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PyMod cannot connect to the network, e.g. by installing External Tools and using Remote BLAST. But the computer network is fine. PyMod runs on Windows 10. On this system I can access github and blast.ncbi through my browser. On the system running PyMod, both pip and conda are able to access the network and download the software.

Dear developers;
Pymod is a really nice tool for a beginner in protein homology modeling,i have install pymol in my linux system,However, I did not find the corresponding command to install and use PyMol from the user manual,How to install and use in linux system without GUI,Looking forward to your reply,thanks

Hi
What is the cause of the uploaded error?

Bio.SubsMat has been deprecated for a while and now has seemingly been removed for Biopython 1.8.
I believe that Biopython now recommends to use Bio.Align.substitution_matrices in its place for getting sub mat data.

It says "An internet connection is not available...",but obviously my computer is connected.So if you can help me to find the real problem that we can fix.
thank you!

Hey... guessing this is similiar issue to DockingPie, no matter the pymol version I use the installation box for modeller says this version of pymol doesnt have conda, even if I used Conda to install that pymol

Easy way to manually add modeller not involving the GUI by chance?

Thanks

Hello all, I want to analyze the Protein Contacts in my structure. I have two chains in my structure and when I want to analyze contact between these two chains and then I click on the Contact Map. but it shows this error.

In the DOPE profile window, the "interact on click" function seems to also interact with hidden plots (deselected models on the right-hand list). This is somewhat unintuitive. (Great software by the way.)

The sequence cannot be displayed in the SEQUENCE ID and SEQUENCES sections after submitting the selected sequence when running NCBI BLAST using pymod 3.0.2. Simultaneously, an error occurs in PyMol, and the traceback is as follows:
Traceback (most recent call last):
File "D:\pymol\pymol_edu\pymol_edu_install\lib\site-packages\pmg_tk\startup\pymod3\pymod_lib\pymod_protocols\similarity_searches_protocols_base_blast.py", line 879, in
self.main_button.clicked.connect(lambda a=None: self.protocol.blast_results_state())
File "D:\pymol\pymol_edu\pymol_edu_install\lib\site-packages\pmg_tk\startup\pymod3\pymod_lib\pymod_protocols\similarity_searches_protocols_base_blast.py", line 445, in blast_results_state
self.import_results_in_pymod()
File "D:\pymol\pymol_edu\pymol_edu_install\lib\site-packages\pmg_tk\startup\pymod3\pymod_lib\pymod_protocols\similarity_searches_protocols_base_blast.py", line 583, in import_results_in_pymod
raise Exception("The query sequence returned by '%s' is not the same of the original one." % self.blast_version)
Exception: The query sequence returned by 'blast' is not the same of the original one.

I used to install the Pymod bundle installer with the install_all.py script pretty easily. However, once I actualized PyMol to its newest version (2.3) the old, good install_all.py script does not work anymore. Many "missing parentheses" appear in the error warnings.

Hi pymod developers,

I have a problem with modeller installation. I am trying to use PyMod 3.0.2 through PyMol 2.3.3.
I am keep getting "No module named tqdm" when I am trying install modeller using the right license key.

I used command prompt on windows for pip install tqdm and the requirement already satisfied.

What am I doing wrong?

-Eunok