Hi Krish, If I understand correctly, the SDF files that you have do not contain 3D atomic coordinates. They only contain 2D "chemical diagrams" -- so they can't be used like real structures. ChimeraX tries to apply chemical detection based on bond lengths and angles, which does not work on these chemical diagrams, since they are typically different in scale as well as being totally flat. Sorry, there is no option to make them into real 3D molecules.

To get 3D structures of the compounds you would instead need to start with something like a SMILES string or a PubChem identifier and use those types of fetches (SMILES or PubChem3D) instead of your SDF files. These types of fetches are done with the "open" command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch

There is no automatic way to read arbitrary values from SDF files. Instead you would need to open all the structures somehow, then create an attribute assignment file to assign the values. Or, you would need to write a custom python script that reads the values from your files. Somebody else would have to advise on that, as I don't know python.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 2, 2023, at 12:24 PM, Krishnan Raman via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi Elaine, Thanks for the quick reply. I think I was not clear about the first request. I have an sdf file with structure and some aasay value(numeric) associated with each structure. . The sdf option to open files brought up the structures in 2D in chimerax but none of the associated numbers. Hence the question. Also is there a way to covert 3d structures into 3d molecules in chimerax with a plugin perhaps? Regards Krish

-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, February 2, 2023 12:47 PM To: Krishnan Raman RKrishnan@BIOCRYST.com Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Your message to ChimeraX-users awaits moderator approval

[EXTERNAL]

Hi Krish, (1) getting data associated with a structure into ChimeraX. If there are specific values you want to assign to atoms or residues, you can do it with "attribute definition format" -- a simple plain-text file described here:

https://link.edgepilot.com/s/0135ec44/fimMJLKy0UmmxsiSc5nMzg?u=https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html

The assigned attributes can be used for coloring, or selecting atoms/residues with values in specific ranges, etc. https://link.edgepilot.com/s/1f7cc291/git0pEihikG9TH_xdQKJgw?u=https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html

Or if you mean something like density map or electrostatic potential map, or sequences and sequence alignments, there are number of formats that ChimeraX reads in addition to atomic coordinates: https://link.edgepilot.com/s/0ae80330/Nb2xJEwhtUWYXSpRHZjCPA?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html%23formats

(2) I don't know how (or whether it is possible) to start multiple instances of chimerax from an HTML file. Somebody else will have to elaborate on that.

My experience with HTML with the special command-execution links is that you start ChimeraX yourself and then can click the links to execute commands in the existing instance. https://link.edgepilot.com/s/b1e84e4d/DNTmcaDwa0uwsSRpqo12Wg?u=https://rbvi.ucsf.edu/chimerax/docs/user/tools/helpviewer.html

I hope this helps, Elaine

---

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 2, 2023, at 10:04 AM, Eric Pettersen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

...

Begin forwarded message:

From: Krishnan Raman Subject: RE: Your message to ChimeraX-users awaits moderator approval Date: February 2, 2023 at 9:47:12 AM PST To: "chimerax-users-owner@cgl.ucsf.edu" chimerax-users-owner@cgl.ucsf.edu

Hi guys

is there a way to get structures + other numerical data into chimerax? I get the structures using a sdf file. I want to get in someother data associated each structure.

How to start multiple instances of chimerax from a html-commands file? Thanks Krish

Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. CONFIDENTIALITY NOTICE

This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Hi Krish, I forgot to mention that there is also a "setattr" command to set one attribute value at a time: https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html

So you could have one such command per structure. It is when you get to a large number of values that it may be nicer to create and read in a separate attribute file (file.defattr opened with "open" command). Best, Elaine

On Feb 2, 2023, at 1:01 PM, Krishnan Raman via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi Elaine, That answered my question accurately. Id id find that reading *.mol files containing 3d coordinates works in chimerax. Let me think about adding numerical values with each structure. Thanks Krish

-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, February 2, 2023 2:58 PM To: Krishnan Raman RKrishnan@BIOCRYST.com Cc: Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: values associated with structures; 2D to 3D?

[EXTERNAL]

Hi Krish, If I understand correctly, the SDF files that you have do not contain 3D atomic coordinates. They only contain 2D "chemical diagrams" -- so they can't be used like real structures. ChimeraX tries to apply chemical detection based on bond lengths and angles, which does not work on these chemical diagrams, since they are typically different in scale as well as being totally flat. Sorry, there is no option to make them into real 3D molecules.

To get 3D structures of the compounds you would instead need to start with something like a SMILES string or a PubChem identifier and use those types of fetches (SMILES or PubChem3D) instead of your SDF files. These types of fetches are done with the "open" command: https://link.edgepilot.com/s/61c9495d/aVeQcBTcUU2_ELnxB5JPKg?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html%23fetch

There is no automatic way to read arbitrary values from SDF files. Instead you would need to open all the structures somehow, then create an attribute assignment file to assign the values. Or, you would need to write a custom python script that reads the values from your files. Somebody else would have to advise on that, as I don't know python.

I hope this helps, Elaine

---

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 2, 2023, at 12:24 PM, Krishnan Raman via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi Elaine, Thanks for the quick reply. I think I was not clear about the first request. I have an sdf file with structure and some aasay value(numeric) associated with each structure. . The sdf option to open files brought up the structures in 2D in chimerax but none of the associated numbers. Hence the question. Also is there a way to covert 3d structures into 3d molecules in chimerax with a plugin perhaps? Regards Krish

-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, February 2, 2023 12:47 PM To: Krishnan Raman RKrishnan@BIOCRYST.com Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Your message to ChimeraX-users awaits moderator approval

[EXTERNAL]

Hi Krish, (1) getting data associated with a structure into ChimeraX. If there are specific values you want to assign to atoms or residues, you can do it with "attribute definition format" -- a simple plain-text file described here:

https://link.edgepilot.com/s/0135ec44/fimMJLKy0UmmxsiSc5nMzg?u=https: //rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html

The assigned attributes can be used for coloring, or selecting atoms/residues with values in specific ranges, etc. https://link.edgepilot.com/s/1f7cc291/git0pEihikG9TH_xdQKJgw?u=https: //rbvi.ucsf.edu/chimerax/docs/user/attributes.html

Or if you mean something like density map or electrostatic potential map, or sequences and sequence alignments, there are number of formats that ChimeraX reads in addition to atomic coordinates: https://link.edgepilot.com/s/0ae80330/Nb2xJEwhtUWYXSpRHZjCPA?u=https: //rbvi.ucsf.edu/chimerax/docs/user/commands/open.html%23formats

(2) I don't know how (or whether it is possible) to start multiple instances of chimerax from an HTML file. Somebody else will have to elaborate on that.

My experience with HTML with the special command-execution links is that you start ChimeraX yourself and then can click the links to execute commands in the existing instance. https://link.edgepilot.com/s/b1e84e4d/DNTmcaDwa0uwsSRpqo12Wg?u=https: //rbvi.ucsf.edu/chimerax/docs/user/tools/helpviewer.html

I hope this helps, Elaine

---

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Feb 2, 2023, at 10:04 AM, Eric Pettersen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

...

Begin forwarded message:

From: Krishnan Raman Subject: RE: Your message to ChimeraX-users awaits moderator approval Date: February 2, 2023 at 9:47:12 AM PST To: "chimerax-users-owner@cgl.ucsf.edu" chimerax-users-owner@cgl.ucsf.edu

Hi guys

is there a way to get structures + other numerical data into chimerax? I get the structures using a sdf file. I want to get in someother data associated each structure.

How to start multiple instances of chimerax from a html-commands file? Thanks Krish

Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. CONFIDENTIALITY NOTICE

This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

---

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Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. CONFIDENTIALITY NOTICE

This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users