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iOS and Android app for remote connections

9/8/2020

Hello all,

Using the app: https://termius.com/

you can connect with ssh to any linux machine (it's a similar app to e.g. Putty in a Windows PC) . So you can connect to your lab desktop and through it you can ssh to a supercomputer or any server you are using to submit/monitor jobs and run any terminal commands you need.

Sofia

ACS Reviewer Lab

8/27/2020

The following tutorial is designed to help you learn how to become a journal reviewer. It is highly recommended as you 'll also learn how reviewers think, so you can better prepare your own manuscripts. It only takes 2-3 hours and it's free.

As a Bonus, a certificate is issued if you answer correctly an easy assessment at the end of the tutorial!

https://www.acsreviewerlab.org/

Alexis

Tips for creating nice images with VMD

4/25/2019

For nice images of proteins in VMD we recommend that you use the Graphics -> Representations -> Drawing Method -> Surf or MSMS visualisation, and then use the "Display -> Display Settings -> Ray Tracing Options -> Amb. Occl -> on" feature.

Here you can download MSMS:
http://mgltools.scripps.edu/downloads#msms

To render:
# smaller render, no normalization, high aasamling
[tachyonpath] -res 1920 1080 -aasamples 36 -add_skylight 1.0 %s -format PSD48 -o %s.psd

# huge render, high aasamling
[tachyonpath] -res 12460 9620 -aasamples 36 -add_skylight 1.0 %s -normalize -format PSD48 -o %s.psd

# below command can be used to set resolution when you don't want to force a resolution in tachyon
display resize 1280 1024

Free webinar by Christopher Lipinski on the Lipinski rules of 5

9/5/2018

Join Christopher Lipinski and Barry Bunin for a discussion on the "Lipinski Rules of 5," which has become the benchmark by which almost all drug discovery analyses are now compared.

Register here: https://info.collaborativedrug.com/lipinski-bunin-ruleof5-0-0

Experts will discuss:

Advanced drug discovery & data screening methods
What is the Lipinski Rule of 5 & How you can go beyond the Rule of 5 to achieve better results
New technologies to better assess the quality of your screening data
Experimental culture and sociology as a factor in clustering your results
How scientists can (and should) respond to the growing opioid addiction crisis – which has actually lowered life expectancy in America

How to display an Electron Density Map in Pymol

3/27/2018

Very often protein crystallography results in ambiguous regions of electron density.

To check that your protein structure is adequately represented by electron dements maps please follow the following tutorial in pymol:

http://www.virology.wisc.edu/acp/tutorials/PyMol-E-density.pdf

Zoe

How to create high quality figures with VMD

3/15/2018

In order to create high quality figures with VMD, go to: File > Render and use the Tachyon module in the File Render Controls panel.

Also, in order to increase the resolution of the figure, go to Render Command, in the same panel, and add the flag: -res xxx yyy, defining the number of pixels of the image.

Example:
"/usr/local/lib/vmd/tachyon_LINUXAMD64" -aasamples 12 %s -format TARGA -res 1600 1200 -o %s.tga

Christina

How to correctly list full or abbreviated journal names in Endnote and change the capitalization of words

1/3/2018

EndNote provides a number of terms list to make sure that the journal names in your bibliography are either the full name or abbreviation as your style requires. To set up your terms list, first make a backup of your library as described here. Then, please follow the steps below. The procedure is also shown in an embedded video following the steps.

In EndNote, go to "Tools > Open Term Lists > Journal Terms List".
Highlight the first journal, and press [Ctrl]+A on the keyboard to highlight all the terms (on a Macintosh, this would be [Command]+A). Note: If the Journal Terms List is empty, skip to step 4.
Next, press the "Delete Term" button to the right to empty the list of old terms.
Go to the "Lists" tab at the top, and click on the "Import List" button.
Browse to the Term Lists folder within the EndNote folder, and choose to open the Medical text file (assuming you want to use the Index Medicus abbreviations).

If you are on a Windows machine, this folder should default to:
C:\Program Files\EndNote (EndNote Version Number)\Terms Lists

If you are on a 64-bit Windows machine, this folder should default to:
C:\Program Files (X86)\EndNote (EndNote Version Number)\Terms Lists

If you are on a Mac, this folder should default to:
Hard Drive: Applications: EndNote (EndNote Version Number): Terms
This will import the correct abbreviations into your library's term list.
Next, to make sure the style is using the correct substitution, go to "Edit > Output Styles > Open Style Manager".
In the list of styles, highlight the style you are using and click the "Edit" button.
Click on "Journal Names" on the left.

If Endnote changes the words of the title to lowercase:

You can add terms to an exclusion list so that EndNote does not change the case of the added terms.
In EndNote, go to: EndnoteX7 -> Preferences.
Click on the first option 'Change Case'.
Enter the terms one by one and click on 'Add'
After entering all terms you can click on 'OK' or 'Apply'.

Source

Chemical Reviews on Nanoparticles, Non Covalent Interactions, Enzyme Allostery and more!

8/23/2017

Reviews published in Chemical Reviews are state of the art and a must-read for all scientists in the Natural Sciences.

We 've chosen the following most recent thematic issues as most relevant to drug design and drug delivery design.

Physical Chemistry

Water - The Most Anomalous Liquid
July 13, 2016 (Volume 116, Issue 13, pp. 7459-7726)
Editorial | Table of Contents

Noncovalent Interactions
May 11, 2016 (Volume 116, Issue 9, pp. 4911-5688)
Editorial | Table of Contents

Nanomaterials

Nanoparticle Chemistry
September 28, 2016 (Volume 116, Issue 18, pp. 10343-11290)
Editorial | Table of Contents

Nanoparticles in Medicine
October 14, 2015 (Volume 115, Issue 19 pp. 10407-11190)
Editorial | Table of Contents

Enzymes

G-Protein Coupled Receptors
January 11, 2017 (Volume 117, Issue 1, pp. 1-246)
Editorial | Table of Contents

Protein Ensembles and Allostery
June 8, 2016 (Volume 116, Issue 11, pp. 6263-6742)
Editorial | Table of Contents
13, pp. 8481-9520)
Editorial | Table of Contents

Enjoy reading!

Drug Design Webinars by Schrodinger

2/21/2017

Schrödinger, Inc will be presenting its 5th European Life Science Bootcamp – a series of live webinars that will cover a wide range of popular topics, and will be fully interactive – each webinar will consist of 10 minutes of presentation, 20 minutes of software demonstration, followed by live Q&A with the presenter.

Schrödinger's 5th European Life Science Bootcamp will run from Monday, March 20th through Thursday, March 24th, covering the following topics:

WaterMap for Lead Optimisation
Introduction and Case Studies in Free Energy Perturbation for Lead Optimisation
Becoming an Expert in PyMOL: Customization and Scripting
Modelling Peptide Binding: From Structure to Properties
Using Phase for Pharmacophore Modelling

Click here to learn more, and to register for any of the sessions. Note that each session will be recorded and all registrants will automatically receive a link to the session recording.

The recordings from previous European Life Science Bootcamps can be found here:

How do I add myself back as a sudo user?

11/30/2016

If you should be a sudoer in ubuntu but somehow the system is broken and you can no longer make administrative changes, follow the procedure below to re-enter the sudoers list.

$ sudo ls
[sudo] password for stephane:
stephane is not in the sudoers file. This incident will be reported.

During boot, press and hold the left Shift key, and you should see the GRUB menu.
Select the entry containing (recovery mode) and wait.
You should now be presented with a menu. Select:
remount Remount / read/write and mount all other file systems

If this option doesn't appear or won't work, you can instead choose the root option and use the following command to mount the system partition:
mount -o remount /
or
mount -o rw,remount /

After applying this variation, adding a user to the admin (11.10 and ealrier) or sudo (12.04 and later) group is done like:
adduser username admin # 11.10 and earlier
adduser username sudo # 12.04 and later