Enquiry about the ligand library generation by scripts in Chimera
Good morning, Dear Professor, My name is Zhenjiao Du, from Kansas State University. I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized by molecular dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job. I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might need to generate thousands of peptide ligands for virtual screening. I find Chimera also supports python programming. Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it. I am looking forward to your reply. Sincerely, Zhenjiao Du Vice president of CAFS Student Committee Ph.D. student, Cereal Chemistry Grain Science & Industry, Kansas State University 150A Waters Hall, Manhattan, KS 66502 Pronouns: He/His
Hi Zhenjiao, You need to resort to Python to do this since there is no command equivalent for peptide building. I don't know how familiar you are with Python programming, but there is some basic information for using Python in Chimera here: Chimera Programmer's Guide <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>. Specifically you would use the BuildStructure.placePeptide() function to construct the peptide ligand(s) and just run the "minimize" command to minimize them. You can run Chimera commands from Python using the runCommand() function as described here: Very Basic Chimera Programming Primer <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>. You would need to write a loop that goes through your peptide sequences (and possibly associated phi/psis). The inside of the loop would have some code similar to: from BuildStructure import placePeptide from chimera import runCommand placePeptide(sequence, [(phi1, psi1), (phi2, psi2), ... (phiN, psiN)]) runCommand("minimize options-you-want") runCommand("write #0 appropriate-file-name") runCommand("close all") Tip, if you want all the residues to start with the same phi/psis, the second argument to placePeptide() could be: [(phi, psi)] * len(sequence) --Eric Eric Pettersen UCSF Computer Graphics Lab
On Oct 6, 2022, at 8:27 PM, Zhenjiao Du via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good morning, Dear Professor,
My name is Zhenjiao Du, from Kansas State University. I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized by molecular dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job.
I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might need to generate thousands of peptide ligands for virtual screening. I find Chimera also supports python programming.
Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it. I am looking forward to your reply. Sincerely,
Zhenjiao Du Vice president of CAFS Student Committee Ph.D. student, Cereal Chemistry Grain Science & Industry, Kansas State University 150A Waters Hall, Manhattan, KS 66502
Pronouns: He/His
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
Good afternoon, Eric, I am so grateful to your reply. I am so happy. That really make my day.đ¤Šđ¤Šđ¤Šđ¤Šđđđđđđđ Based on your suggestions, I successfully built an automatic workflow for peptide ligand generation by combining the available function and PyAutoGUI. It is a little bit stupid approach to implement my job, but finally it works out. đđđđđ Again, thank you so much for your reply, and the amazing software your team is working with. I hope I can go deeper into the molecular docking and dynamics simulation world. One day, I can have the opportunity to study and work at UCSF. Sincerely, Zhenjiao ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Saturday, October 8, 2022 2:26 To: Zhenjiao Du <zhenjiao@ksu.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Enquiry about the ligand library generation by scripts in Chimera This email originated from outside of K-State. Hi Zhenjiao, You need to resort to Python to do this since there is no command equivalent for peptide building. I don't know how familiar you are with Python programming, but there is some basic information for using Python in Chimera here: Chimera Programmer's Guide<https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>. Specifically you would use the BuildStructure.placePeptide() function to construct the peptide ligand(s) and just run the "minimize" command to minimize them. You can run Chimera commands from Python using the runCommand() function as described here: Very Basic Chimera Programming Primer<https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>. You would need to write a loop that goes through your peptide sequences (and possibly associated phi/psis). The inside of the loop would have some code similar to: from BuildStructure import placePeptide from chimera import runCommand placePeptide(sequence, [(phi1, psi1), (phi2, psi2), ... (phiN, psiN)]) runCommand("minimize options-you-want") runCommand("write #0 appropriate-file-name") runCommand("close all") Tip, if you want all the residues to start with the same phi/psis, the second argument to placePeptide() could be: [(phi, psi)] * len(sequence) --Eric Eric Pettersen UCSF Computer Graphics Lab On Oct 6, 2022, at 8:27 PM, Zhenjiao Du via Chimera-users <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> wrote: Good morning, Dear Professor, My name is Zhenjiao Du, from Kansas State University. I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized by molecular dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job. I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might need to generate thousands of peptide ligands for virtual screening. I find Chimera also supports python programming. Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it. I am looking forward to your reply. Sincerely, Zhenjiao Du Vice president of CAFS Student Committee Ph.D. student, Cereal Chemistry Grain Science & Industry, Kansas State University 150A Waters Hall, Manhattan, KS 66502 Pronouns: He/His _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Dear Zhenjiao, I'm glad you got it to work. Have a great weekend! --Eric
On Oct 7, 2022, at 2:26 PM, Zhenjiao Du via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good afternoon, Eric,
I am so grateful to your reply. I am so happy. That really make my day.đ¤Šđ¤Šđ¤Šđ¤Šđđđđđđđ
Based on your suggestions, I successfully built an automatic workflow for peptide ligand generation by combining the available function and PyAutoGUI. It is a little bit stupid approach to implement my job, but finally it works out. đđđđđ
Again, thank you so much for your reply, and the amazing software your team is working with.
I hope I can go deeper into the molecular docking and dynamics simulation world. One day, I can have the opportunity to study and work at UCSF.
Sincerely, Zhenjiao
From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Saturday, October 8, 2022 2:26 To: Zhenjiao Du <zhenjiao@ksu.edu <mailto:zhenjiao@ksu.edu>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Enquiry about the ligand library generation by scripts in Chimera
This email originated from outside of K-State.
Hi Zhenjiao, You need to resort to Python to do this since there is no command equivalent for peptide building. I don't know how familiar you are with Python programming, but there is some basic information for using Python in Chimera here: Chimera Programmer's Guide <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>. Specifically you would use the BuildStructure.placePeptide() function to construct the peptide ligand(s) and just run the "minimize" command to minimize them. You can run Chimera commands from Python using the runCommand() function as described here: Very Basic Chimera Programming Primer <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>. You would need to write a loop that goes through your peptide sequences (and possibly associated phi/psis). The inside of the loop would have some code similar to:
from BuildStructure import placePeptide from chimera import runCommand placePeptide(sequence, [(phi1, psi1), (phi2, psi2), ... (phiN, psiN)]) runCommand("minimize options-you-want") runCommand("write #0 appropriate-file-name") runCommand("close all")
Tip, if you want all the residues to start with the same phi/psis, the second argument to placePeptide() could be: [(phi, psi)] * len(sequence)
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 6, 2022, at 8:27 PM, Zhenjiao Du via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Good morning, Dear Professor,
My name is Zhenjiao Du, from Kansas State University. I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized by molecular dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job.
I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might need to generate thousands of peptide ligands for virtual screening. I find Chimera also supports python programming.
Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it. I am looking forward to your reply. Sincerely,
Zhenjiao Du Vice president of CAFS Student Committee Ph.D. student, Cereal Chemistry Grain Science & Industry, Kansas State University 150A Waters Hall, Manhattan, KS 66502
Pronouns: He/His
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
participants (2)
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Eric Pettersen -
Zhenjiao Du