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.commailto: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 - MSDhttps://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.commailto: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 - MSDhttps://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.
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Hi Greg, I am using ChimeraX 1.6 and the commands you list do not work:
openhelp:user/commands/open.html cir fromDatabase ccd Unknown CCD ligand name openhelp: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 importanthttps://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.commailto:matt.jaremko@merck.com Date: Monday, October 16, 2023 at 11:45 AM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edumailto: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.commailto: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 - MSDhttps://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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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 ccdor:
open ccd:circcd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands.
-- GregOn 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.
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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/.%C2%A0%C2%A0 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. _______________________________________________ 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/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 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/
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 - MSDhttps://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:
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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:
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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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participants (3)
-
Elaine Meng -
Greg Couch -
Jaremko, Matt Joseph