Elaine

Ran into a problem.

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.

Following the steps in the URL you referenced:

Open Chimera
Open Ligand
Open Protein
Open favorites --> Model Pane
��� at this point the only active choice is 'activate all'
Click on Ligand
��� copy/combine is now active
Right click Protein
Copy/Combine
��� 2 combination is now aticve
Save 2.pdb

Edit 2.pdb to conform with LigPlus+ pdb file format (2edited.pdb)

Open 2.pdb in� LigPlot+

Oops - and other not printable comments. Not exactly the expected result.� Just what is the problem?

HETATM�� 25� H� UNLD���� 1���� -25.457� -6.079 183.671� 0.00� 0.00���������� H
MDL
ATOM����� 1� N�� SER A� 13���� -59.051� 40.339 226.398� 0.00� 0.00����� AS1� N
������������������������������� ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ��
Misaligned fields! (Unfortunately, I didn't know this was the problem., but the author of LigPlot+ did)

What did I do/fail to do in Chimera?

Thanks in advance.

��� ��� Steve



On 04/24/2021 06:41 PM, Elaine Meng wrote:
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:
<https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-March/017672.html>

I hope this helps,
Elaine 
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Apr 24, 2021, at 5:42 AM, Stephen P. Molnar <s.molnar@sbcglobal.net> 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.

www.molecular-modeling.net

614.312.7528 (c)
Skype:  smolnar1


<D21.pdb><D21Mod1.pdb><Mod1.pdb>_______________________________________________
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-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1