I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1. Thanks L P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4 Phone: 416-813-5378 (Internal 305378) Web page: https://lab.research.sickkids.ca/howell/ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
Hi, it's also fairly easy to install Boltz-2 in a standalone conda python environment. Best wishes, R Rudy J. Richardson, ScD, DABT Molecular Simulations Laboratory Room M6065 SPH-II 2029 University of Michigan 1415 Washington Heights Ann Arbor, MI 48109-2029 USA Tel: +1-734-936-0769 Fax: +1-734-763-8095 Email: rjrich@umich.edu On Sun, Jun 8, 2025 at 8:56 AM Lynne Howell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1.
Thanks
L
*P. Lynne Howell*
Canada Research Chair (2006-2020)
Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children
Professor, Department of Biochemistry, University of Toronto
*Office and Mailing address: *
Room 20-9-715
Peter Gilgan Centre for Research and Learning (PGCRL)
686 Bay St. Toronto ON M5G 0A4
Phone: 416-813-5378 (Internal 305378)
*Web page: https://lab.research.sickkids.ca/howell <https://lab.research.sickkids.ca/howell>/*
------------------------------
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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/
thanks for the suggestion … the guys in the lab have already done this but it’s very difficult (if not impossible, given the way the hospital has set up security) to access the workstation in the lab when working off site …. Was hoping to be able to work on this in the weekend L ________________________________ From: Rudy Richardson <rjrich@umich.edu> Sent: Sunday, June 8, 2025 9:31:48 AM To: Lynne Howell <howell@sickkids.ca> Cc: Sherwood Casjens via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Boltz-2 You don't often get email from rjrich@umich.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi, it's also fairly easy to install Boltz-2 in a standalone conda python environment. Best wishes, R Rudy J. Richardson, ScD, DABT Molecular Simulations Laboratory Room M6065 SPH-II 2029 University of Michigan 1415 Washington Heights Ann Arbor, MI 48109-2029 USA Tel: +1-734-936-0769 Fax: +1-734-763-8095 Email: rjrich@umich.edu<mailto:rjrich@umich.edu> On Sun, Jun 8, 2025 at 8:56 AM Lynne Howell via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1. Thanks L P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4 Phone: 416-813-5378 (Internal 305378) Web page: https://lab.research.sickkids.ca/howell/ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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 may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
Hi Lynne, I plan on getting Boltz-2 and affinity prediction into ChimeraX probably in late June or July in ChimeraX daily builds. We are planning to release ChimeraX version 1.10 later this week and it will use Boltz-1. I tested Boltz-2 when it was released a few days ago. While it runs on Mac it produces wrong protein folds and ligands with all atoms on top of each other. It worked correctly on Linux. I did not yet try on Windows. A main purpose of putting Boltz into ChimeraX is so that biology researchers can run it on Mac and Windows computers, so I will need to get Boltz-2 working on those before I put it into ChimeraX. Tom
On Jun 8, 2025, at 9:51 AM, Lynne Howell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
thanks for the suggestion … the guys in the lab have already done this but it’s very difficult (if not impossible, given the way the hospital has set up security) to access the workstation in the lab when working off site …. Was hoping to be able to work on this in the weekend L
From: Rudy Richardson <rjrich@umich.edu <mailto:rjrich@umich.edu>> Sent: Sunday, June 8, 2025 9:31:48 AM To: Lynne Howell <howell@sickkids.ca <mailto:howell@sickkids.ca>> Cc: Sherwood Casjens via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Boltz-2
You don't often get email from rjrich@umich.edu <mailto:rjrich@umich.edu>. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> Hi, it's also fairly easy to install Boltz-2 in a standalone conda python environment.
Best wishes,
R
Rudy J. Richardson, ScD, DABT Molecular Simulations Laboratory Room M6065 SPH-II 2029 University of Michigan 1415 Washington Heights Ann Arbor, MI 48109-2029 USA
Tel: +1-734-936-0769 Fax: +1-734-763-8095 Email: rjrich@umich.edu <mailto:rjrich@umich.edu>
On Sun, Jun 8, 2025 at 8:56 AM Lynne Howell via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1.
Thanks
L
P. Lynne Howell
Canada Research Chair (2006-2020)
Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children
Professor, Department of Biochemistry, University of Toronto
Office and Mailing address:
Room 20-9-715
Peter Gilgan Centre for Research and Learning (PGCRL)
686 Bay St. Toronto ON M5G 0A4
Phone: 416-813-5378 (Internal 305378)
Web page: https://lab.research.sickkids.ca/howell/
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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 may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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/
Hi Tom et al., I have Boltz2 running on my local Linux computer. It does rather well with protein folding and co-folding with a protein and small-molecule ligand as long as the ligand is a fairly conventional structure. However, some problems arise with somewhat more exotic structures, such as organophosphorus compounds with chiral phosphorus and/or P=S moieties, which tend to end up as P-SH. I have also tried ferrocene derivatives,which are rejected by Boltz2. Some of the issues with ligands arise when converting 3D structure files in SDF format to SMILES. For this, I get better results using RDKit rather than OpenBabel for the conversion. Best wishes, Rudy Rudy J. Richardson, ScD, DABT Molecular Simulations Laboratory Room M6065 SPH-II 2029 University of Michigan 1415 Washington Heights Ann Arbor, MI 48109-2029 USA Tel: +1-734-936-0769 Fax: +1-734-763-8095 Email: rjrich@umich.edu On Mon, Jun 9, 2025 at 5:09 PM Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Lynne,
I plan on getting Boltz-2 and affinity prediction into ChimeraX probably in late June or July in ChimeraX daily builds. We are planning to release ChimeraX version 1.10 later this week and it will use Boltz-1.
I tested Boltz-2 when it was released a few days ago. While it runs on Mac it produces wrong protein folds and ligands with all atoms on top of each other. It worked correctly on Linux. I did not yet try on Windows. A main purpose of putting Boltz into ChimeraX is so that biology researchers can run it on Mac and Windows computers, so I will need to get Boltz-2 working on those before I put it into ChimeraX.
Tom
On Jun 8, 2025, at 9:51 AM, Lynne Howell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
thanks for the suggestion … the guys in the lab have already done this but it’s very difficult (if not impossible, given the way the hospital has set up security) to access the workstation in the lab when working off site …. Was hoping to be able to work on this in the weekend L
------------------------------ *From:* Rudy Richardson <rjrich@umich.edu> *Sent:* Sunday, June 8, 2025 9:31:48 AM *To:* Lynne Howell <howell@sickkids.ca> *Cc:* Sherwood Casjens via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Subject:* Re: [chimerax-users] Boltz-2
You don't often get email from rjrich@umich.edu. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> Hi, it's also fairly easy to install Boltz-2 in a standalone conda python environment.
Best wishes,
R
Rudy J. Richardson, ScD, DABT Molecular Simulations Laboratory Room M6065 SPH-II 2029 University of Michigan 1415 Washington Heights Ann Arbor, MI 48109-2029 USA
Tel: +1-734-936-0769 Fax: +1-734-763-8095 Email: rjrich@umich.edu
On Sun, Jun 8, 2025 at 8:56 AM Lynne Howell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1.
Thanks
L
*P. Lynne Howell*
Canada Research Chair (2006-2020)
Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children
Professor, Department of Biochemistry, University of Toronto
*Office and Mailing address: *
Room 20-9-715
Peter Gilgan Centre for Research and Learning (PGCRL)
686 Bay St. Toronto ON M5G 0A4
Phone: 416-813-5378 (Internal 305378)
*Web page: https://lab.research.sickkids.ca/howell <https://lab.research.sickkids.ca/howell>/*
------------------------------
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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 may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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/
Hi Rudy, Yep, I have been trying Boltz-2 also, and I saw probably your discussion of this issue with specifying ligands using SMILES strings in Boltz github issue 313 https://github.com/jwohlwend/boltz/issues/313#issuecomment-2956828840 There is a Boltz pull request that tries to allow Boltz to take 3D ligand structures in SDF, Mol2, or PDB format as input instead of SMILES https://github.com/jwohlwend/boltz/pull/40 Unfortunately it describes first converting the 3D structure to SMILES to derive some information Boltz needs, probably bond orders, so this will probably fail in cases where the SMILES string does not capture the molecular structure. I have also been thinking about adding reading of 3D ligand structures for Boltz input and I was intending to not use SMILES at all. But I have not had time. And it probably requires bond orders that may not be in the 3D file. Perhaps we can just have RDKit directly figure out the extra meta-data from the 3D structure instead of going through SMILES. Or possibly SDF or Mol2 has records for all the needed metadata and we could just require that the input files provide the needed data. Tom
On Jun 9, 2025, at 2:24 PM, Rudy Richardson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom et al.,
I have Boltz2 running on my local Linux computer. It does rather well with protein folding and co-folding with a protein and small-molecule ligand as long as the ligand is a fairly conventional structure. However, some problems arise with somewhat more exotic structures, such as organophosphorus compounds with chiral phosphorus and/or P=S moieties, which tend to end up as P-SH. I have also tried ferrocene derivatives,which are rejected by Boltz2. Some of the issues with ligands arise when converting 3D structure files in SDF format to SMILES. For this, I get better results using RDKit rather than OpenBabel for the conversion.
Best wishes,
Rudy
Rudy J. Richardson, ScD, DABT Molecular Simulations Laboratory Room M6065 SPH-II 2029 University of Michigan 1415 Washington Heights Ann Arbor, MI 48109-2029 USA
Tel: +1-734-936-0769 Fax: +1-734-763-8095 Email: rjrich@umich.edu <mailto:rjrich@umich.edu> On Mon, Jun 9, 2025 at 5:09 PM Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Lynne,
I plan on getting Boltz-2 and affinity prediction into ChimeraX probably in late June or July in ChimeraX daily builds. We are planning to release ChimeraX version 1.10 later this week and it will use Boltz-1.
I tested Boltz-2 when it was released a few days ago. While it runs on Mac it produces wrong protein folds and ligands with all atoms on top of each other. It worked correctly on Linux. I did not yet try on Windows. A main purpose of putting Boltz into ChimeraX is so that biology researchers can run it on Mac and Windows computers, so I will need to get Boltz-2 working on those before I put it into ChimeraX.
Tom
On Jun 8, 2025, at 9:51 AM, Lynne Howell via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
thanks for the suggestion … the guys in the lab have already done this but it’s very difficult (if not impossible, given the way the hospital has set up security) to access the workstation in the lab when working off site …. Was hoping to be able to work on this in the weekend L
From: Rudy Richardson <rjrich@umich.edu <mailto:rjrich@umich.edu>> Sent: Sunday, June 8, 2025 9:31:48 AM To: Lynne Howell <howell@sickkids.ca <mailto:howell@sickkids.ca>> Cc: Sherwood Casjens via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Boltz-2
You don't often get email from rjrich@umich.edu <mailto:rjrich@umich.edu>. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> Hi, it's also fairly easy to install Boltz-2 in a standalone conda python environment.
Best wishes,
R
Rudy J. Richardson, ScD, DABT Molecular Simulations Laboratory Room M6065 SPH-II 2029 University of Michigan 1415 Washington Heights Ann Arbor, MI 48109-2029 USA
Tel: +1-734-936-0769 Fax: +1-734-763-8095 Email: rjrich@umich.edu <mailto:rjrich@umich.edu>
On Sun, Jun 8, 2025 at 8:56 AM Lynne Howell via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1.
Thanks
L
P. Lynne Howell
Canada Research Chair (2006-2020)
Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children
Professor, Department of Biochemistry, University of Toronto
Office and Mailing address:
Room 20-9-715
Peter Gilgan Centre for Research and Learning (PGCRL)
686 Bay St. Toronto ON M5G 0A4
Phone: 416-813-5378 (Internal 305378)
Web page: https://lab.research.sickkids.ca/howell/
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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 may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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/
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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/
Hi Tom, It would be great if you could figure out how to bypass SMILES altogether! Good luck! Rudy On Mon, Jun 9, 2025 at 7:27 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Rudy,
Yep, I have been trying Boltz-2 also, and I saw probably your discussion of this issue with specifying ligands using SMILES strings in Boltz github issue 313
https://github.com/jwohlwend/boltz/issues/313#issuecomment-2956828840
There is a Boltz pull request that tries to allow Boltz to take 3D ligand structures in SDF, Mol2, or PDB format as input instead of SMILES
https://github.com/jwohlwend/boltz/pull/40
Unfortunately it describes first converting the 3D structure to SMILES to derive some information Boltz needs, probably bond orders, so this will probably fail in cases where the SMILES string does not capture the molecular structure. I have also been thinking about adding reading of 3D ligand structures for Boltz input and I was intending to not use SMILES at all. But I have not had time. And it probably requires bond orders that may not be in the 3D file. Perhaps we can just have RDKit directly figure out the extra meta-data from the 3D structure instead of going through SMILES. Or possibly SDF or Mol2 has records for all the needed metadata and we could just require that the input files provide the needed data.
Tom
On Jun 9, 2025, at 2:24 PM, Rudy Richardson via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom et al.,
I have Boltz2 running on my local Linux computer. It does rather well with protein folding and co-folding with a protein and small-molecule ligand as long as the ligand is a fairly conventional structure. However, some problems arise with somewhat more exotic structures, such as organophosphorus compounds with chiral phosphorus and/or P=S moieties, which tend to end up as P-SH. I have also tried ferrocene derivatives,which are rejected by Boltz2. Some of the issues with ligands arise when converting 3D structure files in SDF format to SMILES. For this, I get better results using RDKit rather than OpenBabel for the conversion.
Best wishes,
Rudy
Rudy J. Richardson, ScD, DABT Molecular Simulations Laboratory Room M6065 SPH-II 2029 University of Michigan 1415 Washington Heights Ann Arbor, MI 48109-2029 USA
Tel: +1-734-936-0769 Fax: +1-734-763-8095 Email: rjrich@umich.edu
On Mon, Jun 9, 2025 at 5:09 PM Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Lynne,
I plan on getting Boltz-2 and affinity prediction into ChimeraX probably in late June or July in ChimeraX daily builds. We are planning to release ChimeraX version 1.10 later this week and it will use Boltz-1.
I tested Boltz-2 when it was released a few days ago. While it runs on Mac it produces wrong protein folds and ligands with all atoms on top of each other. It worked correctly on Linux. I did not yet try on Windows. A main purpose of putting Boltz into ChimeraX is so that biology researchers can run it on Mac and Windows computers, so I will need to get Boltz-2 working on those before I put it into ChimeraX.
Tom
On Jun 8, 2025, at 9:51 AM, Lynne Howell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
thanks for the suggestion … the guys in the lab have already done this but it’s very difficult (if not impossible, given the way the hospital has set up security) to access the workstation in the lab when working off site …. Was hoping to be able to work on this in the weekend L
------------------------------ *From:* Rudy Richardson <rjrich@umich.edu> *Sent:* Sunday, June 8, 2025 9:31:48 AM *To:* Lynne Howell <howell@sickkids.ca> *Cc:* Sherwood Casjens via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Subject:* Re: [chimerax-users] Boltz-2
You don't often get email from rjrich@umich.edu. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> Hi, it's also fairly easy to install Boltz-2 in a standalone conda python environment.
Best wishes,
R
Rudy J. Richardson, ScD, DABT Molecular Simulations Laboratory Room M6065 SPH-II 2029 University of Michigan 1415 Washington Heights Ann Arbor, MI 48109-2029 USA
Tel: +1-734-936-0769 Fax: +1-734-763-8095 Email: rjrich@umich.edu
On Sun, Jun 8, 2025 at 8:56 AM Lynne Howell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1.
Thanks
L
*P. Lynne Howell*
Canada Research Chair (2006-2020)
Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children
Professor, Department of Biochemistry, University of Toronto
*Office and Mailing address: *
Room 20-9-715
Peter Gilgan Centre for Research and Learning (PGCRL)
686 Bay St. Toronto ON M5G 0A4
Phone: 416-813-5378 (Internal 305378)
*Web page: https://lab.research.sickkids.ca/howell <https://lab.research.sickkids.ca/howell>/*
------------------------------
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ 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/
------------------------------
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participants (3)
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Lynne Howell -
Rudy Richardson -
Tom Goddard