faq
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| faq [2018/12/19 01:40] – flack | faq [2024/04/09 08:33] (current) – rkiss | ||
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| ====== Frequently asked questions (FAQ) ====== | ====== Frequently asked questions (FAQ) ====== | ||
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| + | ====I get an error message " | ||
| + | |||
| + | Please check if you have uploaded a valid PDB file. If so please try to remove any excess lines NOT starting with " | ||
| + | < | ||
| + | cat input.pdb | grep -E " | ||
| + | </ | ||
| + | |||
| + | |||
| + | ====How can I get access to a Linux system if my operating system is Windows? | ||
| + | |||
| + | If you are on Windows 10, we suggest to install WSL to get access to a Linux distribution (for example Ubuntu). You can find WSL install instructions here: | ||
| + | |||
| + | [[https:// | ||
| ====Can I get a Mcule database SMILES file in smaller chunks?==== | ====Can I get a Mcule database SMILES file in smaller chunks?==== | ||
| - | If you have access to a unix based system and the split command you can use the below commands to split large files into smaller chunks. | + | If you have access to a Linux system and the split command you can use the below commands to split large files into smaller chunks. |
| To split a smi.gz / smiles.gz file into multiple **uncompressed chunks** use a command like this: | To split a smi.gz / smiles.gz file into multiple **uncompressed chunks** use a command like this: | ||
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| To split a smi.gz / smiles.gz file into multiple **gzip compressed chunks** use a command like this: | To split a smi.gz / smiles.gz file into multiple **gzip compressed chunks** use a command like this: | ||
| < | < | ||
| - | gzip -dc your.smi.gz | split --verbose --lines=< | + | gzip -dc your.smi.gz | split --verbose --lines=< |
| </ | </ | ||
| For example to split the Mcule Purchasable (Full) smi.gz file into 1M **gzip compressed chunks** use: | For example to split the Mcule Purchasable (Full) smi.gz file into 1M **gzip compressed chunks** use: | ||
| < | < | ||
| - | gzip -dc mcule_purchasable_full_180817.smi.gz | split --verbose --lines=1000000 --numeric-suffixes --suffix-length=10 --additional-suffix=' | + | gzip -dc mcule_purchasable_full_180817.smi.gz | split --verbose --lines=1000000 --numeric-suffixes --suffix-length=10 --additional-suffix=' |
| </ | </ | ||
| If you have pigz installed on your system you can replace gzip with pigz in the commands above to speed up the process, especially when you want compressed chunks. You can typically install it with < | If you have pigz installed on your system you can replace gzip with pigz in the commands above to speed up the process, especially when you want compressed chunks. You can typically install it with < | ||
| + | |||
| + | If you are on Windows 10, we suggest to install WSL to get access to a Linux distribution (for example Ubuntu). You can find WSL install instructions here: | ||
| + | |||
| + | [[https:// | ||
| ====Can I get a Mcule database SDF file in smaller chunks?==== | ====Can I get a Mcule database SDF file in smaller chunks?==== | ||
| - | If you have access to a unix based system and awk you can use the below commands to split large, gzipped SDF files into smaller chunks. | + | If you have access to a Linux system and awk you can use the below commands to split large, gzipped SDF files into smaller chunks. |
| - | To split an sdf.gz file into multiple uncompressed chunks, use a command like this: | + | To split an sdf.gz file into multiple |
| < | < | ||
| gzip -dc your.sdf.gz | awk -v name=< | gzip -dc your.sdf.gz | awk -v name=< | ||
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| Just replace your.sdf.gz with your filename, < | Just replace your.sdf.gz with your filename, < | ||
| - | For example to split the Mcule Purchasable (Full) sdf.gz file into 1M uncompressed chunks use: | + | For example to split the Mcule Purchasable (Full) sdf.gz file into 1M **uncompressed chunks** use: |
| < | < | ||
| gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf -v size=1000000 ' | gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf -v size=1000000 ' | ||
| Line 46: | Line 64: | ||
| - | To split an sdf.gz file into multiple gzip compressed chunks, use a command like this: | + | To split an sdf.gz file into multiple |
| < | < | ||
| gzip -dc your.sdf.gz | awk -v name=< | gzip -dc your.sdf.gz | awk -v name=< | ||
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| Just replace your.sdf.gz with your filename, < | Just replace your.sdf.gz with your filename, < | ||
| - | For example to split the Mcule Purchasable (Full) sdf.gz file into 1M gzip compressed chunks use: | + | For example to split the Mcule Purchasable (Full) sdf.gz file into 1M **gzip compressed chunks** use: |
| < | < | ||
| gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf.gz -v size=1000000 ' | gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf.gz -v size=1000000 ' | ||
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| Please note that the process can take a while. | Please note that the process can take a while. | ||
| + | |||
| + | If you are on Windows 10, we suggest to install WSL to get access to a Linux distribution (for example Ubuntu). You can find WSL install instructions here: | ||
| + | |||
| + | [[https:// | ||
| ====Will my previous searches deleted? | ====Will my previous searches deleted? | ||
| - | We won’t delete any of your search/screen results. However, you can delete them if you’d like by selecting the collection | + | Searches created by anonymous users (not authenticated users) get deleted after some time, but if you registered an Mcule user account and perform searches |
| ====Where can I access my previous search results? | ====Where can I access my previous search results? | ||
| - | Under the “Collections” tab. All your previous search/screen | + | On the "Collections" page. All your previous search/workflow |
| ====How many searches and screens can I run?==== | ====How many searches and screens can I run?==== | ||
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| Under the “find chemicals” tab you can run simple searches ([[exactsearch|Exact]], | Under the “find chemicals” tab you can run simple searches ([[exactsearch|Exact]], | ||
| - | Under the “workflow builder” tab more complex, multistep virtual screens can be built and run. Available tools under the workflow builder tab include [[dockingvina|Docking (Vina)]], [[diversitysel|Diversity selection]], | + | Under the “workflow builder” tab more complex, multistep virtual screens can be built and run. Available tools under the workflow builder tab include [[dockingvina|Docking (Vina)]], [[diversitysel|Diversity selection]], |
| ====Who can see my search/ | ====Who can see my search/ | ||
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| ====How can I get access to extra searching/ | ====How can I get access to extra searching/ | ||
| - | Extra tools, like FTrees Visual Similarites or ChemAxon Properties are provided on a subscription basis. To get access to these tools, go to our [[https:// | + | Extra tools, like ChemAxon Properties are provided on a subscription basis. To get access to these tools, go to our [[https:// |
| ====I’m working at XY University. Can I get a discount for the subscription packages? | ====I’m working at XY University. Can I get a discount for the subscription packages? | ||
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| ====I need to find novel inhibitors of a protein. How should I start?==== | ====I need to find novel inhibitors of a protein. How should I start?==== | ||
| - | There are several ways of doing this. Here is one general example. Go to “workflow builder”, set a “Property filter” (RO5 max 1). If there is a reference ligand available that is a known inhibitor of your protein, you can use it as a query molecule for “FTrees Visual Similarities” or “Similarity search”. If there is an available crystal structure for your protein, you can check if it can be selected from the ~10,000 prepared target structures in the Docking (Vina) workflow step. To make sure you don’t exceed your limits, use the “Sampler filter” or “Diversity selection” to reduce the number of molecules to the required number. Click on “Screen” to run your screening workflow. The results will be displayed as they are generated. To export the results click on “Export”, | + | There are several ways of doing this. Here is one general example. Go to “workflow builder”, set a “Property filter” (RO5 max 1). If there is a reference ligand available that is a known inhibitor of your protein, you can use it as a query molecule for “Similarity search”. If there is an available crystal structure for your protein, you can check if it can be selected from the ~10,000 prepared target structures in the Docking (Vina) workflow step. To make sure you don’t exceed your limits, use the “Sampler filter” or “Diversity selection” to reduce the number of molecules to the required number. Click on “Screen” to run your screening workflow. The results will be displayed as they are generated. To export the results click on “Export”, |
| ====I want to check if a compound is purchasable, | ====I want to check if a compound is purchasable, | ||
faq.1545183639.txt.gz · Last modified: 2018/12/19 01:40 by flack