Hi Kelvin, Chimera uses residue-name lookup to assign charges and molecular mechanics parameters to standard residues, so a modified residue named SER is going to be a problem. You need to change the name of that SER residue so that Chimera treats it as nonstandard. One way is to edit your PDB file. Another is once you have the structure open in Chimera change the residue name with the command (Favorites→Command Line): setattr r type SXR :307.b The run your minimization. After it finished you can change the name back if you want with: setattr r type SER :307.b --Eric Eric Pettersen UCSF Computer Graphics Lab
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 <mailto:meng@cgl.ucsf.edu>> Sent: Saturday, July 13, 2024 4:48 AM To: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>>; CHUNG, WH Kelvin [ABCT] <wh-kelvin.chung@polyu.edu.hk <mailto:wh-kelvin.chung@polyu.edu.hk>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] [chimerax-users] Covalent substrate modeling and minimization
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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/ vi.ucsf.edu <http://vi.ucsf.edu/>%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fvolume.html%23gener al&data=05%7C02%7Cwh-kelvin.chung%40polyu.edu.hk <http://40polyu.edu.hk/>%7Cdf0aae6e55a044d582 3408dca2b3e0ce%7C8f37f760b1874981b82fe5dc6f5bcf44%7C0%7C0%7C638564140 674125188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzI iLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=txZTg%2BntlWPX9yYU HkchG%2Bgt4NRHE6ROd8HHb%2Fynzs4%3D&reserved=0> <https://rb/ vi.ucsf.edu <http://vi.ucsf.edu/>%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fvolume.html%23zone& data=05%7C02%7Cwh-kelvin.chung%40polyu.edu.hk <http://40polyu.edu.hk/>%7Cdf0aae6e55a044d582340 8dca2b3e0ce%7C8f37f760b1874981b82fe5dc6f5bcf44%7C0%7C0%7C638564140674 135253%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLC JBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=zCwphaugzSt%2FQdYfXm2 ksajV5MvgGhjpLN0NfT7rIhA%3D&reserved=0> <https://rb/ vi.ucsf.edu <http://vi.ucsf.edu/>%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fvolumeviewer.html&data =05%7C02%7Cwh-kelvin.chung%40polyu.edu.hk <http://40polyu.edu.hk/>%7Cdf0aae6e55a044d5823408dca 2b3e0ce%7C8f37f760b1874981b82fe5dc6f5bcf44%7C0%7C0%7C6385641406741416 03%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTi I6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=qRlMkmJaWXb8IZjin43lQB091 cIGROdWe119HCV7RBA%3D&reserved=0>
(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 <http://vi.ucsf.edu/>%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fbuildstructure.html&da ta=05%7C02%7Cwh-kelvin.chung%40polyu.edu.hk <http://40polyu.edu.hk/>%7Cdf0aae6e55a044d5823408d ca2b3e0ce%7C8f37f760b1874981b82fe5dc6f5bcf44%7C0%7C0%7C63856414067414 5686%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJB TiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=uU1vrv%2FeuRe2LmATOdUFx LNdMghYqsWh5XxXSC7vWhI%3D&reserved=0>
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/ vi.ucsf.edu <http://vi.ucsf.edu/>%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Ftorsion.html&data=0 5%7C02%7Cwh-kelvin.chung%40polyu.edu.hk <http://40polyu.edu.hk/>%7Cdf0aae6e55a044d5823408dca2b 3e0ce%7C8f37f760b1874981b82fe5dc6f5bcf44%7C0%7C0%7C638564140674149764 %7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6 Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=dTMaux4X3VqtkuWvsKx0eVlyRDY lkyrXZKDMRvfZ8Uo%3D&reserved=0> <https://rb/ vi.ucsf.edu <http://vi.ucsf.edu/>%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fangle.html&data=05% 7C02%7Cwh-kelvin.chung%40polyu.edu.hk <http://40polyu.edu.hk/>%7Cdf0aae6e55a044d5823408dca2b3e 0ce%7C8f37f760b1874981b82fe5dc6f5bcf44%7C0%7C0%7C638564140674153562%7 CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik 1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=9Meo9RoGD1y8xpLQSsGb4u1ZDboMT ESTz0QD2ym3yDo%3D&reserved=0> <https://rb/ vi.ucsf.edu <http://vi.ucsf.edu/>%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fui.html%23mousemode &data=05%7C02%7Cwh-kelvin.chung%40polyu.edu.hk <http://40polyu.edu.hk/>%7Cdf0aae6e55a044d58234 08dca2b3e0ce%7C8f37f760b1874981b82fe5dc6f5bcf44%7C0%7C0%7C63856414067 4157388%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiL CJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=O%2B6r9%2FhkJ1NSE5n% 2FOnC61eqYuLNfUhbvdTaDXc0tYw8%3D&reserved=0>
(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 <mailto: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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