Hi All What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown. Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports "Using Amber 20 recommended default charges and atom types for standard residues" Alternative command 'addcharge standardizeResidues 5BU,CSL,MSE,UMS' reports "Using Amber 20 recommended default charges and atom types for standard residues" and no errors but don't add charges to saved PDB file. Charges are added with another structure editor. Thanks for insights! **CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message.
Hi Daniel, ChimeraX computes partial charges for atoms. As per the PDB format for ATOM records https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM, the "charge" columns are for formal charges -- there are only two columns for charge information which therefore couldn't possibly contain partial charges. Some other formats that ChimeraX can save (such as Sybyl Mol2) can retain partial charge information.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Dec 5, 2023, at 7:35 PM, Daniel Hsu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi All
What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown.
Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports “Using Amber 20 recommended default charges and atom types for standard residues”
Alternative command ‘addcharge standardizeResidues 5BU,CSL,MSE,UMS’ reports “Using Amber 20 recommended default charges and atom types for standard residues” and no errors but don’t add charges to saved PDB file.
Charges are added with another structure editor.
Thanks for insights!
**CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Eric Thank you for this explanation! While not an expert at reading PDB records, I noticed that Protein Prep output in PDB from one program contains annotations that pertain to unit charge. This does not appear to be incorrect because another platform running docking (and other processes) reads it fine. e.g., lines below: ATOM 1 N PRO A 113 6.373 5.875 9.398 1.00 31.24 N1+ . ATOM 256 NH2 ARG A 129 -9.487 -21.448 13.950 1.00 28.43 N1+ . ATOM 567 OD2 ASP A 148 -11.479 2.884 0.139 1.00 15.41 O1-
But what's bothersome, and unfortunate for me, the platform I use rejects ChimeraX PDB output processed with Dock Prep, error message uninsightful, but it may be possible to ask support to what the error pertains. And, it does not support mol2 structure input. Any suggestion/comments are much appreciated. Thanks Dan
From: Eric Pettersen pett@cgl.ucsf.edu Sent: Wednesday, December 6, 2023 9:21 AM To: Daniel Hsu dkhsu@ucdavis.edu Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Add charge to PDB fails
Hi Daniel, ChimeraX computes partial charges for atoms. As per the PDB format for ATOM recordshttps://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM, the "charge" columns are for formal charges -- there are only two columns for charge information which therefore couldn't possibly contain partial charges. Some other formats that ChimeraX can save (such as Sybyl Mol2) can retain partial charge information.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Dec 5, 2023, at 7:35 PM, Daniel Hsu via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi All What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown. Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports "Using Amber 20 recommended default charges and atom types for standard residues" Alternative command 'addcharge standardizeResidues 5BU,CSL,MSE,UMS' reports "Using Amber 20 recommended default charges and atom types for standard residues" and no errors but don't add charges to saved PDB file. Charges are added with another structure editor. Thanks for insights! **CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Dan, As Eric said, those last columns are the formal charge (integer only), whereas Dock Prep adds partial (non-integer) charges to atoms. ChimeraX does not output the formal charge, which is an optional part of PDB format, whereas we do make every effort to adhere to PDB standards when writing the file. However, if you want partial charges included in a file, you have to use a different format, namely Mol2.
Maybe the docking program you mention uses PDBQT or PQR format, neither of which are the same as standard PDB format. Autodock and Autodock Vina use PDBQT format, if I remember correctly. PDBQT format has columns for partial charge (Q) and atom type (T), and PQR has columns for partial charge (Q) and radius (R) even though the first part of each line looks the same as PDB format. However, ChimeraX does not write either of those formats.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2023, at 10:04 AM, Daniel Hsu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Eric
Thank you for this explanation!
While not an expert at reading PDB records, I noticed that Protein Prep output in PDB from one program contains annotations that pertain to unit charge. This does not appear to be incorrect because another platform running docking (and other processes) reads it fine. e.g., lines below:
ATOM 1 N PRO A 113 6.373 5.875 9.398 1.00 31.24 N1+ .
ATOM 256 NH2 ARG A 129 -9.487 -21.448 13.950 1.00 28.43 N1+ .
ATOM 567 OD2 ASP A 148 -11.479 2.884 0.139 1.00 15.41 O1-
But what’s bothersome, and unfortunate for me, the platform I use rejects ChimeraX PDB output processed with Dock Prep, error message uninsightful, but it may be possible to ask support to what the error pertains. And, it does not support mol2 structure input.
Any suggestion/comments are much appreciated.
Thanks
Dan
From: Eric Pettersen pett@cgl.ucsf.edu Sent: Wednesday, December 6, 2023 9:21 AM To: Daniel Hsu dkhsu@ucdavis.edu Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Add charge to PDB fails
Hi Daniel, ChimeraX computes partial charges for atoms. As per the PDB format for ATOM records, the "charge" columns are for formal charges -- there are only two columns for charge information which therefore couldn't possibly contain partial charges. Some other formats that ChimeraX can save (such as Sybyl Mol2) can retain partial charge information.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Dec 5, 2023, at 7:35 PM, Daniel Hsu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi All
What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown.
Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports “Using Amber 20 recommended default charges and atom types for standard residues”
Alternative command ‘addcharge standardizeResidues 5BU,CSL,MSE,UMS’ reports “Using Amber 20 recommended default charges and atom types for standard residues” and no errors but don’t add charges to saved PDB file.
Charges are added with another structure editor.
Thanks for insights!
**CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Oops, I got it wrong, ChimeraX can write PQR format! To do that, you have to use the "save" command with the option "pqr true":
https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb
More about PQR: https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html#PQR
Sorry about that, Elaine
On Dec 6, 2023, at 11:57 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dan, As Eric said, those last columns are the formal charge (integer only), whereas Dock Prep adds partial (non-integer) charges to atoms. ChimeraX does not output the formal charge, which is an optional part of PDB format, whereas we do make every effort to adhere to PDB standards when writing the file. However, if you want partial charges included in a file, you have to use a different format, namely Mol2.
Maybe the docking program you mention uses PDBQT or PQR format, neither of which are the same as standard PDB format. Autodock and Autodock Vina use PDBQT format, if I remember correctly. PDBQT format has columns for partial charge (Q) and atom type (T), and PQR has columns for partial charge (Q) and radius (R) even though the first part of each line looks the same as PDB format. However, ChimeraX does not write either of those formats.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2023, at 10:04 AM, Daniel Hsu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Eric
Thank you for this explanation!
While not an expert at reading PDB records, I noticed that Protein Prep output in PDB from one program contains annotations that pertain to unit charge. This does not appear to be incorrect because another platform running docking (and other processes) reads it fine. e.g., lines below:
ATOM 1 N PRO A 113 6.373 5.875 9.398 1.00 31.24 N1+ .
ATOM 256 NH2 ARG A 129 -9.487 -21.448 13.950 1.00 28.43 N1+ .
ATOM 567 OD2 ASP A 148 -11.479 2.884 0.139 1.00 15.41 O1-
But what’s bothersome, and unfortunate for me, the platform I use rejects ChimeraX PDB output processed with Dock Prep, error message uninsightful, but it may be possible to ask support to what the error pertains. And, it does not support mol2 structure input.
Any suggestion/comments are much appreciated.
Thanks
Dan
From: Eric Pettersen pett@cgl.ucsf.edu Sent: Wednesday, December 6, 2023 9:21 AM To: Daniel Hsu dkhsu@ucdavis.edu Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Add charge to PDB fails
Hi Daniel, ChimeraX computes partial charges for atoms. As per the PDB format for ATOM records, the "charge" columns are for formal charges -- there are only two columns for charge information which therefore couldn't possibly contain partial charges. Some other formats that ChimeraX can save (such as Sybyl Mol2) can retain partial charge information.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Dec 5, 2023, at 7:35 PM, Daniel Hsu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi All
What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown.
Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports “Using Amber 20 recommended default charges and atom types for standard residues”
Alternative command ‘addcharge standardizeResidues 5BU,CSL,MSE,UMS’ reports “Using Amber 20 recommended default charges and atom types for standard residues” and no errors but don’t add charges to saved PDB file.
Charges are added with another structure editor.
Thanks for insights!
**CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you for this information, Elaine!
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, December 6, 2023 12:56 PM To: Daniel Hsu dkhsu@ucdavis.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Add charge to PDB fails
Oops, I got it wrong, ChimeraX can write PQR format! To do that, you have to use the "save" command with the option "pqr true":
https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb
More about PQR: https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html#PQR
Sorry about that, Elaine
On Dec 6, 2023, at 11:57 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dan, As Eric said, those last columns are the formal charge (integer only), whereas Dock Prep adds partial (non-integer) charges to atoms. ChimeraX does not output the formal charge, which is an optional part of PDB format, whereas we do make every effort to adhere to PDB standards when writing the file. However, if you want partial charges included in a file, you have to use a different format, namely Mol2.
Maybe the docking program you mention uses PDBQT or PQR format, neither of which are the same as standard PDB format. Autodock and Autodock Vina use PDBQT format, if I remember correctly. PDBQT format has columns for partial charge (Q) and atom type (T), and PQR has columns for partial charge (Q) and radius (R) even though the first part of each line looks the same as PDB format. However, ChimeraX does not write either of those formats.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2023, at 10:04 AM, Daniel Hsu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Eric
Thank you for this explanation!
While not an expert at reading PDB records, I noticed that Protein Prep output in PDB from one program contains annotations that pertain to unit charge. This does not appear to be incorrect because another platform running docking (and other processes) reads it fine. e.g., lines below:
ATOM 1 N PRO A 113 6.373 5.875 9.398 1.00 31.24 N1+ .
ATOM 256 NH2 ARG A 129 -9.487 -21.448 13.950 1.00 28.43 N1+ .
ATOM 567 OD2 ASP A 148 -11.479 2.884 0.139 1.00 15.41 O1-
But what's bothersome, and unfortunate for me, the platform I use rejects ChimeraX PDB output processed with Dock Prep, error message uninsightful, but it may be possible to ask support to what the error pertains. And, it does not support mol2 structure input.
Any suggestion/comments are much appreciated.
Thanks
Dan
From: Eric Pettersen pett@cgl.ucsf.edu Sent: Wednesday, December 6, 2023 9:21 AM To: Daniel Hsu dkhsu@ucdavis.edu Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Add charge to PDB fails
Hi Daniel, ChimeraX computes partial charges for atoms. As per the PDB format for ATOM records, the "charge" columns are for formal charges -- there are only two columns for charge information which therefore couldn't possibly contain partial charges. Some other formats that ChimeraX can save (such as Sybyl Mol2) can retain partial charge information.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Dec 5, 2023, at 7:35 PM, Daniel Hsu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi All
What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown.
Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports "Using Amber 20 recommended default charges and atom types for standard residues"
Alternative command 'addcharge standardizeResidues 5BU,CSL,MSE,UMS' reports "Using Amber 20 recommended default charges and atom types for standard residues" and no errors but don't add charges to saved PDB file.
Charges are added with another structure editor.
Thanks for insights!
**CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mai/ l.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucs f.edu%2F&data=05%7C01%7Cdkhsu%40ucdavis.edu%7Ce4d9ff1a3eab4b71658408d bf69db46a%7Ca8046f6466c04f009046c8daf92ff62b%7C0%7C0%7C63837492941803 2146%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJB TiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UBQ0xK9ov8daIFL7hxvg 8mhpe2E7zoQz2Z%2BDCDPrPQo%3D&reserved=0
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mai/ l.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucs f.edu%2F&data=05%7C01%7Cdkhsu%40ucdavis.edu%7Ce4d9ff1a3eab4b71658408d bf69db46a%7Ca8046f6466c04f009046c8daf92ff62b%7C0%7C0%7C63837492941803 2146%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJB TiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UBQ0xK9ov8daIFL7hxvg 8mhpe2E7zoQz2Z%2BDCDPrPQo%3D&reserved=0
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail/ .cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf. edu%2F&data=05%7C01%7Cdkhsu%40ucdavis.edu%7Ce4d9ff1a3eab4b71658408dbf6 9db46a%7Ca8046f6466c04f009046c8daf92ff62b%7C0%7C0%7C638374929418032146 %7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6I k1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UBQ0xK9ov8daIFL7hxvg8mhpe2 E7zoQz2Z%2BDCDPrPQo%3D&reserved=0
participants (3)
-
Daniel Hsu -
Elaine Meng -
Eric Pettersen