computational chemtool

[faustina-beep]

Hello everyone, I am Faustina. I am an Mpharm student researching on the design of fragments for Open source antibiotics. I have looked at the current poses that have been done on the Mur D and Mur E receptors and will like to begin to build fragments based on the current hits that have been displayed. My main problem is how to use the computational chem tool to help me dock what I have currently thought of. I have downloaded anaconda and gone through the paper that was posted on the chemtool but it did not help with my ability to use these software. Is there anything else I can do, please.

[drc007]

@faustina-beep Let's start from the beginning. You say you have installed Anaconda, have you installed all the conda packages?

In a terminal window type

conda install jupyter
conda install -c rdkit rdkit
conda install numpy
conda install scipy
conda install scikit-learn
conda install pandas
conda install matplotlib
conda install seaborn

[drc007]

Have you also download and installed SMINA https://sourceforge.net/projects/smina/

[drc007]

You then need to download the Jupyter Notebook https://opensourceantibiotics.github.io/murligase/CompChemTools/UsingSmina.zip

[faustina-beep]

Thanks will do

Get Outlook for iOShttps://aka.ms/o0ukef

---

From: Chris Swain notifications@github.com Sent: Monday, November 4, 2019 8:15:56 AM To: opensourceantibiotics/murligase murligase@noreply.github.com Cc: Nyarko, Faustina faustina.nyarko.16@ucl.ac.uk; Author author@noreply.github.com Subject: Re: [opensourceantibiotics/murligase] computational chemtool (#11)

You then need to download the Jupyter Notebook https://opensourceantibiotics.github.io/murligase/CompChemTools/UsingSmina.ziphttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopensourceantibiotics.github.io%2Fmurligase%2FCompChemTools%2FUsingSmina.zip&data=02%7C01%7C%7C631bd25b3280487854f008d760ff3867%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637084521581717174&sdata=Km%2BzSLYflE9CIdD8bGtOanTFvhN8r955gZpwXz5MU%2Bg%3D&reserved=0

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/opensourceantibiotics/murligase/issues/11?email_source=notifications&email_token=ANMUZ2LHB4Q22CN4HGSBVALQR7K3ZA5CNFSM4JIP3HE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEC6PTHY#issuecomment-549255583, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANMUZ2LWRJOY2FRTNAD6DBLQR7K3ZANCNFSM4JIP3HEQ.

[faustina-beep]

@drc007 I have been able to install Anaconda and used conda to install the mentioned packages and Jupyter Notebook however, I am finding difficulty in opening SMINA after installing it. It keeps giving me messages that it cannot be opened. Please find the image link below.

[drc007]

@faustina-beep Smina is a command line program that can be accessed using the Terminal In a Terminal window type (assuming smina is installed in usr/local/bin/)

/usr/local/bin/smina.osx --help

and you should get a list of the command line options.

If you are not sure where it was installed in the Terminal type

which smina.osx

and it will display the path

[faustina-beep]

@drc007 I have tried it in the terminal but it gave me a message that there is no such file. checking on my downloads I could see the files but it tells me there is no application to open it.

[faustina-beep]

@drc007 please see the message displayed in the download window

[drc007]

@faustina-beep is the smina.osx file in /usr/local/bin/ ?

In the Terminal type

which smina.osx

What is the path returned?

The file you have highlighted above is the Jupyter notebook not Smina

[faustina-beep]

@drc007 yes it is. Please find attached image.

[faustina-beep]

@drc007 But could it be that I deleted it several times yesterday? Also, I have downloaded it a couple of times today to see if it will work

[drc007]

@faustina-beep That is great,

Now what do you get if you type this in a terminal window?

which smina.osx

Just want to check the path to the executable.

[faustina-beep]

@drc007 it comes up with this message.

[drc007]

That looks like you have done the search in the Finder rather than the Terminal.

Terminal is an application you should find in Applications:Utilities

[faustina-beep]

It does not give any response.

[drc007]

Hmmm.

Try typing into a Terminal window

/usr/local/bin/smina.osx --H

[faustina-beep]

@drc007 This is what it gave

[drc007]

@faustina-beep Is there a space between .osx and --H?

/usr/local/bin/smina.osx --H

[faustina-beep]

@drc007 now it tells me its permission denied

[drc007]

@faustina-beep OK looks like need to alter file permission to allow application to run

In Terminal type (it might ask for your password)

chmod +x /usr/local/bin/smina.osx

Then try

/usr/local/bin/smina.osx --H

[faustina-beep]

@drc007 It still denied it

[drc007]

@faustina-beep Looks like you might need a space between +x and /usr/local/bin/smina.osx ?

[faustina-beep]

@drc007 I think a response has been given now.

[drc007]

@faustina-beep Success, well done!

The next step is the Jupyter notebook. This is contained in the folder you displayed earlier.

The notebook is has the file extension .ipynb

I have a folder in my main directory called projects, and I run all the notebooks from this folder. You can have the folder anywhere but it is useful to think about organisation at this point.

You now need to type this in a Terminal window.

cd followed by the path to the folder containing the notebook.

something like

cd /Users/username/Projects/OpenSourceAntibiotics/notebooks

On a Mac the easy way to do this is to type cd in a Terminal window and then drag and drop the folder containing the notebook onto the Terminal window.

Hit return then type

ls

[faustina-beep]

@drc007 this is what I got when I first click on the Jupyter notebook

[drc007]

@faustina-beep In the Terminal you need to first navigate to the folder containing the notebook, then type

jupyter notebook

This should open a web browser window showing the contents of the folder. You can then select the desired Jupyter notebook.

[faustina-beep]

this gave me this result and simultaneously opened Jupyter in the browser

[drc007]

@faustina-beep Looks like you are not in the folder containing the Jupyter notebook.

In the Terminal window use control C twice to stop the notebook server then type

ls

This will give you the listing of the folder in the Terminal

[faustina-beep]

@drc007 this is what it gave me

[drc007]

@faustina-beep That should be a lower case "L"

[faustina-beep]

@drc007 . This is the list it gave me .

[drc007]

@faustina-beep It looks like you are in top level of your user folder. You need to navigate to the folder containing ConformationGenerationDocking.ipynb. This should be a folder called "UsingSmina"?

If you drop this folder onto a Terminal window it will display the path to the folder

Then type cd followed by the path to the folder

something like

cd /Users/username/UsingSmina

[faustina-beep]

@drc007 The highlighted folder was dragged and dropped in the terminal. then it gave this error

[drc007]

@faustina-beep You need to drop the folder containing ConformationGenerationDocking.ipynb

not the ConformationGenerationDocking.ipynb file.

[drc007]

@faustina-beep This link will download the notebook in a folder https://opensourceantibiotics.github.io/murligase/CompChemTools/UsingSmina.zip

The folder will be called UsingSmina, drag the folder from your downloads folder and put it in your preferred locations.

Then drop the folder on a Terminal window.

[faustina-beep]

@drc007 This is what it gave me

[drc007]

@faustina-beep OK, double click on the zip file to unzip and you should have a folder called UsingSmina on your desktop

The in the Terminal type

cd /Users/faustinanyarko/Desktop/UsingSmina

then type

ls

To show the folder contents

[faustina-beep]

@drc007 I don't think anything happened.

[faustina-beep]

@drc007 sorry have sent the wrong picture

[drc007]

@faustina-beep you need a space between cd and the path

[faustina-beep]

@drc007 I did early but I did not get any response that is why I tried without it, but I have put a space between it again and it not responded

[drc007]

@faustina-beep It is case sensitive.

cd /Users/faustinanyarko/Desktop/UsingSmina

[faustina-beep]

@drc007 Have checked and corrected that but no responds.

[drc007]

@faustina-beep What happens if you now type

ls

[faustina-beep]

@drc007 Still no responds

[drc007]

@faustina-beep Hmmm.

Ok close the Terminal window and reopen.

Now type "cd " and then drop the UsingSmina folder from your desktop onto the Terminal window and press return.

[faustina-beep]

@drc007 Again nothing happened. but I have seen a folder named using Smina which is not zipped should I try using that one Screen Shot 2019-11-07 at 17 09 48

[drc007]

@faustina-beep Yes.

[faustina-beep]

@drc007 It did not help.

[drc007]

@faustina-beep I think it did. Your prompt now includes the folder name

Now type ls