[Chimera-users] Problem Saava9ng merged PDB Files

[Stephen P. Molnar]

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 at 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 at 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210430/d093cb8a/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot_2021-04-30_08-15-13.png
Type: image/png
Size: 17826 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210430/d093cb8a/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Ligand.pdb
Type: application/vnd.palm
Size: 2058 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210430/d093cb8a/attachment-0003.pdb>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Protein.pdb
Type: application/vnd.palm
Size: 4771428 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210430/d093cb8a/attachment-0004.pdb>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 2edited.pdb
Type: application/vnd.palm
Size: 4634194 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210430/d093cb8a/attachment-0005.pdb>