prody/ProDy issues and pull requests

#1904 - Fix clustenm saving and loading

Pull Request - State: open - Opened by jamesmkrieger 18 days ago - 6 comments

#1903 - Streamline fixer and water filter for multiple structures

Pull Request - State: closed - Opened by jamesmkrieger 21 days ago - 4 comments

#1902 - bad change to mmCIF chain vs segment?

Issue - State: open - Opened by jamesmkrieger 24 days ago

#1901 - PRS matrix values more than 1

Issue - State: closed - Opened by Vini161 24 days ago - 5 comments

#1900 - cKDTree Problem

Issue - State: closed - Opened by rks5854 about 1 month ago - 47 comments

#1899 - parseMSA

Issue - State: closed - Opened by estrauch about 1 month ago - 3 comments

#1898 - How to set the path for ProDy in VMD

Issue - State: open - Opened by kiran923 about 2 months ago - 2 comments

#1897 - How to set the PATH for the ProDy in VMD

Issue - State: closed - Opened by kiran923 about 2 months ago - 1 comment

#1896 - Changes in external links [People & Bahar Lab]

Pull Request - State: closed - Opened by karolamik13 about 2 months ago

#1887 - people update

Pull Request - State: closed - Opened by karolamik13 2 months ago

#1874 - 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)

Issue - State: closed - Opened by mohad200 2 months ago - 2 comments

#1873 - ADP axes has a problem too

Issue - State: open - Opened by jamesmkrieger 2 months ago

#1872 - fix adp matrix

Pull Request - State: open - Opened by jamesmkrieger 2 months ago - 3 comments

#1871 - suppress problems with ligands in docs

Pull Request - State: open - Opened by jamesmkrieger 2 months ago

#1870 - PDB ligand XML files are replaced by CIF

Issue - State: open - Opened by jamesmkrieger 2 months ago

#1869 - fix setup.py to copy hpb

Pull Request - State: open - Opened by jamesmkrieger 2 months ago

#1868 - add no waters align error

Pull Request - State: closed - Opened by jamesmkrieger 2 months ago

#1867 - fix calcWaterBridgesTraj docs

Pull Request - State: closed - Opened by jamesmkrieger 2 months ago

#1866 - addMissingAtoms PDBFixer fails with InSty/WatFinder tutorial file

Issue - State: open - Opened by jamesmkrieger 2 months ago - 6 comments
Labels: Bug

#1865 - Bioexcel cv19

Pull Request - State: closed - Opened by jamesmkrieger 2 months ago

#1864 - fix consideredAtoms errors

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago

#1863 - add iterpose to catdcd

Issue - State: open - Opened by jamesmkrieger 3 months ago
Labels: Feature request

#1862 - fix bioexcel not timing out

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago

#1861 - add exGNM to save load model

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago - 1 comment

#1860 - split pqr coords by line positions when needed

Pull Request - State: open - Opened by jamesmkrieger 3 months ago - 2 comments

#1859 - It's now difficult to get pfam full alignments

Issue - State: open - Opened by jamesmkrieger 3 months ago

#1858 - set fetchPfamMSA default to seed

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago

#1857 - Failed to build prody / ERROR: Could not build wheels for prody, which is required to install pyproject.toml-based projects

Issue - State: closed - Opened by emilyrkang 3 months ago - 7 comments

#1856 - A weird bug of prody 2.4.1 on Python 3.9.0

Issue - State: closed - Opened by JinyinZha 3 months ago - 1 comment

#1855 - Bug in PQR parser

Issue - State: open - Opened by VonBoss 3 months ago - 12 comments

#1854 - fix missing norm in calcProj

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago

#1853 - Add Bioexcel cv19 database

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago - 6 comments

#1852 - Union on selections in one selstr raises TypeError

Issue - State: closed - Opened by tadsatlawa 3 months ago - 3 comments

#1851 - Pfam fix

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago

#1850 - pop nproc in clustenm app

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago

#1849 - Logistic regression for differences between sub-ensembles

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago - 2 comments

#1848 - add showProj proj input

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago

#1847 - cifheader fixes

Pull Request - State: closed - Opened by jamesmkrieger 3 months ago - 1 comment

#1846 - Errors when parsing mmCIF structures with mismatching chain ids

Issue - State: closed - Opened by sforli 3 months ago - 13 comments

#1845 - limit pyparsing<=3.1.1

Pull Request - State: closed - Opened by jamesmkrieger 4 months ago

#1844 - TypeError: can't multiply sequence by non-int of type 'Forward'

Issue - State: closed - Opened by al979 4 months ago - 3 comments

#1843 - Failure to correctly parse resnames with 4 letters

Issue - State: open - Opened by karolamik13 4 months ago - 3 comments

#1842 - More nucleosides

Pull Request - State: closed - Opened by jamesmkrieger 4 months ago - 3 comments

#1841 - error on tutorial Evolution of sequence, structure and dynamics with Evol and SignDy

Issue - State: open - Opened by Armanda87 4 months ago - 9 comments

#1840 - Failure to correctly parse all ligand chains in complex PDB file

Issue - State: closed - Opened by amorehead 4 months ago - 13 comments

#1839 - CoMD Analysis Issue - Coordsets must have more than 3 coordinate sets

Issue - State: open - Opened by klmcguire 4 months ago - 11 comments

#1838 - Adaptive ANM A to B then B to A, and mode issues

Issue - State: closed - Opened by klmcguire 4 months ago - 3 comments

#1837 - Adaptive ANM Saving Conformations

Issue - State: closed - Opened by klmcguire 4 months ago - 1 comment

#1836 - #ModuleNotFoundError: No module named 'StringIO' on tutorial

Issue - State: closed - Opened by Armanda87 4 months ago - 6 comments

#1835 - more Scipion minimal clustenm changes

Pull Request - State: closed - Opened by jamesmkrieger 4 months ago

#1834 - Frequency from normal mode analysis

Issue - State: closed - Opened by dulalmondal123 4 months ago - 4 comments

#1833 - ClustENM fitting changes needed for Scipion-EM-ProDy

Pull Request - State: closed - Opened by jamesmkrieger 4 months ago

#1832 - Normal Mode analysis of trajectory file using anm

Issue - State: closed - Opened by dulalmondal123 4 months ago - 3 comments

#1831 - Update app docs to include NMA

Pull Request - State: closed - Opened by jamesmkrieger 4 months ago

#1830 - Normal mode analysis of protein

Issue - State: closed - Opened by dulalmondal123 4 months ago - 4 comments

#1829 - does ProDy support non-numeric resnums?

Issue - State: closed - Opened by timodonnell 4 months ago - 6 comments
Labels: Feature request

#1828 - HTMD interface

Issue - State: open - Opened by jamesmkrieger 4 months ago
Labels: Feature request

#1827 - Pfam not completely working

Issue - State: closed - Opened by jamesmkrieger 5 months ago - 13 comments

#1826 - feature request: slice in adaptive ANM

Issue - State: open - Opened by MargotRiggi 5 months ago - 1 comment

#1825 - fix pfam test for pfam changes

Pull Request - State: closed - Opened by jamesmkrieger 5 months ago

#1824 - override GOOD_SEQID and GOOD_COVERAGE with seqid and coverage if higher

Pull Request - State: closed - Opened by jamesmkrieger 5 months ago

#1823 - add kmedoid clustering

Pull Request - State: closed - Opened by jamesmkrieger 5 months ago

#1822 - PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

Issue - State: open - Opened by jamesmkrieger 5 months ago

#1821 - What is the timescale of mode animations in VMD NMWhiz?

Issue - State: closed - Opened by jpajs 5 months ago - 3 comments

#1820 - Any way to predict the structure of a missing domain in state B from a full length structure of state A?

Issue - State: open - Opened by MargotRiggi 5 months ago - 9 comments

#1819 - rmsds of ClustENMD and issue with OpenMM8

Issue - State: closed - Opened by huangjianxiangzju 5 months ago - 5 comments

#1818 - Trouble Installing Prody

Issue - State: closed - Opened by jpajs 5 months ago - 4 comments

#1817 - update docs to include SignDy, InSty and WatFinder names

Pull Request - State: closed - Opened by jamesmkrieger 5 months ago - 1 comment

#1816 - fix alignBioPairwise for updated biopython

Pull Request - State: closed - Opened by jamesmkrieger 5 months ago - 5 comments

#1815 - fix networkx for updated versions

Pull Request - State: closed - Opened by jamesmkrieger 5 months ago - 5 comments

#1814 - Add write mmtf

Issue - State: closed - Opened by jamesmkrieger 5 months ago - 7 comments
Labels: Feature request

#1813 - Write cif via atomic conversion to biopython

Issue - State: closed - Opened by jamesmkrieger 5 months ago
Labels: Feature request

#1812 - add numResidues to Atomic

Pull Request - State: closed - Opened by jamesmkrieger 6 months ago

#1811 - fix default altloc mask size for parseMMCIF

Pull Request - State: closed - Opened by jamesmkrieger 6 months ago

#1810 - remove undefined var spacing

Pull Request - State: closed - Opened by jamesmkrieger 6 months ago

#1809 - add uniteChains to select app

Pull Request - State: closed - Opened by jamesmkrieger 6 months ago

#1808 - Several fixes related to fetching and writing pdb files

Pull Request - State: closed - Opened by jamesmkrieger 6 months ago

#1807 - various fixes for handling ensembles with selections as ref

Pull Request - State: open - Opened by jamesmkrieger 6 months ago - 1 comment

#1806 - add Kmediod clustering for ensembles

Issue - State: closed - Opened by jamesmkrieger 6 months ago - 1 comment
Labels: Feature request

#1805 - Bug in diferent version

Issue - State: closed - Opened by Armanda87 7 months ago - 2 comments

#1804 - fix no attribute _anisous

Pull Request - State: closed - Opened by jamesmkrieger 7 months ago

#1803 - include label 0 in showProjection

Pull Request - State: closed - Opened by jamesmkrieger 7 months ago

#1802 - Add Linear Discriminant Analysis

Pull Request - State: closed - Opened by jamesmkrieger 7 months ago

#1801 - Contacts of a trajectory ensemble

Issue - State: closed - Opened by Yago52 7 months ago - 4 comments

#1800 - fix cif file altloc mask

Pull Request - State: closed - Opened by jamesmkrieger 7 months ago

#1799 - fix ens degen error

Pull Request - State: closed - Opened by jamesmkrieger 7 months ago

#1798 - Options for writePDB TER, REMARK, END lines

Pull Request - State: closed - Opened by jamesmkrieger 7 months ago

#1797 - REMARK and END lines in a PDB file created by writePDB/writePDBStream

Issue - State: closed - Opened by Nick-322 7 months ago - 5 comments

#1796 - New features in calcSminaBindingAffinity

Pull Request - State: closed - Opened by karolamik13 8 months ago

#1795 - add report as argument for ciffile and cifheader

Pull Request - State: closed - Opened by jamesmkrieger 8 months ago

#1794 - Fewer warnings

Pull Request - State: closed - Opened by jamesmkrieger 8 months ago

#1793 - More robust handling of altloc

Pull Request - State: closed - Opened by dkoes 8 months ago - 2 comments

#1792 - adhoc fix for 6uwi for mmCIF

Pull Request - State: closed - Opened by jamesmkrieger 8 months ago - 5 comments

#1791 - look for cif and emd in path

Pull Request - State: closed - Opened by jamesmkrieger 8 months ago

#1790 - 6UWI doesn't parse

Issue - State: closed - Opened by dkoes 8 months ago - 1 comment

#1789 - Interactions

Pull Request - State: closed - Opened by karolamik13 8 months ago

#1788 - only get and set acs ind if hasattr

Pull Request - State: closed - Opened by jamesmkrieger 8 months ago

#1787 - Interactions

Pull Request - State: closed - Opened by karolamik13 8 months ago

#1786 - add seqsep to iterNeighbors

Pull Request - State: closed - Opened by jamesmkrieger 8 months ago - 1 comment

#1786 - add seqsep to iterNeighbors

Pull Request - State: closed - Opened by jamesmkrieger 8 months ago - 1 comment

GitHub / prody/ProDy issues and pull requests