Hello, How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: [cid:image001.png@01DA0026.3D6BC080] Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Sorry, this was the original error message: [cid:image001.png@01DA0026.92BCE0A0] From: "Jaremko, Matt Joseph" <matt.jaremko@merck.com> Date: Monday, October 16, 2023 at 11:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Open small molecule cif Hello, How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: [cid:image002.png@01DA0026.92BCE0A0] Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
We added small molecule cif support in ChimeraX 1.6. So you need to update your version of ChimeraX. If a .cif file isn't a mmCIF, it will try to open it as a small molecule cif file. And, in your case, you can open the CIR ligand without downloading it first with: open cir from ccd or: open ccd:cir ccd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands. -- Greg On 10/16/2023 8:47 AM, Jaremko, Matt Joseph via ChimeraX-users wrote:
Sorry, this was the original error message:
*From: *"Jaremko, Matt Joseph" <matt.jaremko@merck.com> *Date: *Monday, October 16, 2023 at 11:45 AM *To: *ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> *Subject: *Open small molecule cif
Hello,
How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX:
Thank you,
Matt
*Matt J. Jaremko, Ph.D. (He|Him)*
Senior Scientist | Protein & Structural Chemistry
Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033
Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD <https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Greg, I am using ChimeraX 1.6 and the commands you list do not work: open<help:user/commands/open.html> cir fromDatabase ccd Unknown CCD ligand name open<help:user/commands/open.html> ccd:cir Unknown CCD ligand name How can I import these small molecule cifs from a file? This doesn’t seem to be working in 1.6. Thank you, Matt From: Greg Couch <gregc@cgl.ucsf.edu> Date: Tuesday, October 17, 2023 at 2:51 AM To: "Jaremko, Matt Joseph" <matt.jaremko@merck.com>, ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Re: Open small molecule cif You don't often get email from gregc@cgl.ucsf.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> EXTERNAL EMAIL– Use caution with any links or file attachments. We added small molecule cif support in ChimeraX 1.6. So you need to update your version of ChimeraX. If a .cif file isn't a mmCIF, it will try to open it as a small molecule cif file. And, in your case, you can open the CIR ligand without downloading it first with: open cir from ccd or: open ccd:cir ccd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands. -- Greg On 10/16/2023 8:47 AM, Jaremko, Matt Joseph via ChimeraX-users wrote: Sorry, this was the original error message: [cid:image001.png@01DA00D1.71BF7AB0] From: "Jaremko, Matt Joseph" <matt.jaremko@merck.com><mailto:matt.jaremko@merck.com> Date: Monday, October 16, 2023 at 11:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><mailto:chimerax-users@cgl.ucsf.edu> Subject: Open small molecule cif Hello, How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: [cid:image002.png@01DA00D1.71BF7AB0] Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. _______________________________________________ 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/ This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Hi Matt, Both of those commands work for me in ChimeraX version 1.6.1 as well as a recent 1.7 daily build. However, I see that CCD fetch was added way back in version 1.0, so I doubt that version is an issue. Are you able to open anything from CCD? E.g. open ccd:tyr Does capitalizing the residue name help? open ccd:TYR ... actually, can you do any web fetch? E.g. PDB entries open 2d2n Although the error message does not suggest it, maybe there is some issue with web proxy settings, see the ChimeraX preferences, Web Access section: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 17, 2023, at 5:10 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Greg, I am using ChimeraX 1.6 and the commands you list do not work:
open cir fromDatabase ccd Unknown CCD ligand name open ccd:cir Unknown CCD ligand name
How can I import these small molecule cifs from a file? This doesn’t seem to be working in 1.6.
Thank you, Matt
From: Greg Couch <gregc@cgl.ucsf.edu> Date: Tuesday, October 17, 2023 at 2:51 AM To: "Jaremko, Matt Joseph" <matt.jaremko@merck.com>, ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Re: Open small molecule cif
You don't often get email from gregc@cgl.ucsf.edu. Learn why this is important EXTERNAL EMAIL– Use caution with any links or file attachments. We added small molecule cif support in ChimeraX 1.6. So you need to update your version of ChimeraX. If a .cif file isn't a mmCIF, it will try to open it as a small molecule cif file. And, in your case, you can open the CIR ligand without downloading it first with:
open cir from ccd
or:
open ccd:cir
ccd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands.
-- Greg
On 10/16/2023 8:47 AM, Jaremko, Matt Joseph via ChimeraX-users wrote: Sorry, this was the original error message: <image001.png>
From: "Jaremko, Matt Joseph" <matt.jaremko@merck.com> Date: Monday, October 16, 2023 at 11:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Open small molecule cif
Hello,
How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: <image002.png>
Thank you, Matt
Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
_______________________________________________ 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/
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
_______________________________________________ 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/
The commands work for me in 1.6. So this now sounds like a network connectivity issue. ChimeraX fetches the CCD files from https://files.wwpdb.org/. I wouldn't be surprised if your company has a https proxy or firewall that needs to be configured to allow that. Please consult with your local IT folks and let us know what you find out. -- Greg On 10/17/2023 5:10 AM, Jaremko, Matt Joseph wrote:
Hi Greg,
I am using ChimeraX 1.6 and the commands you list do not work:
*open <help:user/commands/open.html> cir fromDatabase ccd***
*Unknown CCD ligand name*
*open <help:user/commands/open.html> ccd:cir*
*Unknown CCD ligand name*
How can I import these small molecule cifs from a file? This doesn’t seem to be working in 1.6.
Thank you,
Matt
*From: *Greg Couch <gregc@cgl.ucsf.edu> *Date: *Tuesday, October 17, 2023 at 2:51 AM *To: *"Jaremko, Matt Joseph" <matt.jaremko@merck.com>, ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> *Subject: *Re: [chimerax-users] Re: Open small molecule cif
You don't often get email from gregc@cgl.ucsf.edu. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification>
*EXTERNAL EMAIL*– Use caution with any links or file attachments.
We added small molecule cif support in ChimeraX 1.6. So you need to update your version of ChimeraX. If a .cif file isn't a mmCIF, it will try to open it as a small molecule cif file. And, in your case, you can open the CIR ligand without downloading it first with:
open cir from ccd
or:
open ccd:cir
ccd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands.
-- Greg
On 10/16/2023 8:47 AM, Jaremko, Matt Joseph via ChimeraX-users wrote:
Sorry, this was the original error message:
*From: *"Jaremko, Matt Joseph" <matt.jaremko@merck.com> <mailto:matt.jaremko@merck.com> *Date: *Monday, October 16, 2023 at 11:45 AM *To: *ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> <mailto:chimerax-users@cgl.ucsf.edu> *Subject: *Open small molecule cif
Hello,
How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX:
Thank you,
Matt
*Matt J. Jaremko, Ph.D. (He|Him)*
Senior Scientist | Protein & Structural Chemistry
Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033
Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD <https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
_______________________________________________
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To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu
Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Hi Elaine, These work for me: open ccd:tyr TYR title: tyrosine Opened CCD TYR open 2d2n Summary of feedback from opening 2d2n fetched from pdb warnings Unable to fetch template for 'OXY': might have incorrect bonds Unable to fetch template for 'MMC': might have incorrect bonds note Fetching mmCIF 2d2n from http://files.rcsb.org/download/2d2n.cif 2d2n title: Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi [more info...] .... But can't find cir. Capitlizaed or not. I'm on the Mac version. Thanks, Matt On 10/17/23, 11:59 AM, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: EXTERNAL EMAIL– Use caution with any links or file attachments. Hi Matt, Both of those commands work for me in ChimeraX version 1.6.1 as well as a recent 1.7 daily build. However, I see that CCD fetch was added way back in version 1.0, so I doubt that version is an issue. Are you able to open anything from CCD? E.g. open ccd:tyr Does capitalizing the residue name help? open ccd:TYR ... actually, can you do any web fetch? E.g. PDB entries open 2d2n Although the error message does not suggest it, maybe there is some issue with web proxy settings, see the ChimeraX preferences, Web Access section: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html>> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 17, 2023, at 5:10 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Greg, I am using ChimeraX 1.6 and the commands you list do not work:
open cir fromDatabase ccd Unknown CCD ligand name open ccd:cir Unknown CCD ligand name
How can I import these small molecule cifs from a file? This doesn’t seem to be working in 1.6.
Thank you, Matt
From: Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> Date: Tuesday, October 17, 2023 at 2:51 AM To: "Jaremko, Matt Joseph" <matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>>, ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Re: Open small molecule cif
You don't often get email from gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>. Learn why this is important EXTERNAL EMAIL– Use caution with any links or file attachments. We added small molecule cif support in ChimeraX 1.6. So you need to update your version of ChimeraX. If a .cif file isn't a mmCIF, it will try to open it as a small molecule cif file. And, in your case, you can open the CIR ligand without downloading it first with:
open cir from ccd
or:
open ccd:cir
ccd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands.
-- Greg
On 10/16/2023 8:47 AM, Jaremko, Matt Joseph via ChimeraX-users wrote: Sorry, this was the original error message: <image001.png>
From: "Jaremko, Matt Joseph" <matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>> Date: Monday, October 16, 2023 at 11:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Open small molecule cif
Hello,
How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: <image002.png>
Thank you, Matt
Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
_______________________________________________ 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 <mailto:chimerax-users@cgl.ucsf.edu>/
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This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
open ccd:tyr worked because it was already cached on your system (ChimeraX comes with residue templates for the most common amino and nucleic acids). Not being able to fetch a residue template (a CCD file) means you have network issues or that the files.wwpdb.org is down. The log output should have been:
Fetching compressed mmCIF 2d2n from http://files.rcsb.org/download/2d2n.cif Fetching CCD OXY from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/OXY/OXY.cif Fetching CCD MMC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/MMC/MMC.cif Again, I suspect it is an issue with your company's https proxy or firewall with fils.wwpdb.org. You need to consult your company's IT support.
-- Greg On 10/17/2023 10:23 AM, Jaremko, Matt Joseph via ChimeraX-users wrote:
Hi Elaine,
These work for me:
open ccd:tyr TYR title: tyrosine
Opened CCD TYR
open 2d2n Summary of feedback from opening 2d2n fetched from pdb warnings Unable to fetch template for 'OXY': might have incorrect bonds Unable to fetch template for 'MMC': might have incorrect bonds note Fetching mmCIF 2d2n from http://files.rcsb.org/download/2d2n.cif 2d2n title: Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi [more info...] ....
But can't find cir. Capitlizaed or not.
I'm on the Mac version.
Thanks, Matt
On 10/17/23, 11:59 AM, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
EXTERNAL EMAIL– Use caution with any links or file attachments.
Hi Matt, Both of those commands work for me in ChimeraX version 1.6.1 as well as a recent 1.7 daily build. However, I see that CCD fetch was added way back in version 1.0, so I doubt that version is an issue.
Are you able to open anything from CCD? E.g.
open ccd:tyr
Does capitalizing the residue name help?
open ccd:TYR
... actually, can you do any web fetch? E.g. PDB entries
open 2d2n
Although the error message does not suggest it, maybe there is some issue with web proxy settings, see the ChimeraX preferences, Web Access section:
<https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html>> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess>>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 17, 2023, at 5:10 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Greg, I am using ChimeraX 1.6 and the commands you list do not work:
open cir fromDatabase ccd Unknown CCD ligand name open ccd:cir Unknown CCD ligand name
How can I import these small molecule cifs from a file? This doesn’t seem to be working in 1.6.
Thank you, Matt
From: Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> Date: Tuesday, October 17, 2023 at 2:51 AM To: "Jaremko, Matt Joseph" <matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>>, ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Re: Open small molecule cif
You don't often get email from gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>. Learn why this is important EXTERNAL EMAIL– Use caution with any links or file attachments. We added small molecule cif support in ChimeraX 1.6. So you need to update your version of ChimeraX. If a .cif file isn't a mmCIF, it will try to open it as a small molecule cif file. And, in your case, you can open the CIR ligand without downloading it first with:
open cir from ccd
or:
open ccd:cir
ccd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands.
-- Greg
On 10/16/2023 8:47 AM, Jaremko, Matt Joseph via ChimeraX-users wrote: Sorry, this was the original error message: <image001.png>
From: "Jaremko, Matt Joseph" <matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>> Date: Monday, October 16, 2023 at 11:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Open small molecule cif
Hello,
How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: <image002.png>
Thank you, Matt
Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>
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Thanks Greg, I've reached out to our IT support. Best, Matt On 10/17/23, 10:16 PM, "Greg Couch" <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote: [You don't often get email from gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification <https://aka.ms/LearnAboutSenderIdentification> ] EXTERNAL EMAIL– Use caution with any links or file attachments. open ccd:tyr worked because it was already cached on your system (ChimeraX comes with residue templates for the most common amino and nucleic acids). Not being able to fetch a residue template (a CCD file) means you have network issues or that the files.wwpdb.org is down. The log output should have been:
Fetching compressed mmCIF 2d2n from http://files.rcsb.org/download/2d2n.cif <http://files.rcsb.org/download/2d2n.cif> Fetching CCD OXY from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/OXY/OXY.cif <https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/OXY/OXY.cif> Fetching CCD MMC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/MMC/MMC.cif <https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/MMC/MMC.cif> Again, I suspect it is an issue with your company's https proxy or firewall with fils.wwpdb.org. You need to consult your company's IT support.
-- Greg On 10/17/2023 10:23 AM, Jaremko, Matt Joseph via ChimeraX-users wrote:
Hi Elaine,
These work for me:
open ccd:tyr TYR title: tyrosine
Opened CCD TYR
open 2d2n Summary of feedback from opening 2d2n fetched from pdb warnings Unable to fetch template for 'OXY': might have incorrect bonds Unable to fetch template for 'MMC': might have incorrect bonds note Fetching mmCIF 2d2n from http://files.rcsb.org/download/2d2n.cif <http://files.rcsb.org/download/2d2n.cif> 2d2n title: Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi [more info...] ....
But can't find cir. Capitlizaed or not.
I'm on the Mac version.
Thanks, Matt
On 10/17/23, 11:59 AM, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu> <mailto:meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>>> wrote:
EXTERNAL EMAIL– Use caution with any links or file attachments.
Hi Matt, Both of those commands work for me in ChimeraX version 1.6.1 as well as a recent 1.7 daily build. However, I see that CCD fetch was added way back in version 1.0, so I doubt that version is an issue.
Are you able to open anything from CCD? E.g.
open ccd:tyr
Does capitalizing the residue name help?
open ccd:TYR
... actually, can you do any web fetch? E.g. PDB entries
open 2d2n
Although the error message does not suggest it, maybe there is some issue with web proxy settings, see the ChimeraX preferences, Web Access section:
<https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html>> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html>> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html>>> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess>> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess>> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess>>>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 17, 2023, at 5:10 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <mailto:chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>> wrote:
Hi Greg, I am using ChimeraX 1.6 and the commands you list do not work:
open cir fromDatabase ccd Unknown CCD ligand name open ccd:cir Unknown CCD ligand name
How can I import these small molecule cifs from a file? This doesn’t seem to be working in 1.6.
Thank you, Matt
From: Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu> <mailto:gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>>> Date: Tuesday, October 17, 2023 at 2:51 AM To: "Jaremko, Matt Joseph" <matt.jaremko@merck.com <mailto:matt.jaremko@merck.com> <mailto:matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>>>, ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <mailto:chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>> Subject: Re: [chimerax-users] Re: Open small molecule cif
You don't often get email from gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu> <mailto:gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>>. Learn why this is important EXTERNAL EMAIL– Use caution with any links or file attachments. We added small molecule cif support in ChimeraX 1.6. So you need to update your version of ChimeraX. If a .cif file isn't a mmCIF, it will try to open it as a small molecule cif file. And, in your case, you can open the CIR ligand without downloading it first with:
open cir from ccd
or:
open ccd:cir
ccd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands.
-- Greg
On 10/16/2023 8:47 AM, Jaremko, Matt Joseph via ChimeraX-users wrote: Sorry, this was the original error message: <image001.png>
From: "Jaremko, Matt Joseph" <matt.jaremko@merck.com <mailto:matt.jaremko@merck.com> <mailto:matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>>> Date: Monday, October 16, 2023 at 11:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <mailto:chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>> Subject: Open small molecule cif
Hello,
How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: <image002.png>
Thank you, Matt
Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com <mailto:matt.jaremko@merck.com> <mailto:matt.jaremko@merck.com <mailto:matt.jaremko@merck.com>>
This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
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This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/> <https://www.msd.com/contact-us/>>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
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participants (3)
-
Elaine Meng -
Greg Couch -
Jaremko, Matt Joseph