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  • Alignment in ezCADD/NGL Open ezCADD website ( the console of your browser. (Here is how to open it in different browser: https://kb.mailster ...
    Posted Jul 2, 2019, 3:05 PM by Danny Xu
  • Outcome server windows 10 remote desktop using rdpwrap RDPWrap on 10.0.17134.706Edit:  C:\Program Files\RDP Wrapper\rdwrap.ini, it worked for me. Add this to the ...
    Posted May 31, 2019, 9:13 AM by Danny Xu
  • Is it possible to use a threading adapter (e.g. M25 to RMS) and use a Nikon lens on the EVOS? The short answer is that Nikon and Olympus objectives are NOT typically compatible on the same optical system (there are a few exceptions). The key reason is that there will ...
    Posted May 15, 2019, 10:30 AM by Danny Xu
  • Confocal and Widefield Image Processing Z-Stack Step Size ...
    Posted May 7, 2019, 8:35 PM by Danny Xu
  • EVOS LED Light Cube for DASPEI DASPEI dye (λEx/λ Em = 461/589 nm). Our EVOS FL system (AMAFD1000) contains these 4 light cubes: AMEP-4652 (RFP, Ex: 531/40 Em: 593/40)  AMEP-4650 (DAPI ...
    Posted May 7, 2019, 2:01 PM by Danny Xu
  • XAMPP  Auto installed Apache, PHP, and Perl, MySQL, can use MariaDB already installed. set up phpMyAdmin to automatically log in as user. I  also created a database user that has full ...
    Posted Feb 7, 2019, 2:24 PM by Danny Xu
  • Windows 10 in-place reinstall an in-place upgrade worked to fix our instance of Windows 10 that couldn't otherwise ...
    Posted Dec 26, 2018, 11:20 AM by Danny Xu
  • sudo preserve environment variables sudo -E su username -c 'commands'
    Posted Dec 3, 2018, 1:42 PM by Danny Xu
  • IP address lookup and block To get country and domain info from IP:geoiplookup IP_addresshost IP_address/domain_namedig whoissudo iptables -I INPUT -s x.x.x.x/32 -j DROP ...
    Posted Dec 3, 2018, 1:34 PM by Danny Xu
  • Schrodinger Installation on OpenSUSE, SUSE vi INSTALLis_sles_sled_12_sp1() {    _sles_12_sp1=`lsb_release -d 2> /dev/null | grep -e "SUSE Linux Enterprise Desktop 12\s*$" -e "SUSE Linux Enterprise Server 12 ...
    Posted Nov 17, 2018, 9:28 PM by Danny Xu
  • Mirror a website using wget and VisualWget VWget for Windows to check:--mirror --convert-links --adjust-extension --page-requisites --no-parent --html-extension--mirror ...
    Posted Nov 8, 2018, 1:33 PM by Danny Xu
  • Hide OneDrive Sync Check Mark
    Posted Oct 31, 2018, 6:38 PM by Danny Xu
  • GPT vs MBR Windows can only boot from GPT on UEFI-based computers running 64-bit versions of Windows 10, 8, 7, Vista, and corresponding server versions. All versions of Windows 10, 8 ...
    Posted Oct 31, 2018, 9:47 AM by Danny Xu
  • error while loading shared libraries: cannot open shared object file: No such file or directorySolution: search for "libstdc" in yast2, most likely libstdc++33-32bit package ...
    Posted Oct 23, 2018, 10:05 AM by Danny Xu
  • Windows 10 update "your virus and threat protection is managed by your organization" ...
    Posted Oct 23, 2018, 8:26 AM by Danny Xu
  • Pin a folder to Task bar from Windows File Explorer and ...
    Posted Oct 31, 2018, 9:56 AM by Danny Xu
  • Adobe Acrobat OCR text recognition renderable text error Issue When you start the Recognize Text Using OCR command, Adobe Acrobat returns the following error:"Acrobat could ...
    Posted Oct 20, 2018, 5:06 PM by Danny Xu
  • Windows Log file for Crash, etc.
    Posted Oct 11, 2018, 2:58 PM by Danny Xu
  • PSCI 6670 CADD I For oddt environment, installed oddt,  openbabel 2.4.0 from oddt channel, rdkit/chemfp from bioconda channel For rotatable bonds in Openbabel, I need to modify plugindefine.txt in this ...
    Posted Oct 1, 2018, 1:21 PM by Danny Xu
  • Create LVM over RAID0 This section will convert the two RAIDs into physical volumes (PVs). Then combine those PVs into a volume group (VG ...
    Posted Sep 25, 2018, 12:27 PM by Danny Xu
  • Dell T5500 Opensuse 42.3 Installation Kernel Parameter Need to tweak ACPI setting to install 42.3 installation, need to set acpi=offAfter installation, remove acpi ...
    Posted Aug 28, 2018, 4:16 PM by Danny Xu
  • Linux strings command Process text in a binary file `which cat` | grep license
    Posted Aug 27, 2018, 9:39 AM by Danny Xu
  • SSD NVME M2 Speed Performance Test For Micron/Crucial SSD, There is Momentum Cache  option. Download and install Storage Executive option. Samsung regular ...
    Posted Oct 12, 2018, 1:50 PM by Danny Xu
  • SAS and Python, SASPy, SAS_Kernel for Jupyter Notebook SAS Programming for R Users (Course Materials) SAS environments outside of SAS University Edition, here's what you need to ...
    Posted Mar 27, 2018, 6:23 PM by Danny Xu
  • Log compilation, installation steps ./configure --prefix=/home/you/mpich-install  2>&1 | tee config.log  (bash)|& tee (csh)make VERBOSE=1 |& tee make.log (for csh and tcsh) make VERBOSE=1 2>&1 | tee ...
    Posted Feb 15, 2018, 9:27 AM by Danny Xu
  • Linux hardware info sudo /usr/sbin/dmidecodFor details:
    Posted Feb 14, 2018, 2:45 PM by Danny Xu
  • M.2 drive SSD vs NVMe Are all M.2 drives NVMe? No. Remember, M.2 is just the form factor. M.2 drives can come in SATA versions (like the Crucial MX300 M.2 for ...
    Posted Feb 7, 2018, 11:13 AM by Danny Xu
  • View and convert SVG file on Linux and Windows On SUSE, install rsvg-view from yast2Viewer:  rsvg-view-3 filename.svgConverter:  -f, --format=[png, pdf, ps, eps, svg, xml, recording] rsvg-convert C2-C1-C3-C6.svg ...
    Posted Feb 6, 2018, 10:58 AM by Danny Xu
  • Sqlite vs MySQL
    Posted Jan 14, 2018, 5:21 PM by Danny Xu
  • tar to stdout tar xvf archive.tar -O | lesstar xvf archive.tar -O | grep [ ]For a file inside tar filetar xvf archive.tar file_with_path -O | lesstar xvf archive ...
    Posted Jan 10, 2018, 9:07 PM by Danny Xu
  • CXX11 compilation error If you get linker errors about undefined references to symbols that involve types in the std::__cxx11 namespace or ...
    Posted Jan 6, 2018, 10:00 AM by Danny Xu
  • Amber16 + AmberTool17 installation sudo conda create -n amber16 python=2.7install the following packages:numpymatplotlibscipyipythonnotebookcythonsudo yast2install  libbz2-1 libbz2-develexport AMBERHOME=/garlic/apps/Downloads ...
    Posted Feb 15, 2018, 3:46 PM by Danny Xu
  • MDL Mol/SDF V2000 vs V3000 Most apps: obabel, ChemAxon etc. can handle the conversion: ...
    Posted Dec 24, 2017, 3:31 PM by Danny Xu
  • CMake find OpenBabel installed in Conda The magic line is in cmake/modules/FindOpenBabel2.cmake                NAMES                        openbabel/obconversion.h                        openbabel-2.0/openbabel/obconversion.h
    Posted Dec 21, 2017, 1:17 PM by Danny Xu
  • Install gnina and Caffe clone cd gninaTip: vi CMakeCache.txt to debugCreate conda env gnina with python2.7 and install ...
    Posted Jan 5, 2018, 8:09 PM by Danny Xu
  • Minerve2 Backup Procedure 1. login to minerve2 and package all files in your home folder to a tar filenohup tar cvpf minerve2_backup.tar . >& minerve2_backup.log &tail -f minerve2_backup.log ...
    Posted Dec 4, 2017, 4:48 PM by Danny Xu
  • LVM commands on an external eSata/USB3 enclosure Volume Group commands vgscan Scans all the disks for volume groups and rebuilds the LVM cache file, also displays the volume groups. vgchange -a n/y my_volume_group Deactivate ...
    Posted Dec 4, 2017, 2:53 PM by Danny Xu
  • Auto delete Gmail Step 1: Go to Settings -> Filters -> Create a new filter Step 2: Type the following into "Has the words" field: category:promotions older_than:90dor before:2011/01/15 ...
    Posted Dec 3, 2017, 9:16 AM by Danny Xu
  • MongoDB and LINCS L1000 1. Open Robot 3T and click create 2. Fill out connection as shown then hit Authentication tab 3. Check Perform authentication and fill out the fields. The password is dxu123 ...
    Posted Nov 28, 2017, 5:59 PM by Danny Xu
  • Map any key to any key on Windows
    Posted Nov 18, 2017, 10:17 AM by Danny Xu
  • Ginger iptables outbound rules -A OUTPUT -m state --state RELATED,ESTABLISHED -j ACCEPT-A OUTPUT -p tcp -m tcp --dport 22 -j ACCEPT-A OUTPUT -p tcp -m tcp --dport 53 -j ACCEPT-A ...
    Posted Nov 6, 2017, 12:39 PM by Danny Xu
  • Add a Domain name to Google Site Follow instructions here 1 Make sure your domain is using our default name servers. Your domain must be using ...
    Posted Nov 4, 2017, 10:17 AM by Danny Xu
  • Cat concatenate gz files file1.gz file2.gz file3.gz > allfiles-cat.gz zcat file1.gz file2.gz file3.gz | gzip -c > allfiles-zcat.gz zcat allfiles ...
    Posted Oct 26, 2017, 1:30 PM by Danny Xu
  • Windows Subsystem for Linux (WSL), Anaconda, Conda, Jupyter Wow!!! Starting in Windows 10 Anniversary Update, the Windows Subsystem for Linux can invoke native Windows binaries from the Linux console and Linux binaries from a Windows console.  https://msdn ...
    Posted Jan 29, 2019, 8:32 PM by Danny Xu
  • Convert SVG to PNG or JPG  I haven't been able to get good results from ImageMagick in this instance ...
    Posted Oct 24, 2017, 10:26 AM by Danny Xu
  • SCM-ADF uses VTK7 and newer OpenGL features to dramatically speed up the visualization of large systems. This comes with a ...
    Posted Apr 26, 2017, 2:09 PM by Danny Xu
  • Encrypt shell script on Linux and BAT file on Windows Linux ShellHow to: shc: -r -f ./script ...
    Posted Oct 17, 2017, 2:39 PM by Danny Xu
  • Rdkit Cairo Fix for Drawing Molecules from rdkit import Chemfrom rdkit.Chem import AllChemfrom rdkit.Chem import DrawAllChem.Compute2DCoords(m)m = Chem.MolFromSmiles('c1nccc2n1ccc2')Draw.MolToFile(m,'/tmp/test.png')Errors pops up ...
    Posted Apr 18, 2017, 5:00 PM by Danny Xu
  • Linux Cheat Sheet
    Posted Apr 11, 2017, 5:30 PM by Danny Xu
  • Anaconda conda in Schrodinger virtual env ipython='python -m ...
    Posted Sep 18, 2017, 12:46 PM by Danny Xu
  • APC Smart UPS The packages are: apcupsd and apcupsd-gui The status of the daemon can be found with: systemctl status apcupsd.service The graphical interface is: gapcmon And the config file is ...
    Posted Feb 23, 2017, 3:34 PM by Danny Xu
  • Ginger iptables/firewall It's turned on. To change config: vi /etc/iptables/rules.v4
    Posted Jan 30, 2017, 6:34 PM by Danny Xu
  • netcat/nc port scan if a port is opennc -z -v -w5 <host> <port/range>-w5: 5s timeout is optionalExample: nc -zv domain ...
    Posted Nov 2, 2017, 1:20 PM by Danny Xu
  • Firefox 48 update on SLES 12 SP1 Initial update caused breaking of default Gnome Login Screen, the following will prevent it: 1. Open Yast2-->Software-->Software Management 2. Search for firefox 3. Select MozillaFirefox and bring up ...
    Posted Dec 15, 2016, 3:06 PM by Danny Xu
  • awk over ssh all "ps aux|grep virtualgrid|awk '{print \$2}'|head -1|xargs -ti kill {}" all 'nohup virtualgrid -nogui >& virtualgrid_`hostname`.log&'
    Posted Oct 14, 2016, 4:11 PM by Danny Xu
  • Real CPU Load top -b -n2 -p 1 | fgrep "Cpu(s)" | tail -1 | awk -F'id,' -v prefix="$prefix" '{ split($1, vs, ","); v=vs[length(vs)]; sub("%", "", v); printf "%s%.1f%%\n", prefix ...
    Posted Oct 1, 2016, 8:23 PM by Danny Xu
  • Check python unicode version ucs2 vs ucs4 This is for python 2.7When built with --enable-unicode=ucs4: >>> import sys >>> print sys.maxunicode 1114111 When built with --enable-unicode=ucs2: >>> import sys >>> print sys.maxunicode 65535 ...
    Posted Feb 23, 2017, 10:04 AM by Danny Xu
  • Remove python apps installed through “python install” "You need to remove all files manually, and also undo any other stuff that installation did manually. If you don't know the list of all files, you can reinstall ...
    Posted Sep 6, 2016, 11:59 PM by Danny Xu
  • Anaconda env for multi-users!topic/anaconda/qinxkmvlnSg sudo su - adduser anaconda mkdir /opt/anaconda ./path/to/ -b -p /opt/anaconda chown -R anaconda ...
    Posted Sep 6, 2016, 10:03 PM by Danny Xu
  • Monitor Installer/Program Changes in Windows 8 suggested tools suggested tools ...
    Posted Aug 26, 2016, 12:00 PM by Danny Xu
  • SUSE12 clone OS Disk Grub2 ext4 1. Use ddrescue to close to a new disk via USB3. Note that the source OS drive does not need umount2. The new disk should be able to boot ...
    Posted Aug 23, 2016, 5:38 PM by Danny Xu
  • GPU Overclock ...
    Posted Aug 17, 2016, 4:13 PM by Danny Xu
  • GPU fan speed control 1. Do this only onceEnabling Control of Fan Speed and generate xorg.conf file, Adds coolbits to the xorg filesudo nvidia-xconfig -a --cool-bits=28 --allow-empty ...
    Posted Aug 30, 2016, 3:57 PM by Danny Xu
  • Windows 8 AppLocker ...
    Posted Aug 12, 2016, 5:42 PM by Danny Xu
  • Windows 8 NSF NFSv4 Support!! only NFSv3 supportFor v4 support, try UMich program ...
    Posted Aug 12, 2016, 5:48 PM by Danny Xu
  • Windows 8 and 10 Remote Desktop RDP Hack Windows 10 ...
    Posted Feb 12, 2019, 10:55 AM by Danny Xu
  • NVRM: os_schedule: Attempted to yield the CPU while in atomic or interrupt context This is GPU0 Titan Z in peppersee[   26.328777] nvidia-modeset: Loading NVIDIA Kernel Mode Setting Driver for UNIX platforms  361 ...
    Posted Aug 14, 2016, 8:35 AM by Danny Xu
  • File encryption using OpenSSL and PGP Tar the directory tar cvf backup.tar /path/to/folder You can remove the [v] switch from the tar command to switch off the verbose mode. Encrypt openssl aes-256 ...
    Posted Aug 3, 2016, 10:29 AM by Danny Xu
  • Startup scipt for ubuntu 1. simple, requires rootvi /etc/rc.local2. upstart systemA simple command (one which doesn't need to remain running) could use an Upstart job like: start on ...
    Posted Aug 2, 2016, 5:18 PM by Danny Xu
  • Bash commands usage examples: sed, awk etc. #awk one liner one-liner ...
    Posted Oct 8, 2016, 11:10 PM by Danny Xu
  • Well said about GPUs, applicable to computing Always use the latest NVIDIA drivers! (some older versions can cause crashing of FurryBall) Remember, if you will use FurryBall with OLD ...
    Posted Aug 2, 2016, 5:20 PM by Danny Xu
  • BUG: soft lockup - CPU#1 stuck for 22s! [Xorg:2982] Solution: disabling C-states in the BIOS  and other CPU power-saving options such as Turbo Mode/Turbo Boost  etc.. should fix this.Some people also tried adding clocksource=jiffies ...
    Posted Feb 19, 2018, 9:30 AM by Danny Xu
  • Remove an IP address that DenyHosts blocked? /etc/denyhosts.confWORK_DIR=/var/lib/denyhostsIf you have been accidentally locked out of one of your hosts (because DenyHosts has added it to /etc/hosts.deny you ...
    Posted Apr 25, 2017, 3:34 PM by Danny Xu
  • Check Linux distro version, LSB, and diagnose binary file Count number of CPUsgrep -c ^processor /proc/cpuinfo mpstat -P ALL|head -1|cut -d'(' -f3|cut -d')' -f1Distro version (this will also show LSB version): lsb_release ...
    Posted Aug 2, 2016, 4:50 PM by Danny Xu
  • MAC address Start/stop network interfaceOld SUSE ifup, ifdown, ifstatus ...
    Posted Jul 26, 2016, 1:09 AM by Danny Xu
  • Basename ${variable%pattern} Trim the shortest match from the end ${variable##pattern} Trim the longest match from the beginning ${variable%%pattern} Trim the longest match from the end ${variable#pattern} Trim ...
    Posted Jul 22, 2016, 8:23 PM by Danny Xu
  • Passwordless for sudo over ssh 1) sudo vi /etc/sudoers: jenkins ALL=(ALL) NOPASSWD: ALL 2) Put the line after all other lines in the sudoers file! That worked for Ubuntu 14.4 and SUSE12 ...
    Posted Jul 21, 2016, 12:10 AM by Danny Xu
  • Configure sshd openssh you made a change to /etc/ssh/sshd_config you must restart the SSHD or make it reload its configuration by typing ...
    Posted Jul 21, 2016, 12:04 AM by Danny Xu
  • After.local You can also write your scripts and then execute them from /etc/init.d/after.local and /etc/init.d/halt.local The after.local script will be run after ...
    Posted Jul 20, 2016, 7:16 PM by Danny Xu
  • IPTables persistent ...
    Posted Jul 20, 2016, 6:57 PM by Danny Xu
  • Schrodinger Docs Maestro-11 Reference Card ...
    Posted May 28, 2018, 5:15 PM by Danny Xu
  • clusterssh/cssh - multiple host ssh/exec to install package for perlas root cpan -i Tk
    Posted Jul 14, 2016, 4:54 PM by Danny Xu
  • GPU nvidia-smi and Schrodinger Schrodinger:Second, ensure that all your cards have ECC memory turned off, are set to Exclusive Process Mode, and Persistence Mode is on. Disable ECC by running the following command ...
    Posted Aug 11, 2016, 10:10 PM by Danny Xu
  • Disable VMD GPU use You must set the CUDA-related environment variables in your shell prior to launching VMD. In the case of Unix systems, you'd do this: /bin/csh syntax: setenv VMDNOCUDA ...
    Posted Jul 15, 2016, 1:13 PM by Danny Xu
  • IPTables Block IP and IP Range This is the correct way: iptables -A INPUT -p tcp --match multiport --dport 1024:3000 -j ACCEPT As an example. Source here. iptables -A INPUT -p tcp --dport 1000:2000 ...
    Posted Jul 12, 2016, 7:57 AM by Danny Xu
  • SUSE12 Desktop Login Problems 1. If login windows does not show up, press CTRL-ALT-Backspace2. If still doesn't work, login as root, init 3init 5rm /run/nologinOtherwise "System ...
    Posted Jul 11, 2016, 3:34 PM by Danny Xu
  • Fail2ban unban IP   With Fail2Ban before v0.8.8: fail2ban-client get YOURJAILNAMEHERE actionunban IPADDRESSHERE With Fail2Ban v0.8.8 and later: fail2ban-client set YOURJAILNAMEHERE unbanip IPADDRESSHERE The hard part is finding ...
    Posted Jul 12, 2016, 7:46 AM by Danny Xu
  • Xargs ~$ echo 10 20 30 40 50 60 | xargs -n 1 -P 4 sleep The use of “-n 1” is vital if you want to pass only one command-line argument ...
    Posted Jul 9, 2016, 10:12 AM by Danny Xu
  • Super fast backup. copy, move many files To copy a large amount of data, tar is generally faster than rsync. The idea is to start with tar and finish off with a final rsync,tar -cpf - src ...
    Posted Jul 6, 2016, 11:09 PM by Danny Xu
  • Find examples 1. Recursively delete empty directories The find command is the primary tool for recursive, filesystem operations. Use the -type d expression to tell find you're interested in finding directories ...
    Posted Jul 5, 2016, 6:58 PM by Danny Xu
  • Super fast delete a folder with large number of files perl -e 'for(<*>){((stat)[9]<(unlink))}'time find ./ -type f -delete (the BEST)time rsync ...
    Posted Jul 6, 2016, 9:20 AM by Danny Xu
  • Memory editing read: scanmem ...
    Posted Aug 2, 2016, 3:45 PM by Danny Xu
  • White Label hard drives For Windows, use freeware test ...
    Posted Oct 12, 2018, 5:17 PM by Danny Xu
  • GPU stress test gpu_burn-0.6.tar.gz (compatible with nvidia-smi and nvcc as of 04-12-2015)This is the best GPU test along with megadock.Note: must run the ...
    Posted Aug 9, 2016, 10:52 AM by Danny Xu
  • SUSE Rescue mode and chroot 1. Start the system with the rescue CD 2. Login with root (no password needed) 3. Mount the / partition. mount /dev/sdc3 /mntmount /dev/sdc1 /mnt/boot4. Give ...
    Posted May 23, 2016, 6:51 PM by Danny Xu
  • How to search DTP/NCI Compounds An easier option is to use Enhanced NCI Database Browser 2.2 Query Data Value, paste SMILES string and set Tc threshold ...
    Posted Sep 5, 2016, 2:34 PM by Danny Xu
  • Python install pip, scipy, numpy, matplotlib Get pip first:Just follow the instructions here: Securely download sure the python version is in the current SEARCH PATH , run sudo python ...
    Posted Mar 1, 2016, 11:12 AM by Danny Xu
  • Adduser vs Useradd (Debian/Ubuntu) Should use adduser which is a perl script that calls useradd and has enhanced features: First off ...
    Posted Dec 3, 2018, 4:59 PM by Danny Xu
  • Intel WiDi installation 1. download and run Intel® WiDi Compatibility Tool Get WiDi update tool ...
    Posted Feb 5, 2016, 11:12 AM by Danny Xu
  • Configure X11/Xorg gdm after switching monitors or video cards A potential universal solution is:1. backup the current /etc/X11/xorg.conf2. reinstall nvidia driver3. use xorg.conf.saxsave and replace Device Section as follows. Note that ...
    Posted Feb 3, 2016, 2:24 PM by Danny Xu
Showing posts 1 - 100 of 231. View more »

Alignment in ezCADD/NGL

posted Jul 2, 2019, 3:05 PM by Danny Xu

Open the console of your browser. (Here is how to open it in different browser:
1. Load chain A of 1y6q to ezCADD main window (attached) => stage.compList[0]
2. Load chain B of 1nc1 to ezCADD main window (attached) => stage.compList[1]
3. Align chain A of 1y6q to chain B of 1nc1 => NGL.superpose(stage.compList[0].structure, stage.compList[1].structure, false)
4. Update the position of chain A of 1y6q => stage.compList[0].updateRepresentations({ 'position': true })

So the commands in Blue background above should be pasted in console.

Outcome server windows 10 remote desktop using rdpwrap

posted May 31, 2019, 9:06 AM by Danny Xu   [ updated May 31, 2019, 9:13 AM ]

RDPWrap on 10.0.17134.706

Edit:  C:\Program Files\RDP Wrapper\rdwrap.ini

Hi, it worked for me. Add this to the end of your file C:\Program Files\RDP Wrapper\rdwrap.ini
Then restart the Remote Desktop services (run services.msc as Admin):


bInitialized.x86 =CBF38
bServerSku.x86 =CBF3C
lMaxUserSessions.x86 =CBF40
bAppServerAllowed.x86 =CBF44
bMultimonAllowed.x86 =CBF4C
bFUSEnabled.x86 =CBF54

bServerSku.x64 =F1378
lMaxUserSessions.x64 =F137C
bAppServerAllowed.x64 =F1380
bInitialized.x64 =F2430
bMultimonAllowed.x64 =F2438
bFUSEnabled.x64 =F2440

Is it possible to use a threading adapter (e.g. M25 to RMS) and use a Nikon lens on the EVOS?

posted May 15, 2019, 10:28 AM by Danny Xu   [ updated May 15, 2019, 10:30 AM ]

The short answer is that Nikon and Olympus objectives are NOT typically compatible on the same optical system (there are a few exceptions). The key reason is that there will be one shared tube lens in the optical path. Nikon is optimized for a 200mm tube lens focal length (modern objectives) and Olympus is optimized for a 180mm tube length. So the optical performance will be sub-par for the Nikon objective because the tube lens focal length is incorrect. The other key thing is that Nikon objectives are built on a 60mm parfocal distance (the distance from the in focus sample to the back of the objective), and the Olympus/AMG objectives are built on a 45mm parfocal distance. This will make a HUGE impact if switching between Nikon and Olympus objectives for focusing, since they will always me a minimum of 15mm out of focus, which is a giant length in microscopy. In an automated system, it also creates the risk of crashing, since the software will not know that the Nikon objective is a 60mm parfocal lens.

Some Zeiss lenses can be mixed and matched with Olympus objectives, because they are close enough in tube length. However, one drawback of some modern Zeiss objectives is that some of the optical corrections (like Chromatic Aberrations) are fixed in the tube lens, NOT the objective itself. Olympus corrects everything in the Objectives. That means that a Zeiss objective with an Olympus or AMG tube lens will be inferior optically because chromatic aberration will be more pronounced.

Confocal and Widefield Image Processing

posted May 7, 2019, 7:37 PM by Danny Xu   [ updated May 7, 2019, 8:35 PM ]

Z-Stack Step Size

Microscope Calibration

Have you gone through the entire process of aligning the optical path? Are your phase plate and annulus properly matched? Is your Kohler illumination aligned? Are your samples sitting flat on the stage? Is your camera in the correct alignment in the optical port?
The microscope itself is professional grade. You should be able to take clear images in any mode so long as it is in working order.

Image Overlay

3D reconstruction of 2D confocal image stacks

Chimera software ( for 3D visualisation of confocal stack (after processing with ImageJ).

Amira for 3D visualization. It is a very expensive software. But they generously enable all the features for the trial version.
ImageJ (Fiji, just a new name for ImageJ) has many plugins for 3D visualization like 3D Viewer, Volume Viewer.

Bitplane Imaris vs. Amira
That depends on what kind of analysis do you need mostly. Amira is good at 3D/4D visualization, segmentation; you can easily generate workflow and apply to other dataset. Imaris has lots of isolated modules you can buy for particular applications, such as deconvolution, co-localization. Imaris can also connect to MATLAB, if my memory is correct. If you do not really need some particular functions/algorithms of Amira or Imaris, I suggest you start from Imagej or Fiji. It's free and has covered most common image processing and analysis algorithms, and highly flexible and extendable, if you are little background of programming.

Cell Counting with Imaris


There are some for ImageJ, but it is suggested that the best bling algorithm is implemented in commercial software AutoQuant. The list of interesting blind and nonblind algorithms can be found here
The one of blind methods I like most among mentioned is LASIP.
But why do you prefer blind deconvolution? Nonblind ones usually give better results and are less computational intesive. The best among commercial is Huygens Suite (week trial available in, the best among freeware is COSMOS ( , new release will be ready in several weeks). For WF microscopy the mentioned ones give very high image quality improvement.

The point spread function (PSF) is the hardest to get. Without a good PSF deconvolution is meaningless.
I am skeptical of blind deconvolution in general (estimating the entire PSF image using an iterative process)

First create the PSF-file using your exact settings (mounting, oil, objective, NA,...) and use this for the deconvolution.

One generally deconvolves z-stack images. You can first acquire a z-stack of a stuck bead under the same magnification to generate the PSF. Open the image z-stack after this and then go to the 3D-Deconvolve function. Select the image stacks there: one sample stack and the other PSF genrated. Play with the parameters and you will get your deconvolved image from this

"Two plugins can be used in ImageJ to perform 3D deconvolution, DeconvolutionLab and Parallel Iterative Deconvolution.
They both need a stack containing the PSF, they are based on iterative algorithms, that is to say they first compute the estimated original signal. Then this estimated original signal is convolved with the PSF, so it should reproduce the deformation induced by the system and give the actual image. Different algorithms are then used to minimise this difference. A commonly used algorithm in fluorescence microscopy is Richardson-Lucy".

Free:  ImageJ/Image2, FIJI, ICY

co-localization plugins are available for the open source java application ImageJ ( and its various distributions, including Fiji ( Two plugins that implement all the co-localization methods described above are JaCoP (ImageJ) and Coloc_2 (Fiji)."

EpiDEMIC plugin on icy ( It is a blind deconvolution (ie no need of a PSF) algorithm for epifluorescence

The implication that "ImageJ is not appropriate for deconvolution" is not correct. ImageJ/Icy and other open source programs can produce results as good or better as commercial deconvolution if used properly. In fact in the most recent Deconvolution Grand Challenge, one of Ferreol's algorithms beat all the commercial entries (the best commercial entry was actually the Olympus implementation by David Biggs). In a recent paper, several algorithms from Deconvolutionlab2 were tested against Huygens and produced comparable results

I encourage anyone interested in ImageJ and/or Icy deconvolution implementations to post questions on the respective listservs and forums, and share images. If you interact with the developers and community you will be able to obtain very good results.

Commercial:  Huygens (SVI, Inc), Imaris (Bitplane), Autoquant X (Media Cybernetics) and Volocity (Perkin Elmer).

EVOS LED Light Cube for DASPEI

posted Apr 4, 2019, 10:25 AM by Danny Xu   [ updated May 7, 2019, 2:01 PM ]

DASPEI dye (λEx/λ Em = 461/589 nm). Our EVOS FL system (AMAFD1000) contains these 4 light cubes:

AMEP-4652 (RFP, Ex: 531/40 Em: 593/40) 
AMEP-4650 (DAPI, Ex: 357/44 Em: 447/60)
AMEP-4651 (GFP, Ex: 470/22 Em: 525/50)
AMEP-4669 (CFP-YFP EM     Ex: 445/45 Em: 542/27)
AMEP4660 QDot 585 (Ex: 445/45 Em: 586/20)

FM1-43 479 598
YOYO-1 / YO-PRO-1 491 509
Cy3   550 570
DsRed (Red Fluorescent Protein) 558 583
Texas Red® / Texas Red®-X 595 613

Courtenay@ThermoFisher: The peaks of DASPEI do not fit commonly available filters, but the dye spectra is broad enough that you should be able to use the RFP filter cube with this dye. 

AMEP4652 is the RFP cube that has Ex 531/40  Em 593/40 and is the only cube you have that will work with DASPEI. The RFP 531/40 nm excitation filter will just catch the upper edge of the excitation spectra and the 593/40 nm emission filter matches the emission peak very well. 

531/40 means 531 +/- 20 nm, or 511 -551 nm.  The excitation range is not ideal for DASPEI but there is enough excitation of the dye at 511 to about 530 nm, that this filter should work OK.  The 593/40 emission filter is a perfect match for DASPEI.

The best match, if you wanted to purchase a cube, would be the AMEP4660 QDot 585 cube with 445/45 excitation and 586/20 emission.  Other cubes that could be used are AMEP6470 Acridine orange cube (442/46, 488LP) and the AMEP4666 QDot general cube (445/45, 525-800)


posted Feb 7, 2019, 2:24 PM by Danny Xu

 Auto installed Apache, PHP, and Perl, MySQL, can use MariaDB already installed.

set up phpMyAdmin to automatically log in as user. I  also created a database user that has full control over (minus grant and lock tables).

XAMPP has a very well designed configuration tool so if we do need to update anything it should be super easy.

Windows 10 in-place reinstall

posted Dec 26, 2018, 11:20 AM by Danny Xu

Running an in-place upgrade worked to fix our instance of Windows 10 that couldn't otherwise be repaired with Command Prompt commands such as

SFC /scannow


DISM /Online /Cleanup-Image /RestoreHealth – neither of which would finish their operation on our installation.

SFC works correctly when run from a console in the preinstall environment (PE).  Component store corruption can be repaired from within Windows without an in place re-install.

sudo preserve environment variables

posted Dec 3, 2018, 1:42 PM by Danny Xu

sudo -E su username -c 'commands'

IP address lookup and block

posted Nov 27, 2018, 3:40 PM by Danny Xu   [ updated Dec 3, 2018, 1:34 PM ]

To get country and domain info from IP:

geoiplookup IP_address
host IP_address/domain_name

sudo iptables -I INPUT -s x.x.x.x/32 -j DROP 
This will put the drop at the start of the INPUT chain.

Schrodinger Installation on OpenSUSE, SUSE

posted Nov 17, 2018, 9:25 PM by Danny Xu   [ updated Nov 17, 2018, 9:28 PM ]


is_sles_sled_12_sp1() {
    _sles_12_sp1=`lsb_release -d 2> /dev/null | grep -e "SUSE Linux Enterprise Desktop 12\s*$" -e "SUSE Linux Enterprise Server 12\s*$" -e "SUSE Linux Enterprise Desktop 12 SP1\s*$" -e "SUSE Linux Enterprise Server 12 SP1\s*$"`
    if [ -n "$_sles_12_sp1" ]; then
        unset _sles_12_sp1
        false #true
        unset _sles_12_sp1

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