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…..
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-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Sent: Thursday, March 28, 2024 3:37 PM To: Krishnan Raman <RKrishnan@BIOCRYST.com mailto:RKrishnan@BIOCRYST.com> Cc: chimerax-users@cgl.ucsf.edu mailto: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.... 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.... 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 mailto: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.
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