[Chimera-users] Problem Saava9ng merged PDB Files

[Elaine Meng]

HI Stephen,
I do not use LigPlot+ but as far as I know Chimera writes correct PDB format no matter which steps you use.

Your message (see below) has lots of unreadable characters and is nearly impossible to decipher.  Also whenever you have a problem with a specific file it is not useful to merely describe it in e-mail.  Instead you should attach the file to the message so we can actually take a look at it.  (Or, for future reference, if you believe it's a bug, don't send e-mail here but instead use menu: Help... Report a Bug, fill out the form, and attach any file needed to reproduce the problem to the bug report form.)

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

> On Apr 30, 2021, at 5:22 AM, Stephen P. Molnar <s.molnar at sbcglobal.net> wrote:
> 
> 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+
> <Screenshot_2021-04-30_08-15-13.png>
> 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
> 
> 
> <Ligand.pdb><Protein.pdb><2edited.pdb>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users