haddocking / disvis Goto Github PK

Dear disvis maintainers,

I have found a typo in the main.py script, line 411. Here it says except Queue.Empty, which should read mp.Queue.Empty.

Regards, Henk

Specifying residues with multiple occupancies e.g.

ATOM      5  CA AARG A   1  ...
ATOM      6  CA BARG A   1  ...

in the interaction analysis causes Disvis to fail with following error:

ValueError: Some selected residues where not found in the PDB file. Please check your input residues.

This should probably either not fail at all or fail with a more specific error message.

Hi developer,

wonder how to generate figure 1 in your paper? Any script to do that? Thanks!

Provide either documentation or a script to visualize the AIC score in molecular visualization software. E.g. put numbers in BFactor column and visualize using spectrum.

refer to:
https://github.com/indigo-dc/ansible-role-disvis-powerfit/blob/master/dockers/docker-disvis/Dockerfile

I get this when building the docker image, don't know if it will affect later when running

building 'disvis.libdisvis' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-MW0004/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c src/libdisvis.c -o build/temp.linux-x86_64-2.7/src/libdisvis.o -ffast-math
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from src/libdisvis.c:283:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by "
^~~~~~~
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from src/libdisvis.c:283:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1453:1: warning: '_import_array' defined but not used [-Wunused-function]
_import_array(void)
^~~~~~~~~~~~~

Hi,

I got TabErrors:

  File "/home/almara/anaconda3/envs/disvis/lib/python3.10/site-packages/disvis-2.0.0-py3.10-linux-x86_64.egg/disvis/IO/mrc.py", line 84
    self._header['xstart'] = raw_header[49]
TabError: inconsistent use of tabs and spaces in indentation

File "/home/almara/anaconda3/envs/disvis/lib/python3.10/site-packages/disvis-2.0.0-py3.10-linux-x86_64.egg/disvis/IO/mrc.py", line 157
    else:
TabError: inconsistent use of tabs and spaces in indentation

The identations of lines 84-86 as well as 157-158 in the file disvis/IO/mrc.py are different to the rest of the file.

Thanks
A

Currently we learn about the how often a given restraint is violated, but have no info by how much.
A small violation (in terms of distance) might not be a big deal considering we are doing rigid body sampling.

An idea would be to analyse the set of models consistent with the largest possible number of restraints (i.e. not the total number of restraints) - this would be the value of N for which we still find acceptable models. For those models, we could then calculate the average distance violation for all restraints. This would this tell us by how much on average a distance is violated, and would allow to prioritise them for removal - a large violation should be more likely a real false positive than a small violation.

Hi,

I'm getting the following errors when compiling

src/_extensions.c:193:5: error: implicit declaration of function 'PyArray_XDECREF_ERR' is invalid in C99 [-Werror,-Wimplicit-function-declaration] PyArray_XDECREF_ERR(py_out);

src/_extensions.c:208:12: error: implicit declaration of function 'Py_InitModule' is invalid in C99 [-Werror,-Wimplicit-function-declaration] (void) Py_InitModule("_extensions", mymethods);

I am compiling on a M1 Mac running OS 12.6 (Monterey) using python 3.9.

Any assistance resolving this issue would be appreciated.

Cheers,
Mike

Would be nice to add back the reporting of the percentage of space already searched or remaining in disvis3 as for the previous version. Tells us what to expect as running time.

Allow inclusion of ambiguous distance restraints.

PyMol has proper capabilities of visualizing the densities, there are however a few less obvious commands to get a proper representation.