Search found 26 matches

by nmarkham
Mon May 15, 2023 11:18 pm
Forum: mfold
Topic: Segmentation fault issue when plotting with sir_graph_ng
Replies: 6
Views: 51965

Re: Segmentation fault issue when plotting with sir_graph_ng

This is puzzling. I should be clear that I am not the author of mfold_util, but I'm fairly confident there are no limitations like what you described. I wonder if you can download this binary: http://www.unafold.org/for-julie/sir_graph_ng and try it in place of the one you have. It's statically link...
by nmarkham
Mon May 15, 2023 11:10 pm
Forum: UNAFold
Topic: type of DNA Sequence
Replies: 1
Views: 26188

Re: type of DNA Sequence

The fact that you've written them all with 5' at one end and 3' at the other suggests to me that they're linear. However, they're your sequences, not mine :D so only you know for sure!
by nmarkham
Thu May 11, 2023 8:39 pm
Forum: mfold
Topic: Segmentation fault issue when plotting with sir_graph_ng
Replies: 6
Views: 51965

Re: Segmentation fault issue when plotting with sir_graph_ng

This is odd. I tried that file and it worked for me.

Can you tell me what version of UNAFold you have, and how you installed it?
by nmarkham
Wed May 10, 2023 8:06 pm
Forum: mfold
Topic: Segmentation fault issue when plotting with sir_graph_ng
Replies: 6
Views: 51965

Re: Segmentation fault issue when plotting with sir_graph_ng

Hi Julie,

Can you post a ct file that shows this problem? I tried a few I had lying around, but none generated a SEGV even with the exact command line you used.

Thanks,
Nick
by nmarkham
Thu Feb 16, 2023 3:27 pm
Forum: UNAFold
Topic: UNAFold vs. mfold
Replies: 1
Views: 27921

Re: UNAFold vs. mfold

First, I want like to clarify that mfold and UNAFold both require licenses for commercial use. However, it does appear to be true that mfold is freely available for non-commercial use while UNAFold is not. (The "processing fee" associated with an academic license for UNAFold it not intende...
by nmarkham
Mon Jan 30, 2023 7:47 pm
Forum: mfold
Topic: mfold -predition with folding temp from dinamelt
Replies: 2
Views: 30965

Re: mfold -predition with folding temp from dinamelt

The Quikfold server at http://www.unafold.org/Dinamelt/applications/quickfold.php is powered by UNAFold rather than mfold, and we generally steer new users to UNAFold for a handful of reasons. However, I know it is possible to generate this kind of output from mfold, because Quikfold was powered by ...
by nmarkham
Tue Dec 20, 2022 9:36 pm
Forum: UNAFold
Topic: UnaFold avaibility? Or lack there of
Replies: 4
Views: 40620

Re: UnaFold avaibility? Or lack there of

Argh! I'm sorry they've ignored you. I responded to your email in hopes of getting RPI's attention. If this doesn't pan out soon, I'll explore some other ways of contacting someone at RPI. It occurs to me that it's probably between semesters now at RPI. There's a tiny chance we won't be able to get ...
by nmarkham
Wed Nov 30, 2022 5:11 pm
Forum: UNAFold
Topic: OligoArrayAux v3.8 compilation fail
Replies: 13
Views: 102672

Re: OligoArrayAux v3.8 compilation fail

Thank you for your patience and for helping me work this out! Now that we know what changes are necessary, I've updated http://www.unafold.org/Dinamelt/software/oligoarrayaux.php to have a source download for 3.8.1. For anyone interested in building OAA on an ARM Mac, now or in the future, version 3...
by nmarkham
Fri Nov 25, 2022 5:13 pm
Forum: UNAFold
Topic: OligoArrayAux v3.8 compilation fail
Replies: 13
Views: 102672

Re: OligoArrayAux v3.8 compilation fail

Hmm, maybe my C89-compatibility idea was half-baked. :( I'm baffled at those error messages from clang. Going back to getting the build to work "naturally", I think the next step would be to edit energy.h and change line 19 to "# define isFinite(x) isfinite(x)", i.e. add "is...
by nmarkham
Thu Nov 24, 2022 12:59 am
Forum: UNAFold
Topic: OligoArrayAux v3.8 compilation fail
Replies: 13
Views: 102672

Re: OligoArrayAux v3.8 compilation fail

Sorry, I should have been clear that it isn't the same line numbers in hybrid-min.c. The equal() function appears at line 2195, so it's lines 2200–2211 to delete. I didn't know what conda was until I Googled it just now. I don't really understand it; I don't think it has any relevance here, but I co...