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 Best Wishes, Roger H ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 08 July 2017 15:08 To: Roger Hawksworth Cc: chimera-users@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/> NLOPredict - Nonlinear Optical Prediction<http://nlopredict.sourceforge.net/> 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> UCSF Chimera Release Notes<http://www.cgl.ucsf.edu/chimera/docs/relnotes.html> 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> Download UCSF Chimera<http://www.cgl.ucsf.edu/chimera/olddownload.html> 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@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

Hello Francois, (There is a chimerax-users e-mail list, CC’d here.) Note that the surface displayed in Chimera and ChimeraX is the SES, not the SAS. For spacing of points, see the “surface” command option “gridSpacing” — use ChimeraX command “help surface” or view the help at our website: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> Use ChimeraX command “save formats” to see what formats you can save. STL or X3D would include the surface vertices, I believe. For full details on “save” use command “help save” or see the copy here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> 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 10, 2017, at 2:01 AM, Francois BERENGER <berenger@bioreg.kyushu-u.ac.jp> wrote:

Hello, I am not interested by surface normals, the 3D coordinates would be enough.

Is it possible to control the surface sampling of the surfacing algorithm? Like with a number of points per Angstrom^2 parameter? Thanks a lot, Francois.