prody/ProDy

Issues

• Any way to predict the structure of a missing domain in state B from a full length structure of state A?

  #1820 opened 7 months ago by MargotRiggi
  11

• feature request: slice in adaptive ANM

  #1826 opened 4 days ago by MargotRiggi
  2

• ProDy support for Mac M1 chips

  #1913 opened 9 days ago by nbruciaferri
  1

• PDB ligand XML files are replaced by CIF

  #1870 opened 13 days ago by jamesmkrieger
  0

• Re-Install

  #1939 opened 20 days ago by rks5854
  10

• searchPfam fails to parse XML

  #1933 opened 23 days ago by NicholasMcCarthy
  1

• Troubleshooting COMD on ProDy with VMD 1.9.2

  #1930 opened a month ago by amarye
  6

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

  #1932 opened a month ago by TangYiChing
  9

• Cannot Find/Import Interactions module

  #1924 opened a month ago by ZlatomirTodorov
  7

• Average spring constant kappa calculation

  #1916 opened 2 months ago by Vini161
  7

• ImportError: druggability package was not found

  #1917 opened 2 months ago by accibio
  0

• Ensemble superpose

  #1912 opened 2 months ago by Yago52
  1

• Python 3.12 Support

  #1915 opened 2 months ago by xavierholt
  6

• PCA Calcmodes

  #1911 opened 2 months ago by Yago52
  4

• compatibility between tutorial data and generated data

  #1909 opened 2 months ago by juliaggggggg55555
  3

• Incompatibility with latest SciPy version 1.14.0

  #1906 opened 2 months ago by melschneider
  3

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

  #1905 opened 2 months ago by nbruciaferri
  1

• bad change to mmCIF chain vs segment?

  #1902 opened 3 months ago by jamesmkrieger
  0

• PRS matrix values more than 1

  #1901 opened 3 months ago by Vini161
  5

• cKDTree Problem

  #1900 opened 3 months ago by rks5854
  47

• How to set the path for ProDy in VMD

  #1898 opened 4 months ago by kiran923
  2

• Bug in PQR parser

  #1855 opened 5 months ago by VonBoss
  12

• addMissingAtoms PDBFixer fails with InSty/WatFinder tutorial file

  #1866 opened 5 months ago by jamesmkrieger
  6

• parseMSA

  #1899 opened 4 months ago by estrauch
  3

• How to set the PATH for the ProDy in VMD

  #1897 opened 4 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 4 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 5 months ago by emilyrkang
  7

• ADP axes has a problem too

  #1873 opened 5 months ago by jamesmkrieger
  0

• add iterpose to catdcd

  #1863 opened 5 months ago by jamesmkrieger
  0

• It's now difficult to get pfam full alignments

  #1859 opened 5 months ago by jamesmkrieger
  0

• A weird bug of prody 2.4.1 on Python 3.9.0

  #1856 opened 5 months ago by JinyinZha
  1

• Errors when parsing mmCIF structures with mismatching chain ids

  #1846 opened 5 months ago by sforli
  13

• Adaptive ANM A to B then B to A, and mode issues

  #1838 opened 5 months ago by klmcguire
  3

• Union on selections in one selstr raises TypeError

  #1852 opened 5 months ago by tadsatlawa
  3

• Pfam not completely working

  #1827 opened 5 months ago by jamesmkrieger
  13

• Failure to correctly parse all ligand chains in complex PDB file

  #1840 opened 6 months ago by amorehead
  13

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

  #1844 opened 6 months ago by al979
  3

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

  #1841 opened 6 months ago by Armanda87
  9

• Failure to correctly parse resnames with 4 letters

  #1843 opened 6 months ago by karolamik13
  3

• CoMD Analysis Issue - Coordsets must have more than 3 coordinate sets

  #1839 opened 6 months ago by klmcguire
  11

• Adaptive ANM Saving Conformations

  #1837 opened 6 months ago by klmcguire
  1

• #ModuleNotFoundError: No module named 'StringIO' on tutorial

  #1836 opened 6 months ago by Armanda87
  6

• Frequency from normal mode analysis

  #1834 opened 6 months ago by dulalmondal123
  4

• Normal Mode analysis of trajectory file using anm

  #1832 opened 6 months ago by dulalmondal123
  3

• Normal mode analysis of protein

  #1830 opened 6 months ago by dulalmondal123
  4

• does ProDy support non-numeric resnums?

  #1829 opened 6 months ago by timodonnell
  6

• HTMD interface

  #1828 opened 7 months ago by jamesmkrieger
  0

• rmsds of ClustENMD and issue with OpenMM8

  #1819 opened 7 months ago by huangjianxiangzju
  5

• What is the timescale of mode animations in VMD NMWhiz?

  #1821 opened 7 months ago by jpajs
  3

• PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

  #1822 opened 7 months ago by jamesmkrieger
  0