prody/ProDy

Issues

• Error using calcModes()

  #1955 opened 3 months ago by Tuyt691
  10

• How to get original SEQRES?

  #1949 opened 2 months ago by lokapal
  9

• Problem with calcADPAxes

  #1975 opened 2 months ago by karolamik13
  2

• writePDB writes improper file

  #1973 opened 3 months ago by hnguyentt
  10

• Missing some residues for hetero atom (hetatm)

  #1968 opened 3 months ago by hnguyentt
  21

• update clustenm for openmm 8

  #1971 opened 3 months ago by jamesmkrieger
  0

• new cif fields (Annotation of Protein Modifications in the PDB)

  #1970 opened 3 months ago by jamesmkrieger
  0

• Average spring constant kappa calculation

  #1916 opened 3 months ago by Vini161
  7

• ExtendModel Nodes and Atoms Incompatible

  #1962 opened 3 months ago by rks5854
  20

• Issue installing ProDy on Windows through anaconda prompt

  #1966 opened 3 months ago by dmk125
  4

• `turbo` option is depriciated from SciPy 1.14.0

  #1964 opened 3 months ago by igorsdub
  1

• Python 3.12 Support

  #1915 opened 5 months ago by xavierholt
  21

• findClusterCenters

  #1951 opened 4 months ago by mmuratyas
  15

• ImportError While Using the ProDy Interface in NMWizard

  #1961 opened 3 months ago by DaddyDaddyFish
  9

• Error using calcCrossCorr with n_cpus > 1

  #1960 opened 3 months ago by apbusia
  12

• Pytorch 2.4 compatibility

  #1956 opened 3 months ago by itrase
  2

• Pdb ligand format changes

  #1957 opened 3 months ago by jamesmkrieger
  0

• GNM works but not ANM

  #1952 opened 3 months ago by rks5854
  3

• ProDy support for Mac M1 chips

  #1913 opened 4 months ago by nbruciaferri
  1

• PDB ligand XML files are replaced by CIF

  #1870 opened 4 months ago by jamesmkrieger
  0

• Re-Install

  #1939 opened 4 months ago by rks5854
  10

• searchPfam fails to parse XML

  #1933 opened 4 months ago by NicholasMcCarthy
  1

• Troubleshooting COMD on ProDy with VMD 1.9.2

  #1930 opened 5 months ago by amarye
  6

• InSty: NameError: name 'Interactions' is not defined

  #1932 opened 5 months ago by TangYiChing
  9

• Cannot Find/Import Interactions module

  #1924 opened 5 months ago by ZlatomirTodorov
  7

• ImportError: druggability package was not found

  #1917 opened 5 months ago by accibio
  0

• Ensemble superpose

  #1912 opened 5 months ago by Yago52
  1

• PCA Calcmodes

  #1911 opened 5 months ago by Yago52
  4

• compatibility between tutorial data and generated data

  #1909 opened 6 months ago by juliaggggggg55555
  3

• Incompatibility with latest SciPy version 1.14.0

  #1906 opened 6 months ago by melschneider
  3

• float division by zero exception raised if using prody_align with mmCIF files

  #1905 opened 6 months ago by nbruciaferri
  1

• bad change to mmCIF chain vs segment?

  #1902 opened 7 months ago by jamesmkrieger
  0

• PRS matrix values more than 1

  #1901 opened 7 months ago by Vini161
  5

• cKDTree Problem

  #1900 opened 7 months ago by rks5854
  47

• How to set the path for ProDy in VMD

  #1898 opened 7 months ago by kiran923
  2

• Bug in PQR parser

  #1855 opened 9 months ago by VonBoss
  12

• addMissingAtoms PDBFixer fails with InSty/WatFinder tutorial file

  #1866 opened 8 months ago by jamesmkrieger
  6

• parseMSA

  #1899 opened 7 months ago by estrauch
  3

• How to set the PATH for the ProDy in VMD

  #1897 opened 7 months ago by kiran923
  1

• dear all researcher, can you guide me, I have install ProDy in Windows , using pip install -U prody and found an error please see the attached file (Capture-1 and Capture-2) when opened ProDy in VMD, i found this error please see the attached file because am not able to find the path of ProDy (Capture-3 to 5)

  #1874 opened 8 months ago by mohad200
  2

• Failed to build prody / ERROR: Could not build wheels for prody, which is required to install pyproject.toml-based projects

  #1857 opened 8 months ago by emilyrkang
  7

• ADP axes has a problem too

  #1873 opened 8 months ago by jamesmkrieger
  0

• add iterpose to catdcd

  #1863 opened 9 months ago by jamesmkrieger
  0

• It's now difficult to get pfam full alignments

  #1859 opened 9 months ago by jamesmkrieger
  0

• A weird bug of prody 2.4.1 on Python 3.9.0

  #1856 opened 9 months ago by JinyinZha
  1

• Errors when parsing mmCIF structures with mismatching chain ids

  #1846 opened 9 months ago by sforli
  13

• Union on selections in one selstr raises TypeError

  #1852 opened 9 months ago by tadsatlawa
  3

• TypeError: can't multiply sequence by non-int of type 'Forward'

  #1844 opened 9 months ago by al979
  3

• error on tutorial Evolution of sequence, structure and dynamics with Evol and SignDy

  #1841 opened 9 months ago by Armanda87
  9

• Failure to correctly parse resnames with 4 letters

  #1843 opened 9 months ago by karolamik13
  3