electrostatic surface of docking model
Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454). When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff! Matteo
Hi Matteo, I guess you need to figure out why there is a hydrogen bonded to the backbone C of residue 244. The C of an amino acid shouldn't have any hydrogens bonded to it. If you wanted, you could send the structure to me and I'd try to offer further insight as to what is happening (I don't have permission to access your job via the link you included). --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 20, 2023, at 4:01 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454 <https://cluspro.bu.edu/models.php?job=898454>). When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff!
Matteo _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Hi Eric, Thanks for your reply and explanation! Attached here is my model. I already tried to directly delete residue 244, but then I get the same error message for residue 243. I have no clue to understand why that is happening, so thank you very much for digging into it! Have a nice day! Matteo ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Friday, January 20, 2023 6:50 PM To: Citterico, Matteo <matteo.citterico@helsinki.fi> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] electrostatic surface of docking model Hi Matteo, I guess you need to figure out why there is a hydrogen bonded to the backbone C of residue 244. The C of an amino acid shouldn't have any hydrogens bonded to it. If you wanted, you could send the structure to me and I'd try to offer further insight as to what is happening (I don't have permission to access your job via the link you included). --Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 20, 2023, at 4:01 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454). When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff! Matteo _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Matteo, The problem is that both your chains have chain ID A. They need to have different IDs. --Eric
On Jan 23, 2023, at 9:29 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric, Thanks for your reply and explanation! Attached here is my model. I already tried to directly delete residue 244, but then I get the same error message for residue 243. I have no clue to understand why that is happening, so thank you very much for digging into it! Have a nice day!
Matteo From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Friday, January 20, 2023 6:50 PM To: Citterico, Matteo <matteo.citterico@helsinki.fi> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] electrostatic surface of docking model
Hi Matteo, I guess you need to figure out why there is a hydrogen bonded to the backbone C of residue 244. The C of an amino acid shouldn't have any hydrogens bonded to it. If you wanted, you could send the structure to me and I'd try to offer further insight as to what is happening (I don't have permission to access your job via the link you included).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 20, 2023, at 4:01 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454 <https://cluspro.bu.edu/models.php?job=898454>). When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff!
Matteo _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> <model.000.01.pdb>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Thank you for the quick reply! I am not very experienced in modifying pdb files. The only option I can think of is changing to "B" the chain ID of every residue of the second protein in the pdb text. Could you suggest me a faster way to do this? Thank you very much for your help! Matteo ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Monday, January 23, 2023 7:44 PM To: Citterico, Matteo <matteo.citterico@helsinki.fi> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] electrostatic surface of docking model Hi Matteo, The problem is that both your chains have chain ID A. They need to have different IDs. --Eric On Jan 23, 2023, at 9:29 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Eric, Thanks for your reply and explanation! Attached here is my model. I already tried to directly delete residue 244, but then I get the same error message for residue 243. I have no clue to understand why that is happening, so thank you very much for digging into it! Have a nice day! Matteo ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Sent: Friday, January 20, 2023 6:50 PM To: Citterico, Matteo <matteo.citterico@helsinki.fi<mailto:matteo.citterico@helsinki.fi>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] electrostatic surface of docking model Hi Matteo, I guess you need to figure out why there is a hydrogen bonded to the backbone C of residue 244. The C of an amino acid shouldn't have any hydrogens bonded to it. If you wanted, you could send the structure to me and I'd try to offer further insight as to what is happening (I don't have permission to access your job via the link you included). --Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 20, 2023, at 4:01 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454). When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff! Matteo _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <model.000.01.pdb>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Matteo, I guess my suggestion is to use a text editor to split the chains into two PDB files. Then open those files in ChimeraX and use the "combine" command to combine them into a single model ("combine #1-2 close true"). That will rename one of the chains to 'B'. You could then save the combined model as a new PDB ("save some_folder/combined.pdb"). --Eric
On Jan 23, 2023, at 10:37 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you for the quick reply! I am not very experienced in modifying pdb files. The only option I can think of is changing to "B" the chain ID of every residue of the second protein in the pdb text. Could you suggest me a faster way to do this? Thank you very much for your help!
Matteo From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Monday, January 23, 2023 7:44 PM To: Citterico, Matteo <matteo.citterico@helsinki.fi> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] electrostatic surface of docking model
Hi Matteo, The problem is that both your chains have chain ID A. They need to have different IDs.
--Eric
On Jan 23, 2023, at 9:29 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Eric, Thanks for your reply and explanation! Attached here is my model. I already tried to directly delete residue 244, but then I get the same error message for residue 243. I have no clue to understand why that is happening, so thank you very much for digging into it! Have a nice day!
Matteo From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Friday, January 20, 2023 6:50 PM To: Citterico, Matteo <matteo.citterico@helsinki.fi <mailto:matteo.citterico@helsinki.fi>> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] electrostatic surface of docking model
Hi Matteo, I guess you need to figure out why there is a hydrogen bonded to the backbone C of residue 244. The C of an amino acid shouldn't have any hydrogens bonded to it. If you wanted, you could send the structure to me and I'd try to offer further insight as to what is happening (I don't have permission to access your job via the link you included).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 20, 2023, at 4:01 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454 <https://cluspro.bu.edu/models.php?job=898454>). When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff!
Matteo _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> <model.000.01.pdb>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
It worked!! Thank you so much again! Matteo ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Monday, January 23, 2023 8:49 PM To: Citterico, Matteo <matteo.citterico@helsinki.fi> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] electrostatic surface of docking model Hi Matteo, I guess my suggestion is to use a text editor to split the chains into two PDB files. Then open those files in ChimeraX and use the "combine" command to combine them into a single model ("combine #1-2 close true"). That will rename one of the chains to 'B'. You could then save the combined model as a new PDB ("save some_folder/combined.pdb"). --Eric On Jan 23, 2023, at 10:37 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Thank you for the quick reply! I am not very experienced in modifying pdb files. The only option I can think of is changing to "B" the chain ID of every residue of the second protein in the pdb text. Could you suggest me a faster way to do this? Thank you very much for your help! Matteo ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Sent: Monday, January 23, 2023 7:44 PM To: Citterico, Matteo <matteo.citterico@helsinki.fi<mailto:matteo.citterico@helsinki.fi>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] electrostatic surface of docking model Hi Matteo, The problem is that both your chains have chain ID A. They need to have different IDs. --Eric On Jan 23, 2023, at 9:29 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Eric, Thanks for your reply and explanation! Attached here is my model. I already tried to directly delete residue 244, but then I get the same error message for residue 243. I have no clue to understand why that is happening, so thank you very much for digging into it! Have a nice day! Matteo ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Sent: Friday, January 20, 2023 6:50 PM To: Citterico, Matteo <matteo.citterico@helsinki.fi<mailto:matteo.citterico@helsinki.fi>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] electrostatic surface of docking model Hi Matteo, I guess you need to figure out why there is a hydrogen bonded to the backbone C of residue 244. The C of an amino acid shouldn't have any hydrogens bonded to it. If you wanted, you could send the structure to me and I'd try to offer further insight as to what is happening (I don't have permission to access your job via the link you included). --Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 20, 2023, at 4:01 AM, Citterico, Matteo via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454). When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff! Matteo _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <model.000.01.pdb>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
-
Citterico, Matteo -
Eric Pettersen