Christian Seitz

icon indicating a website link https://christianseitz21.owlstown.net/

icon company University of Chicago icon location Chicago, Illinois icon location Postdoc in computer science at the University of Chicago and Argonne National Laboratory, working on machine learning and viruses

Results 17 comments of Christian Seitz

System size limitation in writeNMD and/or NMWiz

Alright thanks! I dug a bit more and believe this is actually two issues. I don't think that writeNMD can handle this many residues; when I save and then reload...

System size limitation in writeNMD and/or NMWiz

Hi James, Thanks for looking into this. Using writeNMD and then parseNMD gives the expected output - the loaded modes look identical to the previously created modes, both in atom...

System size limitation in writeNMD and/or NMWiz

that would be great!! If you make any progress I would surely use an ANM animation in my upcoming publication~

System size limitation in writeNMD and/or NMWiz

Sorry for the delay. I've tried to make an ensemble through traverseMode. From there I could use setAtoms and then writePDB and the load this pdb in pymol or chimera...

System size limitation in writeNMD and/or NMWiz

Hi James, Sorry for another silly question, but can you tell me what I'm doing wrong here? I have selected the alpha carbons and created GNM modes from those. I...

System size limitation in writeNMD and/or NMWiz

thanks, that works now!

Tips on combining features across systems

Ah thanks for this explanation and the paper reference, it also contains clear explanations. The only part I don't understand is when you say, "Make sure you're taking care of...

Standard library logic error (bug): (exception type: St12out_of_range) vector::_M_range_check: __n (which is 2) >= this->size() (which is 2)

Hi Gianni, I am not a regular user of Gromacs and forgot it uses nm as distance units, thanks for reminding me. When I convert these values to appropriate units,...

Standard library logic error (bug): (exception type: St12out_of_range) vector::_M_range_check: __n (which is 2) >= this->size() (which is 2)

In VMD, the pore found from the ```pf-cutoff 0 ``` looks more or less normal. Adjusting the cutoff values to 20 or 30 angstroms still gives the same error, that...

Standard library logic error (bug): (exception type: St12out_of_range) vector::_M_range_check: __n (which is 2) >= this->size() (which is 2)

Hello, I am still finding this error: ``` (exception type: St13runtime_error) Could not converge error bound without exceeding maximum truncation number p = 500. ``` Normally, when I use syntax...