On Jul 14, 2024, at 9:47 PM, CHUNG, WH Kelvin [ABCT] via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine,

Greatly appreciate for your support, and sorry for posting my question in a wrong place, I was talking about ChimeraX.
I successfully made the "pre-model" (attached as KP-piperacillin no H.pdb ) by following your suggestion.

I saved the file as  .pdb and tried the minimization in Chimera. However, after clicking "Tools-->structure editing-->minimize structure--> minimize" in Chimera (version 1.18, 2024-06-27), and using al the default parameter, an error message " Residue #0:307.B (SER/serine) is missing atom H_gamma" appeared at the last step.
Indeed, the oxygen atom at ser 307 is the position that I make bond with the ligand (piperacillin), and thus there should be no gamma hydrogen.

Shall I edit the pdb file before the minimization ?

Thank you very much

Kelvin

-----Original Message-----
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Saturday, July 13, 2024 4:48 AM
To: Tom Goddard <goddard@sonic.net>; CHUNG, WH Kelvin [ABCT] <wh-kelvin.chung@polyu.edu.hk>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] [chimerax-users] Covalent substrate modeling and minimization

CAUTION: External email. Do not click links or open attachments unless you recognize the sender and know the content is safe.




Doh!  Apologies for the confusing reply, due to my mistake of entering PDB IDs that started with 1 instead of 4.

Elaine

On Jul 12, 2024, at 1:31 PM, Tom Goddard via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Kelvin,

 Sometimes the PDB model of an X-ray structure lies outside the
crystal unit cell map provide by the EDS and that is what you see with
4kqo.  To get the map to cover the atomic model by using crystall
symmetry use ChimeraX command volume cover

     open 4kqo
     open 4kqo from eds
     volume cover #2 atomBox #1

That creates map #3 that covers the atomic model.  Then it is useful
to hide the density except near the piperacillin ligand (residue JPP)
in chain A using

     volume zone # 3 near /A:JPP

Then I lower the threshold of the map

     volume #3 level 0.09

To get a better view of the density near the ligand you can also hide
the atomic structure except near the ligand by first selecting the
part near the ligand (within 8 Angstroms)

     sel /A:JPP :< 8

then hiding the part not selected

     hide ~sel atoms,ribbon

 There are ways to do these things with toolbar buttons and menus but it is easier for me to tell you the commands.

     Tom

<4kqo_JPP.png>

On Jul 12, 2024, at 9:33 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Kelvin,
First make sure of which program you are using.  You sent this to the chimera-users mailing list which is for the program Chimera.  However, the commands that you mention are for ChimeraX, so you must really be using chimeraX instead.  In the future, please use chimerax-users@cgl.ucsf.edu for ChimeraX questions (CC'd here).  I included both since the answer may involve both.

Everything below is for ChimeraX unless stated otherwise:

(1) Is this substrate included in the experimental structure?  If the experiment was not done with the substrate bound, there is no reason to expect the density map to include density for it.  4kqo does not have a density map in EDS, so I guess you meant 4kq0.  4kq0 has plenty of density near the ligand residue MED, if that's what you meant by "substrate."  You just need to use the slider in the Volume Viewer to change the isosurface level of the density ("volume" command below "level" option, but for interactive use, it is easier to use the slider in the GUI).  To make it easier to view you can also limit the density to a zone near that ligand with the command "volume zone"

open 1kq0
open 1kq0 from eds
view ligand
volume #2 level 0.01339
volume zone #2 near :MED

The isosurface level in the example above is lower than what is shown initially when you open the map.  However, I have no opinion as to what value exactly you should use.   See help for "volume" and "Volume Viewer"

<https://rb/
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<https://rb/
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(2) if you use "Join Models" section of "Build Structure" to create the bond (before combining) it will move one model to use your specified input bond distance and angles, and automatically combine the models.
<https://rb/
vi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fbuildstructure.html&da
ta=05%7C02%7Cwh-kelvin.chung%40polyu.edu.hk%7Cdf0aae6e55a044d5823408d
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If you combine first and then add a bond, it won't move the atoms and
the bond distance and angles may be poor, but it depends on your
situation as to which approach is better, i.e. I'm not saying the way
you did it was wrong.  You may also be interested in using the other
sections in Build Structure (see link above): Adjust Bonds, Adjust
Torsions

You can also measure and change angles with "angle" and "torsion" commands.  You can also rotate bonds manually using the "rotate bond" mousemode.
<https://rb/
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<https://rb/
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(3) there isn't a simple minimization tool that handles nonstandard residues in ChimeraX yet.  You could save a PDB file of the result from the above and use Chimera instead, which has a Minimize Structure tool.

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

On Jul 12, 2024, at 3:26 AM, Kelvin Chung via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Good day
I am a researcher studying antibiotic interaction and trying to make a model with a substrate covalently bound to the active site.
There is a homolog with a crystal structure (PDB: 4KQO), and I am going to add the bound substrate in this pdb file to my target protein where the mode was generated by alphafold server.

Although the workflow shall be simple, I still have some problems, could you kindly help?

1. Firstly, I would like to check whether the model of 4KQO is good enough for modeling, by examining the electron density map (open 4KQO, open 4KQO from eds). However, I found that it is a bit different from the tutorial (https://www.cgl.ucsf.edu/chimerax/docs/quickstart/index.html, pdb:1a0m) that the electron density of 4KQO did not cover the substrate molecule. I am totally ignorant in crystallography, so, how could I visualize the electron density of the substrate? by any symmetry operation / command so that I could check whether there is "electron density in the substrate" ?

2. I aligned 4KQO with the alphafold generated model, and I deleted the protein from 4KQO, and combined the two model, make a bond between the active residue with the substrate, however, I am not sure how to (1) check the bond length and angle is appropriately assigned, and (2) do energy minimization to reorientate side change to eliminate the crash with the substrate.

Thank you very much for your help in advance

Have a nice weekend

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