I didn't know this was the
problem., but the author of LigPlot+ did)<br>
<br>
What did I do/fail to do in Chimera?<br>
<br>
Thanks in advance.<br>
<br>
��� ��� Steve<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 04/24/2021 06:41 PM, Elaine Meng
wrote:<br>
</div>
<blockquote
cite="mid:65154B98-0607-4DDA-B13A-F0C0D159ED7C@cgl.ucsf.edu"
type="cite">
<pre wrap="">Hi Stephen,
Probably you just need to combine the ligand and receptor into a single model before saving to a PDB file, instead of saving the two models to a single multimodel PDB file. This is usually the problem when you want to use some other program afterward for ligand-receptor analysis, and I see that your file has two models in it instead of a single model with both receptor and ligand.
For example, see instructions in this recent post on how to combine the models before saving:
<a class="moz-txt-link-rfc2396E" href="https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-March/017672.html"><https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-March/017672.html></a>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
</pre>
<blockquote type="cite">
<pre wrap="">On Apr 24, 2021, at 5:42 AM, Stephen P. Molnar <a class="moz-txt-link-rfc2396E" href="mailto:s.molnar@sbcglobal.net"><s.molnar@sbcglobal.net></a> wrote:
I am using Chimera v-1.14 (build 42094) on my Debian Buster Linux computer and have run into a problem saving a pdb file containing two pdb files.
The files are attached to this email.This is a portion of the combined flies:
<Screenshot_2021-04-24_08-29-16.png>
The structure of the D21.pdb file isthe ball image.
I followed the instructions in the Building Structures, Modifying and Saving Data in the Help pages.
However, when I open DD21Mod1 in LigPlot to identify the docked ligand I get:
<Screenshot_2021-04-24_08-30-37.png>
Clearly, this is not the ligand docked int the active site. I have used LigPlot on a number of pdb files with good results and am forced to conclude that there is a problem with D21Mod1.pdb.
I would appreciate help in solving this problem.
Thanks in advance.
--
Stephen P. Molnar, Ph.D.
<a class="moz-txt-link-abbreviated" href="http://www.molecular-modeling.net">www.molecular-modeling.net</a>
614.312.7528 (c)
Skype: smolnar1
<D21.pdb><D21Mod1.pdb><Mod1.pdb>_______________________________________________
Chimera-users mailing list: <a class="moz-txt-link-abbreviated" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a>
Manage subscription: <a class="moz-txt-link-freetext" href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Stephen P. Molnar, Ph.D.
<a class="moz-txt-link-abbreviated" href="http://www.molecular-modeling.net">www.molecular-modeling.net</a>
614.312.7528 (c)
Skype: smolnar1
</pre>
</body>
</html>