[Chimera-users] Problem using Chimera with NLOpredict

Eric Pettersen pett at cgl.ucsf.edu
Mon Jul 10 12:24:54 PDT 2017


Yeah, those files and the instructions no longer match the plugin.  For instance, the instructions say to open the Amide_I.cfg file using the menu entry File->Import -> .cfg file.  Well, there is no such menu entry.  I think you’re going to have to try to figure out the interface by trial and error.  Sorry!

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jul 9, 2017, at 10:45 AM, Roger Hawksworth <r_hawksworth at hotmail.co.uk> wrote:
> 
> Hi Elaine,
> 
> thank you for the info and suggestions.
> 
> I managed to find a separate source for the cfg files but they still seem to be in some "funny" format. If interested see at
> 
> http://sda.iu.edu/nlopredict/index.shtml <http://sda.iu.edu/nlopredict/index.shtml>
> 
> 
> Best Wishes,
>                              Roger H
> 
> From: Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
> Sent: 08 July 2017 15:08
> To: Roger Hawksworth
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Problem using Chimera with NLOpredict
>  
> Hi Roger,
> So (to repeat what was in your Word document):
> 
> Sounds like Chimera in general is working, but then there is an error in the NLOPredict plugin when you follow the example on the NLOPredict site and open one of the data files provided at that site, 
> <http://nlopredict.sourceforge.net/ <http://nlopredict.sourceforge.net/>>
> NLOPredict - Nonlinear Optical Prediction <http://nlopredict.sourceforge.net/>
> nlopredict.sourceforge.net <http://nlopredict.sourceforge.net/>
> NLOPredict. NLOPredict is a nonlinear optical prediction and data analysis tool. Currently, it is implemented as a plugin for the UCSF CHIMERA molecular modeling system.
> 
> 
> 
> We do not develop or distribute that plugin, and my knowledge of it is limited.  Other than your contacting the NLOPredict developers about this problem, my only other idea is that maybe something has changed in Chimera and that the plugin may work better with an older version.  
> 
> I don’t see anything on their website about which version of Chimera is recommended, but NLOPredict was developed several years ago, so instead of version 1.11.2 you might try going back a couple versions and seeing what happens. However, it may be more efficient to contact the NLOPredict developers and just ask what version of Chimera they recommend.
> 
> Chimera release notes (dates of different versions):<http://www.cgl.ucsf.edu/chimera/docs/relnotes.html <http://www.cgl.ucsf.edu/chimera/docs/relnotes.html>>
> UCSF Chimera Release Notes <http://www.cgl.ucsf.edu/chimera/docs/relnotes.html>
> www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>
> Chimera Release Notes. All releases with the same version number have the same feature set across all supported platforms. There will be some visual ...
> 
> 
> Chimera download old versions:
> <http://www.cgl.ucsf.edu/chimera/olddownload.html <http://www.cgl.ucsf.edu/chimera/olddownload.html>>
> Download UCSF Chimera <http://www.cgl.ucsf.edu/chimera/olddownload.html>
> www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>
> Platform Installer, Size, and Checksum Date Notes; Mac OS X: chimera-1.11.1-mac.dmg Size: 104050363 bytes MD5: d9c1c7576a3f42c49b871a818257580b: Sep 22, 2016
> 
> 
> 
> Before all that, probably should try downloading that cfg file afresh to make sure that it just didn’t get into some weird state before you tried to open it.  The cfg files at the NLOPredict website seem to binary, or some format that is not easily viewed, so I can’t really tell anything from looking at 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 Jul 8, 2017, at 3:46 AM, Roger Hawksworth <r_hawksworth at hotmail.co.uk <mailto:r_hawksworth at hotmail.co.uk>> wrote:
> > 
> > Hi,
> > Please see attached Word .docx file which is also contained within the attached .zip file.
> > 
> > Today, 08th July 2017, is the first time that I have used Chimera. Perhaps the .cfg file I tried to use is somehow "corrupt"?
> > Best Wishes,
> >                          Roger H
> > 
> 
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