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>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1
