Opened 19 months ago

Closed 19 months ago

Last modified 18 months ago

#14942 closed enhancement (fixed)

MOE docking results

Reported by: RKrishnan@… Owned by: Eric Pettersen
Priority: moderate Milestone:
Component: Surface/Binding Analysis Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Hi Eric,
Thanks. I have attached a mol2 format file saved from moe mdb.
You can go ahead and add me to the feature request recipients…
Regards
krish

From: Eric Pettersen <pett@…>
Sent: Thursday, March 28, 2024 6:24 PM
To: Krishnan Raman <RKrishnan@…>
Cc: ChimeraX Users Help <chimerax-users@…>
Subject: Re: [chimerax-users] *.mdb files from MOE (chemcomp)

[EXTERNAL]

Hi Krish,
As per that ViewDockX help page, the Mol2 files that ViewDockX can handle come from UCSF DOCK versions 4-7, and GOLD. MOE apparently writes its own variant of Mol2 format, which isn't surprising. It might be easy to extend ViewDockX to handle the MOE version of Mol2, and it might not. In either case I would need an example of a MOE Mol2 file, which could be a trivial toy example with just a few compounds in it. If you were willing to supply such a file, I would open a feature-request ticket in our bug-tracking database with you on the recipient list so that you would be kept informed about progress on implementing ViewDockX support for MOE Mol2.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Mar 28, 2024, at 2:51 PM, Krishnan Raman via ChimeraX-users <chimerax-users@…> wrote:

Hi Elaine,
MOE can write *.mol2 files. I used one of those. I could not use viewdockx on that model.
Wonder what was missing in that file…..

<image001.png>

From: Elaine Meng <meng@…>
Sent: Thursday, March 28, 2024 3:37 PM
To: Krishnan Raman <RKrishnan@…>
Cc: chimerax-users@…
Subject: Re: [chimerax-users] *.mdb files from MOE (chemcomp)

[EXTERNAL]

Hello Krish,
It all depends on what format the MOE docking results are, or can optionally be written, in. Further, not all formats that ChimeraX can read and display as atomic coordinates are interpreted specifically as docking results that will be listed in and interact properly with the ViewDockX interface. Some formats are merely shown as atomic structures but do not "talk" to ViewDockX because they don't have the specific score records expected for a specific format.

For a list of the atomic formats that ChimeraX reads, see:
<​https://link.edgepilot.com/s/cee5f41f/3qU0LsnJYE6FzcLQpoC5qA?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html%23atomic>

For a list of the types of docking results recognized as such by the ChimeraX ViewDockX, see:
<​https://link.edgepilot.com/s/18baa070/AzeY3IWbekutdI3S9h4WzQ?u=https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>

So if the above are not included amongst the MOE output options, you would have to develop a format conversion process to generate one of them.

I hope this helps,
Elaine

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

On Mar 28, 2024, at 12:22 PM, Krishnan Raman via ChimeraX-users <chimerax-users@…> wrote:

how to convert docking poses from MOE software to be read into chimerax?
thanks
Krish
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Attachments (1)

7353.mol2​ (41.6 KB ) - added by RKrishnan@… 19 months ago.
Added by email2trac

Download all attachments as: .zip

Change History (7)

comment:1 by RKrishnan@…, 19 months ago 

Hi Eric,
Have attached a *.mol2 file saved from MOE for chimerax read and using viewDOCKx command.
Thanks
Krish

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, April 9, 2024 12:40 PM
To: Krishnan Raman <RKrishnan@BIOCRYST.com>; pett@cgl.ucsf.edu
Cc: meng@cgl.ucsf.edu
Subject: [ChimeraX] #14942: MOE docking results

[EXTERNAL]

#14942: MOE docking results
--------------------------------------+-------------------------------
 Reporter:  RKrishnan@…               |               Owner:  pett
     Type:  enhancement               |              Status:  assigned
 Priority:  moderate                  |           Milestone:
Component:  Surface/Binding Analysis  |             Version:
 Keywords:                            |          Blocked By:
 Blocking:                            |  Notify when closed:
 Platform:  all                       |             Project:  ChimeraX
--------------------------------------+-------------------------------
 Hi Eric,
 Thanks. I have attached a mol2 format file saved from moe mdb.
 You can go ahead and add me to the feature request recipients…  Regards  krish

 From: Eric Pettersen <pett@cgl.ucsf.edu>
 Sent: Thursday, March 28, 2024 6:24 PM
 To: Krishnan Raman <RKrishnan@BIOCRYST.com>
 Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
 Subject: Re: [chimerax-users] *.mdb files from MOE (chemcomp)

 [EXTERNAL]

 Hi Krish,
 As per that ViewDockX help page, the Mol2 files that ViewDockX can handle  come from UCSF DOCK versions 4-7, and GOLD.  MOE apparently writes its own  variant of Mol2 format, which isn't surprising.  It might be easy to  extend ViewDockX to handle the MOE version of Mol2, and it might not.  In  either case I would need an example of a MOE Mol2 file, which could be a  trivial toy example with just a few compounds in it.  If you were willing  to supply such a file, I would open a feature-request ticket in our bug-  tracking database with you on the recipient list so that you would be kept  informed about progress on implementing ViewDockX support for MOE Mol2.

 --Eric

 Eric Pettersen
 UCSF Computer Graphics Lab



 On Mar 28, 2024, at 2:51 PM, Krishnan Raman via ChimeraX-users <chimerax-  users@cgl.ucsf.edu> wrote:

 Hi Elaine,
 MOE can write *.mol2 files. I used one of those. I could not use viewdockx  on that model.
 Wonder what was missing in that file…..

 <image001.png>

 -----Original Message-----
 From: Elaine Meng <meng@cgl.ucsf.edu>
 Sent: Thursday, March 28, 2024 3:37 PM
 To: Krishnan Raman <RKrishnan@BIOCRYST.com>
 Cc: chimerax-users@cgl.ucsf.edu
 Subject: Re: [chimerax-users] *.mdb files from MOE (chemcomp)

 [EXTERNAL]

 Hello Krish,
 It all depends on what format the MOE docking results are, or can  optionally be written, in. Further, not all formats that ChimeraX can read  and display as atomic coordinates are interpreted specifically as docking  results that will be listed in and interact properly with the ViewDockX  interface.  Some formats are merely shown as atomic structures but do not  "talk" to ViewDockX because they don't have the specific score records  expected for a specific format.

 For a list of the atomic formats that ChimeraX reads, see:
 <https://link.edgepilot.com/s/cee5f41f/3qU0LsnJYE6FzcLQpoC5qA?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html%23atomic>

 For a list of the types of docking results recognized as such by the  ChimeraX ViewDockX, see:
 <https://link.edgepilot.com/s/18baa070/AzeY3IWbekutdI3S9h4WzQ?u=https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>

 So if the above are not included amongst the MOE output options, you would  have to develop a format conversion process to generate one of them.

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

 > On Mar 28, 2024, at 12:22 PM, Krishnan Raman via ChimeraX-users  <chimerax-users@cgl.ucsf.edu> wrote:
 >
 > how to convert docking poses from MOE software to be read into chimerax?
 > thanks
 > Krish
 > 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.



 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.
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 <bcx7353.mol2>
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7353.mol2​

by RKrishnan@…, 19 months ago

Attachment: 7353.mol2​ added

Added by email2trac

comment:2 by Eric Pettersen, 19 months ago

Resolution: → fixed
Status: assigned → closed

Okay, tomorrow's build will support the MOE files you supplied in ViewDockX. Currently is shows all the contents of the PROPERTY_DATA section of those files as columns in the ViewDock table, but if there are columns that are never useful please let me know and I can suppress them.

comment:3 by RKrishnan@…, 18 months ago 

Hi Eric,
thanks for implementing viewdockx to read MOE's version of  *.mol2. works great.
regards,
Krishnan
________________________________
From: Krishnan Raman
Sent: Tuesday, April 9, 2024 3:00 PM
To: ChimeraX-bugs@cgl.ucsf.edu <ChimeraX-bugs@cgl.ucsf.edu>
Subject: RE: [ChimeraX] #14942: MOE docking results

Hi Eric,
Have attached a *.mol2 file saved from MOE for chimerax read and using viewDOCKx command.
Thanks
Krish

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, April 9, 2024 12:40 PM
To: Krishnan Raman <RKrishnan@BIOCRYST.com>; pett@cgl.ucsf.edu
Cc: meng@cgl.ucsf.edu
Subject: [ChimeraX] #14942: MOE docking results

[EXTERNAL]

#14942: MOE docking results
--------------------------------------+-------------------------------
 Reporter:  RKrishnan@…               |               Owner:  pett
     Type:  enhancement               |              Status:  assigned
 Priority:  moderate                  |           Milestone:
Component:  Surface/Binding Analysis  |             Version:
 Keywords:                            |          Blocked By:
 Blocking:                            |  Notify when closed:
 Platform:  all                       |             Project:  ChimeraX
--------------------------------------+-------------------------------
 Hi Eric,
 Thanks. I have attached a mol2 format file saved from moe mdb.
 You can go ahead and add me to the feature request recipients…  Regards  krish

 From: Eric Pettersen <pett@cgl.ucsf.edu>
 Sent: Thursday, March 28, 2024 6:24 PM
 To: Krishnan Raman <RKrishnan@BIOCRYST.com>
 Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
 Subject: Re: [chimerax-users] *.mdb files from MOE (chemcomp)

 [EXTERNAL]

 Hi Krish,
 As per that ViewDockX help page, the Mol2 files that ViewDockX can handle  come from UCSF DOCK versions 4-7, and GOLD.  MOE apparently writes its own  variant of Mol2 format, which isn't surprising.  It might be easy to  extend ViewDockX to handle the MOE version of Mol2, and it might not.  In  either case I would need an example of a MOE Mol2 file, which could be a  trivial toy example with just a few compounds in it.  If you were willing  to supply such a file, I would open a feature-request ticket in our bug-  tracking database with you on the recipient list so that you would be kept  informed about progress on implementing ViewDockX support for MOE Mol2.

 --Eric

 Eric Pettersen
 UCSF Computer Graphics Lab



 On Mar 28, 2024, at 2:51 PM, Krishnan Raman via ChimeraX-users <chimerax-  users@cgl.ucsf.edu> wrote:

 Hi Elaine,
 MOE can write *.mol2 files. I used one of those. I could not use viewdockx  on that model.
 Wonder what was missing in that file…..

 <image001.png>

 -----Original Message-----
 From: Elaine Meng <meng@cgl.ucsf.edu>
 Sent: Thursday, March 28, 2024 3:37 PM
 To: Krishnan Raman <RKrishnan@BIOCRYST.com>
 Cc: chimerax-users@cgl.ucsf.edu
 Subject: Re: [chimerax-users] *.mdb files from MOE (chemcomp)

 [EXTERNAL]

 Hello Krish,
 It all depends on what format the MOE docking results are, or can  optionally be written, in. Further, not all formats that ChimeraX can read  and display as atomic coordinates are interpreted specifically as docking  results that will be listed in and interact properly with the ViewDockX  interface.  Some formats are merely shown as atomic structures but do not  "talk" to ViewDockX because they don't have the specific score records  expected for a specific format.

 For a list of the atomic formats that ChimeraX reads, see:
 <https://link.edgepilot.com/s/cee5f41f/3qU0LsnJYE6FzcLQpoC5qA?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html%23atomic>

 For a list of the types of docking results recognized as such by the  ChimeraX ViewDockX, see:
 <https://link.edgepilot.com/s/18baa070/AzeY3IWbekutdI3S9h4WzQ?u=https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>

 So if the above are not included amongst the MOE output options, you would  have to develop a format conversion process to generate one of them.

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

 > On Mar 28, 2024, at 12:22 PM, Krishnan Raman via ChimeraX-users  <chimerax-users@cgl.ucsf.edu> wrote:
 >
 > how to convert docking poses from MOE software to be read into chimerax?
 > thanks
 > Krish
 > 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.



 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.



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 Archives:
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 /chimerax-users@cgl.ucsf.edu/



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 <bcx7353.mol2>
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comment:4 by Eric Pettersen, 18 months ago

Glad to hear it's working for you.

--Eric

comment:5 by RKrishnan@…, 18 months ago 

hide #1.2-11 models
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read properties of undefined (reading 'id')
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read properties of undefined (reading 'id')
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read properties of undefined (reading 'id')
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read properties of undefined (reading 'id')
Compositor returned null texture
Hi Eric,

I get this eeror messages when trying plot my S values (they  are -ve numbers)?
Can I do anything to fix this?
thanks
krish

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, April 25, 2024 11:51 AM
To: Krishnan Raman <RKrishnan@BIOCRYST.com>; pett@cgl.ucsf.edu
Cc: meng@cgl.ucsf.edu
Subject: Re: [ChimeraX] #14942: MOE docking results

[EXTERNAL]

#14942: MOE docking results
-----------------------------------------------+--------------------
          Reporter:  RKrishnan@\u2026               |      Owner:  pett
              Type:  enhancement               |     Status:  closed
          Priority:  moderate                  |  Milestone:
         Component:  Surface/Binding Analysis  |    Version:
        Resolution:  fixed                     |   Keywords:
        Blocked By:                            |   Blocking:
Notify when closed:                            |   Platform:  all
           Project:  ChimeraX                  |
-----------------------------------------------+--------------------
Comment (by pett):

 Glad to hear it's working for you.

 --Eric
--
Ticket URL: <https://link.edgepilot.com/s/de128b44/7R50iieDMEiKtjQSJfafsg?u=https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/14942%23comment:4>
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comment:6 by Eric Pettersen, 18 months ago

I have applied a fix. Try tomorrow's build and let me know if it helps.

--Eric

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