Warning notification for copying an ornament

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Somayeh Zeinalilathori

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Feb 22, 2021, 2:37:06 PM2/22/21
to NMR POKY/SPARKY USER GROUP
Hi, 

I use NMR-FAM sparky for the manual chemical shift assignments of my protein. I used the oc/op command for copying ornaments between CBCACONH/HNCACB. Everything was ok except recently, I kept receiving this notification " you need to select a spectrum to copy the assignment from..." with every single click on any spectra- even when I didn't use this command. I tried restarting NMR-FAM sparky and my laptop (MacBook pro, Catalina) and unfortunately, neither one worked. It is very annoying and makes the manual assignments very slower than it is. Is there any way to fix this?

Regards, 
Somayeh

Lee, Woonghee

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Feb 22, 2021, 2:47:20 PM2/22/21
to Somayeh Zeinalilathori, NMR POKY/SPARKY USER GROUP

Dear Somayeh,

 

Can you try Poky and see if that still exists?

https://poky.clas.ucdenver.edu

 

Poky is a superset of NMRFAM-SPARKY so you can just use as you did.

Let me know if that solves the problem.

 

Best,

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://sites.google.com/view/wlee-group 

https://poky.clas.ucdenver.edu

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

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Somayeh Zeinalilathori

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Feb 22, 2021, 3:56:55 PM2/22/21
to NMR POKY/SPARKY USER GROUP
Dear Woonghee, 

Thanks for quick reply. It sounds Poky is not compatible with my laptop version (Dyld Error Message:
  Library not loaded: /opt/X11/*/libX11.6.dylib
  Referenced from: /private/var/folders/*/poky.app/Contents/MacOS/poky
  Reason: Incompatible library version: poky requires version 11.0.0 or later, but libX11.6.dylib provides version 10.0.0)

Regrads, 
Somayeh
  

Here is the whole error message: 
Process:               poky [2553]
Path:                  /private/var/folders/*/poky.app/Contents/MacOS/poky
Identifier:            com.yourcompany.poky
Version:               0
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           poky [2553]
User ID:               501

Date/Time:             2021-02-22 15:47:47.061 -0500
OS Version:            macOS 11.2.1 (20D74)
Report Version:        12
Bridge OS Version:     5.2 (18P4346)
Anonymous UUID:        0019512E-D9BA-406F-EB93-A42375FD144C

Sleep/Wake UUID:       3D4B2F09-193E-489F-B0E4-058DD5141EA2

Time Awake Since Boot: 1000 seconds

System Integrity Protection: enabled

Notes:                 Translocated Process

Crashed Thread:        0

Exception Type:        EXC_CRASH (SIGABRT)
Exception Codes:       0x0000000000000000, 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

Termination Reason:    DYLD, [0x3] Wrong version

Application Specific Information:
dyld: launch, loading dependent libraries

Dyld Error Message:
  Library not loaded: /opt/X11/*/libX11.6.dylib
  Referenced from: /private/var/folders/*/poky.app/Contents/MacOS/poky
  Reason: Incompatible library version: poky requires version 11.0.0 or later, but libX11.6.dylib provides version 10.0.0

Binary Images:
       0x107d0a000 -        0x107ffdfff +com.yourcompany.poky (0) <A8D716C8-8517-3DEA-8453-0E32DF534A77> /var/folders/*/poky.app/Contents/MacOS/poky
       0x108099000 -        0x10827cfff +libpython3.7m.dylib (0) <10E72354-B49D-3E2C-9898-231688810F22> /var/folders/*/poky.app/Contents/Frameworks/libpython3.7m.dylib
       0x108329000 -        0x10844efff +libtcl8.6.dylib (8.6.8 - 8.6.8) <2482C58E-F209-3A0D-AD87-93984A18E413> /var/folders/*/poky.app/Contents/Frameworks/tcl-tk-x11/lib/libtcl8.6.dylib
       0x108484000 -        0x108559fff +libtk8.6.dylib (8.6.8 - 8.6.8) <841BC240-4CF1-3A83-B74F-2ECCBF8C9960> /var/folders/*/poky.app/Contents/Frameworks/tcl-tk-x11/lib/libtk8.6.dylib
       0x1097a3000 -        0x10983efff  dyld (832.7.3) <0D4EA85F-7E30-338B-9215-314A5A5539B6> /usr/lib/dyld

Model: MacBookPro15,4, BootROM 1554.80.3.0.0 (iBridge: 18.16.14346.0.0,0), 4 processors, Quad-Core Intel Core i5, 1.4 GHz, 16 GB, SMC 
Graphics: kHW_IntelIrisGraphics645Item, Intel Iris Plus Graphics 645, spdisplays_builtin
Memory Module: BANK 0/ChannelA-DIMM0, 8 GB, LPDDR3, 2133 MHz, SK Hynix, -
Memory Module: BANK 2/ChannelB-DIMM0, 8 GB, LPDDR3, 2133 MHz, SK Hynix, -
AirPort: spairport_wireless_card_type_airport_extreme, wl0: Dec  9 2020 01:09:28 version 16.20.293.6.3.6.96 FWID 01-72ab9dcc
Bluetooth: Version 8.0.3d9, 3 services, 27 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
USB Device: USB 3.1 Bus
USB Device: Apple T2 Bus
USB Device: Touch Bar Backlight
USB Device: Touch Bar Display
USB Device: Apple Internal Keyboard / Trackpad
USB Device: Headset
USB Device: Ambient Light Sensor
USB Device: FaceTime HD Camera (Built-in)
USB Device: Apple T2 Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 63.3


Lee, Woonghee

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Feb 22, 2021, 3:59:21 PM2/22/21
to Somayeh Zeinalilathori, NMR POKY/SPARKY USER GROUP

Hi Somayeh,

 

It looks your XQuartz is old. Just update it and it will work

 

Best,

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://sites.google.com/view/wlee-group 

https://poky.clas.ucdenver.edu

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

Somayeh Zeinalilathori

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Feb 22, 2021, 4:12:46 PM2/22/21
to NMR POKY/SPARKY USER GROUP
Ok, Thanks!

Lee, Woonghee

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Feb 22, 2021, 4:14:01 PM2/22/21
to Somayeh Zeinalilathori, NMR POKY/SPARKY USER GROUP

Let us know here if that resolves the issue. That will help following users.

Thanks,

Somayeh Zeinalilathori

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Feb 22, 2021, 7:24:53 PM2/22/21
to NMR POKY/SPARKY USER GROUP
Dear Woonghee, 
Unfortunately, because of some software issues, I cannot use the newer version of XQuartz. 
For the ac/ap warning I reported, it was just because of the pointer mode which I mistakenly set in the assignment copy mode. Going back to zoom/select mode solved the warning issue. 
Thanks again. 

Regards, 
Somayeh

Lee, Woonghee

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Feb 22, 2021, 7:30:13 PM2/22/21
to Somayeh Zeinalilathori, NMR POKY/SPARKY USER GROUP

Okay. It is good to know you found the problem and no longer an issue anyways.

One of the XQuartz issue that I’ve found is that, sometimes when you install XQuartz through non official way besides xquartz.org, X11 libraries are installed in other places not /opt/X11 and make links to /opt/X11 and it makes the user unable to install XQuartz from xquartz.org. In that case, you have to remove /opt/X11 manually before installation XQuartz. I am sure if that was it though.

 

W   

Lee, Woonghee

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Mar 6, 2021, 2:54:36 PM3/6/21
to Somayeh Zeinalilathori, NMR POKY/SPARKY USER GROUP
It looks like the latest XQuartz brings 32 bits libraries again. You would not have the issue related to tha.

From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Somayeh Zeinalilathori <szei...@udel.edu>
Sent: Monday, February 22, 2021 5:24:53 PM
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