Re: [Rdkit-discuss] Minimising bits of molecules?
Dear Paolo, Is it possible to add also the option to freeze certain internal coordinates (I am particularly interested in freezing the dihedral angles)? Best wishes, Michal On 26 November 2013 18:09, Paolo Tosco paolo.to...@unito.it wrote: Dear James, I will try to get it done during the weekend - I'll get back to you once it's ready. Best, Paolo On 11/26/2013 05:51 PM, James Davidson wrote: Dear All, I think this is probably one for Paolo – I was looking at fixing certain atoms during MMFF minimisation, but couldn’t find the option… Then I re-read the UGM slides, and found the one titled “Force-field wish list”, and “fixed atoms” were one of the listed items! My intended use-case is the following: 1. Load protein-ligand complex into PyMOL 2. Make some changes to the bound ligand (using the Builder functionality) 3. Select atoms that are allowed to move (manual selection, then use of PyMOL’s ‘flag’ command) 4. Pass the molecule over to RDKit (already incorporated in a plugin we use), to minimise and then pass back (either as a new object, or apply the new coordinates to the existing object in situ) Actually, this process is already well-used by some of our chemists here – as a way of doing some simple modelling / idea exploration – but is currently using a much ‘flakier’ MMFF implementation. So I would definitely like to move to RDKit for the minimisation – any idea when a ‘fixed atoms’ option is likely to be added? Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it http://open3dqsar.org | http://open3dalign.org == -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
[Rdkit-discuss] Minimising bits of molecules?
Dear All, I think this is probably one for Paolo - I was looking at fixing certain atoms during MMFF minimisation, but couldn't find the option... Then I re-read the UGM slides, and found the one titled Force-field wish list, and fixed atoms were one of the listed items! My intended use-case is the following: 1. Load protein-ligand complex into PyMOL 2. Make some changes to the bound ligand (using the Builder functionality) 3. Select atoms that are allowed to move (manual selection, then use of PyMOL's 'flag' command) 4. Pass the molecule over to RDKit (already incorporated in a plugin we use), to minimise and then pass back (either as a new object, or apply the new coordinates to the existing object in situ) Actually, this process is already well-used by some of our chemists here - as a way of doing some simple modelling / idea exploration - but is currently using a much 'flakier' MMFF implementation. So I would definitely like to move to RDKit for the minimisation - any idea when a 'fixed atoms' option is likely to be added? Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __-- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Minimising bits of molecules?
Dear James, I will try to get it done during the weekend - I'll get back to you once it's ready. Best, Paolo On 11/26/2013 05:51 PM, James Davidson wrote: Dear All, I think this is probably one for Paolo -- I was looking at fixing certain atoms during MMFF minimisation, but couldn't find the option... Then I re-read the UGM slides, and found the one titled Force-field wish list, and fixed atoms were one of the listed items! My intended use-case is the following: 1.Load protein-ligand complex into PyMOL 2.Make some changes to the bound ligand (using the Builder functionality) 3.Select atoms that are allowed to move (manual selection, then use of PyMOL's 'flag' command) 4.Pass the molecule over to RDKit (already incorporated in a plugin we use), to minimise and then pass back (either as a new object, or apply the new coordinates to the existing object in situ) Actually, this process is already well-used by some of our chemists here -- as a way of doing some simple modelling / idea exploration -- but is currently using a much 'flakier' MMFF implementation. So I would definitely like to move to RDKit for the minimisation -- any idea when a 'fixed atoms' option is likely to be added? Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- == Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it http://open3dqsar.org | http://open3dalign.org == -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Minimising bits of molecules?
Excellent!
Let me know if there is anything I can do to help.
-greg
On Tuesday, November 26, 2013, Paolo Tosco wrote:
Dear James,
I will try to get it done during the weekend - I'll get back to you once
it's ready.
Best,
Paolo
On 11/26/2013 05:51 PM, James Davidson wrote:
Dear All,
I think this is probably one for Paolo – I was looking at fixing certain
atoms during MMFF minimisation, but couldn’t find the option… Then I
re-read the UGM slides, and found the one titled “Force-field wish list”,
and “fixed atoms” were one of the listed items!
My intended use-case is the following:
1. Load protein-ligand complex into PyMOL
2. Make some changes to the bound ligand (using the Builder
functionality)
3. Select atoms that are allowed to move (manual selection, then
use of PyMOL’s ‘flag’ command)
4. Pass the molecule over to RDKit (already incorporated in a
plugin we use), to minimise and then pass back (either as a new object, or
apply the new coordinates to the existing object in situ)
Actually, this process is already well-used by some of our chemists here –
as a way of doing some simple modelling / idea exploration – but is
currently using a much ‘flakier’ MMFF implementation. So I would
definitely like to move to RDKit for the minimisation – any idea when a
‘fixed atoms’ option is likely to be added?
Kind regards
James
__
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intended for the named addressee(s) only and access to it by anyone else is
unauthorised. If you are not an addressee, any disclosure or copying of the
contents of this email or any action taken (or not taken) in reliance on it
is unauthorised and may be unlawful. If you have received this email in
error, please notify the sender or postmas...@vernalis.comjavascript:_e({},
'cvml', 'postmas...@vernalis.com');.
Email is not a secure method of communication and the Company cannot accept
responsibility for the accuracy or completeness of this message or any
attachment(s). Please check this email for virus infection for which the
Company accepts no responsibility. If verification of this email is sought
then please request a hard copy. Unless otherwise stated, any views or
opinions presented are solely those of the author and do not represent
those of the Company.
The Vernalis Group of Companies
100 Berkshire Place
Wharfedale Road
Winnersh, Berkshire
RG41 5RD, England
Tel: +44 (0)118 938
To access trading company registration and address details, please go to
the Vernalis website at www.vernalis.com and click on the Company
address and registration details link at the bottom of the page..
__
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affects their revenue. With AppDynamics, you get 100% visibility into your
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Paolo Tosco, Ph.D.
Department of Drug Science and Technology
Via Pietro Giuria, 9 - 10125 Torino (Italy)
Tel: +39 011 670 7680 | Mob: +39 348 5537206
Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it javascript:_e({},
'cvml', 'paolo.to...@unito.it');http://open3dqsar.org |
http://open3dalign.org
==
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Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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