Activity for Sarkis Dallakian
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Sarkis Dallakian posted a comment on discussion General Discussion
Edit run.sh and replace: $PYRX_HOME/bin/python $PYRX_HOME/runPyRx.py &> /dev/null with $PYRX_HOME/bin/python $PYRX_HOME/runPyRx.py When you run from the command line it should tell what libraries are missing.
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I was able to start PyRx after yum install sdl12-compat.x86_64 Please let me know if it works.
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Thank you for the message. I plan to install Fedora 43 over the weekend. I'll keep you posted on the progress.
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Please send me your order number.
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Please provide steps to reproduce this error. You can use https://sourceforge.net/p/pyrx/discussion/general/thread/1ba8825cf0/?limit=25#09f9 to fix it. However, I need to know how to reproduce this to fix it.
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Dear Abdul. I need more information about your High-Performance Computing (HPC) cluster. Is this a Windows system with 120 CPU cores? You need a Linux version with PBS to run PyRx on HPC.
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Please undo it and use the same logic you used to set the workspace to C:\pyrx_dir\latihan01 and set it to the same with added _workspace. You can also change the workspace by editing the PyRx_workspace/preferences.ini in your home folder.
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Replace C:\pyrx_dir\latihan01 with C:\pyrx_dir\latihan01_workspace
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Hi Stephen, Yes, you need to restart PyRx for it to pick up the new workspace. It is better to use multiple workspaces rather than one big one for performance.
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Include SMINA box only if the smina path exists
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Fix for https://sourceforge.net/p/pyrx/discussion/general/thread/d5fcde628e/?limit=25#9c26
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Hi Stephen, It seems to happen because D:\Docking\PyRx doesn't include 'workspace'. You can fix it by replacing D:\Docking\PyRx with D:\Docking\PyRx_workspace, for instance. I'll look into fixing this in the next release. Thanks, Sargis
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Hi Stephen, The new version requires an executable that can't be included with updates. I'll PM you a coupon code. Thanks, Sargis
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Changelog
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1,2
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If you know a little Python, you can modify the code to set Num modes for Vina: https://sourceforge.net/p/pyrx/discussion/general/thread/b70524ed/
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Dear Sir, Thank you for the message. For 1, I would need the specs of your computer, the size of the protein and ligand, and the search space. My guess is that the search space is too large. I recommend making the search space smaller, otherwise,, it would take a long time for Vina to run. For 2) I need steps to reproduce it. In other words how did you get that error? 3) is a warning message that can be ignored.
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The current version only supports python 2. I don't know what's causing this. I'm happy to help with any issues that happen with the paid version.
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You can get the 64-bit version. I'll give a full refund, if it doesn't solve this issue .
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Assuming that your computer has sufficient memory this can be solved buy getting the paid version. The free version is 32-bit while the paid version is 64-bit. I'm also happy to fix any issues you encounter with the paid version.
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Yes, in the latest version, there is an option to set Num modes for Vina https://sourceforge.net/p/pyrx/discussion/general/thread/cef07fd6ea/
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Please get the latest version and let me know if this error remains. You could have started with thanking me for the free version, but no you want more. What are you expecting with the free version?
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Please get the latest version and let me know if this error is still there,
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Please get the latest version an let me know if this error is still there,
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You can also use this link for tax question https://fastspring.com/consumer-support-form/tax-vat-gst/ or this for questions related to https://fastspring.com/consumer-support-form/ to purchasing.
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@anchikam you just enter purchase order number in the checkout. If you do a purchase order through the site it would give you a link where you can make a payment.
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@anchikam you are welcome. You can do Wire Transfer, Check or Money Order or Purchase Order.
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Hi @anchikam , that link I provided list all the info needed plus has W-9. They can email b2b@fastspring.com for more info.
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Hi sure, you can get quotes for free from https://pyrx.sourceforge.io. Please let me know if you have any questions.
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Hi Irene, I DM you a coupon code. MacOS version doesn't work on 64-bit Mac.
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Hello, please dm me your order number and I can't send you a discount code.
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Hi @anchikam , you can use this document that has al the info needed for vendor on-boarding: https://fastspring.com/wp-content/uploads/2023/07/2024-FastSpring-Vendor-Onboarding-Fact-Sheet-CONFIDENTIAL-1-2.pdf
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No, sorry, I don't have time, space, or energy for a 64 bit macintosh version. If I can find a co-founder who uses Mac maybe.
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Changelog
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addin Omar Al-Attraqchi
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Dear Flavio, Sorry, I don't have bandwidth for this currently. I have Ubuntu 20.04 vm and don't have time to get a newer vm. Best regards
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You need to download from https://github.com/oddt/rfscorevs_binary/tree/master. There an option to set the path as shown in https://pyrx.sourceforge.io/pyrx-11-release-announcement/
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Hello, Thank you for being PyRx customer. You can use "Help > Check for Updates..." within the PyRx application; this will initiate a search for available updates to your current version. If this doesn't work, you can use the manual procedure described in https://pyrx.sourceforge.io/recent-changes-in-vina-web-services-and-mac-os-x-updates/ The 1.1 version includes a new “rf-score-vs.exe” executable, that you'll need to download separately.
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Please purchase the latest version. If this bug is there, I'll fix it and give you a refund.
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added bndIndex
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Try renaming the ligand with a shorter name.
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use EVT_CONTEXT_MENU since the original was not working with py3
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py3 fixes
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adding requiments
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From https://pyrx.sourceforge.io/faq#cluster PyRx enables Cluster execution mode when, in addition to AutoDock binaries, you also have qsub (PBS or SGE) in your path. Please install PyRx on the head node and make sure that AutoDock binaries are available from all the nodes. PyRx creates individual job files for each protein-ligand docking and submit all the jobs to your cluster. Does this answer your question?
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Hi, where did you get /home/koby/Y/bin/vina from? Does it segfault if you run it by itself? You might need to compile Vina from the source.
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Dear Flavio, Sorry, no. The best option is to get the latest version for Windows. You can try using Download Snapshot on this version https://sourceforge.net/p/pyrx/code/472/tree/PyRxDev/PyRx/
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Look inside lib64/python2.6/site-packages/PyRx
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There is no estimated release date for the next version of PyRx yet. I'm planning to transition from python2 to python3 and that's taking too much time.
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Good question. I was thinking to include latest versions of Autodock and Vina in the next version of PyRx. I hope simply replacing the executables in the PyRx program folder works, but I haven't tried it yet.
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Great, thank you for using PyRx.
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You can run PyRx.bat instead. This is in the same folder as PyRx.vbs.
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Is these files exists, try making them with shorter names.
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Dear Flavio, Yes, the Linux version has this issue. You can try updating using instructions from https://pyrx.sourceforge.io/blog/127-recent-changes-in-vina-web-services-and-mac-os-x-updates- Best regards, Sargis
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Hi Flavio, Thanks for the message. I had to remove &> /dev/null part from run.sh so it can show the error message. These are packages I installed to make it work: sudo yum install https://rpmfind.net/linux/epel/9/Everything/x86_64/Packages/l/libpng12-1.2.57-18.el9.x86_64.rpm gtk2 sdl12-compat.x86_64 mesa-libGLU.x86_64 Let me know if it works for you. Best regards, Sarkis
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Please find out what ligand is causing the problem. You might be able to skip it and continue with the rest.
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Are you seeing the same error or is this a different error? Where did you download the latest version of PyRx, from?
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It adds Gasteiger charges for the proteins.
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You are welcome. Click on the + sign next to AutoDock to show more options.
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That is true. You can change what type of changes it makes using Edit-> Preferences menu. You can also set the charge calculation method there. There is no force field involved in this process. For AutoDock Vina in PyRx v0.9.8 you can refer to Vina paper and call it Vina scoring function. Docking is using a scoring function rather than a force field. There is a nice paragraph about this in the Vina paper- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641/ "Importantly, while molecular dynamics...
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I have googled the error message for you and found this https://github.com/ccsb-scripps/AutoDock-Vina/issues/268. Does that answer your 1st questions? Regarding 2nd question, you can apply the same settings. You can also copy the vina config file and use it for the command line.
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You are welcome. You can check if you can update following https://pyrx.sourceforge.io/blog/127-recent-changes-in-vina-web-services-and-mac-os-x-updates-
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You are welcome. You can check if you can update the following https://pyrx.sourceforge.io/blog/127-recent-changes-in-vina-web-services-and-mac-os-x-updates-
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Yes, you can ignore this if it works. It tries to set the path for one of your macromolecules and it comes up empty. If it is able to detect your macromolecule and run the docking then it is fine.
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Application Error during PyRx Installation Process
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Delete C:/Program Files (x86)/PyRx folder and try again.
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You are welcome. Are you an administrator of that laptop? Try installing and running PyRx using an account that has administrator privileges.
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I suggest opening a command terminal and copy/paste the content of pyrx.bat line by line in there.
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Try reinstalling. Which version of Windows are you running? Also, try running PyRx.bat from the installation folder to see if any error messages pop up.
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This is most likely version 0.8. You can use Help > About menu to show PyRx version number.
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Hello, PyRx doesn't work in 64-bit Mac's yet. You can use a VM for that https://www.pcmag.com/how-to/how-to-run-32-bit-apps-in-macos-catalina
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Thank you for the message. I'll PM a coupon code for additional discount.
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enable add tool
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You can either create the folder it is trying to use or delete .PyRx_workspacepreferences.ini from your home folder (C:\Users\farma?). I think you have changed workspace folder using Preferences menu and something happened to that folder.
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You can import Alpha Fold pdb in PyRx line any other pdb. What kind integration you have in mind? To run visual screening you need a HPC cluster instead of Kubernetes. PyRx can utilize HPC cluster on perm as well as Amazon HPC cluster.
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Decrease the search space/box
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Error Starting PyRx
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Have you or some other application you installed included 32-bit python ? You can rename C:\Users\renan\AppData\Roaming\Python\Python27 to something else (e.g. Python27_) to see if that works.
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Thanks. Please open cmd prompt, run these commands and send me the output. "C:\Program Files\PyRx\0.9.9\python.exe" import sys sys.path Attaching the output from my PC.
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Thanks. Please open cmd prompt, run these commands and send me the output. "C:\Program Files\PyRx\0.9.9\pythonw.exe" import sys sys.path Attaching the output from my PC.
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Yes, I haven't seen this error before and it seems that this can happen when you mix 32 and 64 python versions. Please run "C:\Program Files\PyRx\0.9.9\PyRx.bat" and send me the screenshot that shows entire screen from start to end like in the attached file.
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changed Structure Details Pane to show when Open Babel molecule is selected
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I wander what happened? To fix this, delete C:\Program Files\PyRx\0.9.9 folder and reinstall it again. What is your order number? Please let me know if this doesn't work so we can think about plan B.
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For AutoDock you can use Docking Parameters.. button on the Run AutoDock page to set the seed. For Vina, look at this post https://sourceforge.net/p/pyrx/discussion/general/thread/b70524ed/#c769
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Hello, this probably means that the results are not converged. You can get the same result using the same seed. For the publication, you'll probably need a higher exhaustiveness.
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Yes, you can run AutoGrid locally, or you can use Vina.
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The latest version is 1.0 and it is not free https://sites.fastspring.com/pyrx/instant/pyrx_windows
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I haven't seen this error before but you are probably running out of memory. You can get the latest version, which is 64-bit to see if that fixes this error.
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Dockamon changes from Omar Al-Attraqchi
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