PyMol saves mmCIF without auth_seq_id, fall back to label_seq_id #325
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milot-mirdita
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Jul 9, 2024
gamcil
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Oct 26, 2024
d2d09b58 Merge pull request #330 from stromjm/interface_v2.0 4e514a2a Merge branch 'steineggerlab:master' into interface_v2.0 8daecacc except overlap e1f38a1e Merge pull request #362 from rachelse/master 6b00c5d9 Merge pull request #366 from rachelse/steineggerlab c18727e4 Deleted search-clust pipeline from README 3d85d5c4 minor d692f966 there could exist no match against itself e1f238df error a078fb9f typo in readme 24c8c92b treat monomer as singleton when scoremultimer uses --monomer-include-mode 1 1d5f9369 fix interface extraction exceptions c27a629a single chain alignment bug fixed 19c8820c Merge pull request #359 from steineggerlab/multimer 079a5a13 monomer related update done 06275df3 rollback to 43fd26f3d3e043c8f9fd4c2b193a8b68f8781689 4046f00f test rbh filter off 13e9883c Merge branch 'multimer' of https://github.com/steineggerlab/foldseek into multimer 2dadffc0 test rbh filter off 83cc643b update single chain cluster a17598cd build exceptions for interface mode 43fd26f3 remove tmscore threshold 704c3a82 fix chain cov ratio 1800e6a9 update for single chained alignments cd26d54c implement complex-tm-threshold 0b1fa423 typo c74a1a5f replace singlechain mode into monomer mode 34104148 merged steineggerlab/foldseek d414d908 merged steineggerlab/foldseek 232a4c43 Merge pull request #353 from rachelse/master 19595fd5 order in LocalParameters c5412cf7 Merge remote-tracking branch 'upstream/master' into interface_v2.0 c1a6b76c merged steineggerlab/foldseek 88093635 Merge pull request #354 from steineggerlab/test d267b3d8 bug fixed 7f2c6219 bug fix try4 abff375e bug fix try3 25e9629c bug fix try2 d9b2913b bug fix try1 8711f6b7 minor things 48666e18 typo in Readme 154019b6 Merge remote-tracking branch 'upstream/master' a2ec51d4 fix parameter explain 306ffb82 add parameter for single chained assignments b7c58acb Update regression 2c6b809d Update regression and convertalis ALNTMSCORE score 7e6be60a Revise alignment TMscore computation ab20120e scoremultimer 319144b4 minor 7112fccb minor e9b0f234 check alinged chain num when interfacelddt 2256e219 Merge pull request #345 from steineggerlab/foldseek_multiple_with_singlechain 9a2b7da4 bug fixed: single elemented vector for single chain alignment d99d79c1 single chain allowing multimersearch 52029c06 Added BFVD as a foldseek database (#344) af1e86e5 default parameters e1d15f64 alnLen seems much better 5b76247b minor ac0a32b1 minor 06016bdd minor fd87b160 added parameters in example in Readme 17402748 added coverage in Readme f1fc6a96 minor 1b39c482 big complex first to prevent big ones to be left and run alone for few hours using 1 thread 08b7e9ce previous version is twice faster de945b2b simd returns segfault 602ff37b Merge branch ‘steineggerlab:master’ into master be9fc339 Merge pull request #343 from steineggerlab/foldseek_multimer_bottleneck 3bcdabae checkChainRedundancy with unordered_sets 5a4ad0be foundNeighbors as an unordered_set b15e236a foldseek-multimer bottleneck solved b947f688 implement foundNeighbors 89f371bb DBSCAN as non-recursive function 9f603b29 check new scoremultimer 4f70b3f4 Readme 50c1df1b Readme 4f1592a4 Readme c3093cd3 outputs filtcov too 420038de chaging readme 3fd78777 chaging readme aa2ced33 all_seqs.fasta not working d1605fe7 SIMD for tmscore 72f5028c map to vector, complex to multimer, [TODO] check if speed improved 63bca7b2 remove distMap 73e41342 seq3di.clear() in GemmiWrapper 2758b96e Merge branch 'master' into interface_v2.0 9d74a1bf orders of Parameters 94874214 make mergeable 2b731d3c Updated regression 02fb1e58 Updated submodule 17986f4c code styles 6db582ea made filtermultimer to get one argument as output. 'output' and 'outout_info' will be the actual outputs a6bee293 important issue solved, thread_idx while writing 4bbdca4f minor aeacb68b changed way to buffer for ustring, tstring 05a80c58 filtcov.tsv to complex_filt_info file. createtsv query query complex_filt_info filtcov.tsv possible 51197117 minor 868bfb1c Update README.md 3ed737c0 Add --tmscore-threshold-mode to allow to switch normalization 552e18dc Fix convertalis and alignment normalization 6b77a4f6 code styles b40729c1 Fix issue steineggerlab/foldseek#312 alntmscore is now normalized by the backtrace length 0415c37c minor issues edef0856 two db lines for each interface 9730f059 minor 2639127a Camel ce4528b1 Use MathUtil squaredist 69d397b2 consistency loss with multithreading solved a21576a0 mergeable, also only if at least 4 residues 0d82857c mergeable, only if at least 4 residues aefcffca Addition of interface code 6740f823 merged steineggerlab/foldseek 71b1f38f complex_h 56d3adbd monomer in scoremultimer aa30bec5 NogridInterface 928984bf Add BFMD database to repository bde99a74 Add ungappedprefilter to it. profile searches 16dc9150 complex-multimer DBSCAN earlystop with maxClusterNum 04876ca2 Merge commit '97d4c6cfb57bb7f0994015580579f31a18aaf9c5' 97d4c6cf Squashed 'lib/mmseqs/' changes from 804bb2af6d..ffb05619ca 0f6bb3cc Deleted original interfaceLDDT code file 22d24ffc Separated interface retrieving and saving 7b5e7287 Implemented interfaceLDDT but naive e478a324 Saved aligned coordinates into vector but cannot use SIMD operations 75013627 Sync with master branch c86d2ce3 solved complex_db_h for monomers 50208e9b Merged commit with review 3d26d2ee commit before pull 27756597 changed order of elements in struct and class for memory e35f355f setting default parameter collides with existing default values 543db3ad createtsv with --threads 1 to make complex_db_h in order a8f0a091 The mistake was not a big problem. One stage before putting iLDDT code 3fd0dab7 Corrected targetcomplexid mistake & chain number comparison 6a94924e Corrected mistake: Saved dbKey as target complex id so far.. 3123bae1 Removed redundant loops and improved performance cdf6e786 minor, input->query e44ea30e Made Complex struct and implementation is in progress 3922544e Inactivated filter-mode param: chainNum & conformation is affected 7e3e4764 Recovery point : saved previous iLDDT implementation b6943b8e Merge branch 'steineggerlab:master' into master 6494f8a6 minor bc212bc8 FoldseekBase.cpp update (#306) 3df6bc46 solved everything 7635ea3d minor a82587c6 minor c5f59d20 Merge branch 'steineggerlab:master' ee77f9d7 Merge 4604c238 complex to multimer 25812ffa Try moving to macos 11 in azure pipelines CI ebfdc666 Revert "Fix GCC 14 warnings" 044806f3 Fix GCC 14 warnings 59d2a253 Fix pymol mmcif files breaking gemmi (upstreamed here project-gemmi/gemmi#325) e06bc508 octant 1da321c2 not done, but added vector check e8469df0 Update filtercomplex.cpp 5b10e67f Update filtercomplex.cpp cb0a43ec minor b31f2ada reset 8bc07703 reset cb277387 [MAYBE SOLVED} chainTM c411e323 DbKey to AlnId/DbId 01a39259 Check if no aligned chain exists 693d723d res.Len seems right 3855d2e8 Look at this. ChainTM goes higher than 1 a8f6588f simple 09b4e410 Solved Multithreading fe0c9383 [TODO] multithreading segfault e4abea41 Revert "maybe solved chain TM" 27f9ac86 maybe solved chain TM 0430e9e5 Calculate chain TM everytime a78bbd5d Set default param as set4final when computing chaintmscore e333ad48 Made few comments reviewing filtercomplex.cpp 8f2ab715 simplify building complex header cf28e076 parsing problem solved 55b5338c memcpy error solve 6f3ac2b6 parsing with pdb d02373d8 parsing 961b8cf0 removing extension a2ea4743 make filtcov.tsv not db 0bc9d97d minor f3a9c22b minor 36490d18 minor change 77936ab3 handling monomer & calculate chainTM if complexTM satisfied a0b426ef Merge branch 'steineggerlab:master' into master 79ad721c Solved weird chain TM-score behavior 81fbfd99 Implemented per-chain-tm but tmscore is suspicious e44034e6 Implemented realloc function in Coordinate.h 6ef9dc7b modified complex header 94da95c4 complex header make 5e47a2ac still 99251fd6 complexheader, but still issue exists 4e7c3624 Revised code of filter complex a27efde9 tmthreshold parameter 52f0459a TODO maybe TMthreshold c1294530 both tm for all cov modes 7367a247 assID, query, target, coverage(1 or 2), tm(1 or 2) ff5a8e5f filtercomplex tmp coverage.tsv 73c2aa7a Merge branch 'steineggerlab:master' into master 369842e2 Solved argument list too long issue 4329b254 Finalized rmdb 81ac5ef5 Generates comment about rep complex in fastafile b7a27454 easy-cc description b25de75f remove tmp files 4ceb9ada Completed to output rep seqs fasta file 560c6e49 temporary Result2repseq d16ac100 tmp remove 7e5bd089 changed tmp dir 86f5fe9e colsed easycc 412b51d0 header file fa875fdf making complex header file fe9865cb small changes 819a75a8 add description 06945aed Parameters 7d34bcbb default parameters e3defcd4 separated buildCmplDb from filtercomplex 83100b8e Solved complexsearch parameter not applied problem 607c14fc Success command run 9b183905 share status 7e054b6f [DONE] Build successed. [TODO] Default Parameter setting 6ac16224 finally make works c3a7c959 [TODO] Solve conflicts during make 8dd17b24 Organized shell scripts a36b8c7e git conflicts 6db40b57 tmp LocalParameters.cpp dd34d670 still build failed aebd3fd8 small changes b9d73150 .cpp files 02a89148 easycc and cc .sh dbd9b076 To Complexclusterworkflow f7b9508e Changes 03c635e5 Changed ComplexCluster into FilterComplex ec234b1d revised parameters for filtercomplex 39b2f062 renamed complexcluster.sh to filtercomplex.sh and finalized 47cfb386 share status 40a0e719 to share status 413faeeb Add filtercomplex parameter for coverage 8667be3d [TODO] Build failed. check localparameters, workflowfiles, etc. 3782b550 Made workflow file e15a2241 [IN PROGRESS] separated complexcluster and easycomplexcluster but need to organize 84c5279f FoldSeelBase.cpp should be changed though, easy-complexcluster output instruction 017ad0fe Updated LocalParameter files 83a46549 clustered results to flatfiles 38b60958 data/CMakeLists update 46611c48 CMakeLists update 51d29b8c Changed complexcluster.sh to easycomplexcluster.sh 69876616 Merge branch 'master' of https://github.com/rachelse/foldseek b5c45c37 minor modification ef00e785 [IN PROGRESS] Draft state complexcluster.sh 5ac175fd erased default -c 0.8 aaf1a6b1 complexclust.sh e52c527a cleaned code b7bc37fc -c default 0.8 d81811f9 TODO: select highest aligned alignments among same complex-complex & what if user wants to use -c 0.0? 5adeb999 no errors, not debugged yet 03860d19 has error, but for sharing status. Coverge criteria 47c37e08 Merge branch 'steineggerlab:master' into master 35c5914a Merge branch 'steineggerlab:master' into master bb7ec93b First version for complex filter git-subtree-dir: lib/foldseek git-subtree-split: d2d09b588f50d5f8e2fd7a958377a33b2f725415
gamcil
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Dec 4, 2024
33103374 Add parameter for taxonomy report in easy-search (#389) 3cad1360 Fix cluster reassign + tm-align #383 b43e63d7 Rework residue mapping to combine most gemmi AAs with prev FS AAs #387 8c3e3938 Merge pull request #385 from rachelse/master 7a3a9db3 Merge branch 'steineggerlab:master' into master 214886bb Update citations d295eec6 Replace rust with rustup in github CI 8485aaf9 Switch mac arm test to github hosted runner b011b8e4 lddt works when chaintm 0 d6056322 Fix convertalis for FS multimer d2d09b58 Merge pull request #330 from stromjm/interface_v2.0 4e514a2a Merge branch 'steineggerlab:master' into interface_v2.0 8daecacc except overlap e1f38a1e Merge pull request #362 from rachelse/master 6b00c5d9 Merge pull request #366 from rachelse/steineggerlab c18727e4 Deleted search-clust pipeline from README 3d85d5c4 minor d692f966 there could exist no match against itself e1f238df error a078fb9f typo in readme 24c8c92b treat monomer as singleton when scoremultimer uses --monomer-include-mode 1 1d5f9369 fix interface extraction exceptions c27a629a single chain alignment bug fixed 19c8820c Merge pull request #359 from steineggerlab/multimer 079a5a13 monomer related update done 06275df3 rollback to 43fd26f3d3e043c8f9fd4c2b193a8b68f8781689 4046f00f test rbh filter off 13e9883c Merge branch 'multimer' of https://github.com/steineggerlab/foldseek into multimer 2dadffc0 test rbh filter off 83cc643b update single chain cluster a17598cd build exceptions for interface mode 43fd26f3 remove tmscore threshold 704c3a82 fix chain cov ratio 1800e6a9 update for single chained alignments cd26d54c implement complex-tm-threshold 0b1fa423 typo c74a1a5f replace singlechain mode into monomer mode 34104148 merged steineggerlab/foldseek d414d908 merged steineggerlab/foldseek 232a4c43 Merge pull request #353 from rachelse/master 19595fd5 order in LocalParameters c5412cf7 Merge remote-tracking branch 'upstream/master' into interface_v2.0 c1a6b76c merged steineggerlab/foldseek 88093635 Merge pull request #354 from steineggerlab/test d267b3d8 bug fixed 7f2c6219 bug fix try4 abff375e bug fix try3 25e9629c bug fix try2 d9b2913b bug fix try1 8711f6b7 minor things 48666e18 typo in Readme 154019b6 Merge remote-tracking branch 'upstream/master' a2ec51d4 fix parameter explain 306ffb82 add parameter for single chained assignments b7c58acb Update regression 2c6b809d Update regression and convertalis ALNTMSCORE score 7e6be60a Revise alignment TMscore computation ab20120e scoremultimer 319144b4 minor 7112fccb minor e9b0f234 check alinged chain num when interfacelddt 2256e219 Merge pull request #345 from steineggerlab/foldseek_multiple_with_singlechain 9a2b7da4 bug fixed: single elemented vector for single chain alignment d99d79c1 single chain allowing multimersearch 52029c06 Added BFVD as a foldseek database (#344) af1e86e5 default parameters e1d15f64 alnLen seems much better 5b76247b minor ac0a32b1 minor 06016bdd minor fd87b160 added parameters in example in Readme 17402748 added coverage in Readme f1fc6a96 minor 1b39c482 big complex first to prevent big ones to be left and run alone for few hours using 1 thread 08b7e9ce previous version is twice faster de945b2b simd returns segfault 602ff37b Merge branch ‘steineggerlab:master’ into master be9fc339 Merge pull request #343 from steineggerlab/foldseek_multimer_bottleneck 3bcdabae checkChainRedundancy with unordered_sets 5a4ad0be foundNeighbors as an unordered_set b15e236a foldseek-multimer bottleneck solved b947f688 implement foundNeighbors 89f371bb DBSCAN as non-recursive function 9f603b29 check new scoremultimer 4f70b3f4 Readme 50c1df1b Readme 4f1592a4 Readme c3093cd3 outputs filtcov too 420038de chaging readme 3fd78777 chaging readme aa2ced33 all_seqs.fasta not working d1605fe7 SIMD for tmscore 72f5028c map to vector, complex to multimer, [TODO] check if speed improved 63bca7b2 remove distMap 73e41342 seq3di.clear() in GemmiWrapper 2758b96e Merge branch 'master' into interface_v2.0 9d74a1bf orders of Parameters 94874214 make mergeable 2b731d3c Updated regression 02fb1e58 Updated submodule 17986f4c code styles 6db582ea made filtermultimer to get one argument as output. 'output' and 'outout_info' will be the actual outputs a6bee293 important issue solved, thread_idx while writing 4bbdca4f minor aeacb68b changed way to buffer for ustring, tstring 05a80c58 filtcov.tsv to complex_filt_info file. createtsv query query complex_filt_info filtcov.tsv possible 51197117 minor 868bfb1c Update README.md 3ed737c0 Add --tmscore-threshold-mode to allow to switch normalization 552e18dc Fix convertalis and alignment normalization 6b77a4f6 code styles b40729c1 Fix issue steineggerlab/foldseek#312 alntmscore is now normalized by the backtrace length 0415c37c minor issues edef0856 two db lines for each interface 9730f059 minor 2639127a Camel ce4528b1 Use MathUtil squaredist 69d397b2 consistency loss with multithreading solved a21576a0 mergeable, also only if at least 4 residues 0d82857c mergeable, only if at least 4 residues aefcffca Addition of interface code 6740f823 merged steineggerlab/foldseek 71b1f38f complex_h 56d3adbd monomer in scoremultimer aa30bec5 NogridInterface 928984bf Add BFMD database to repository bde99a74 Add ungappedprefilter to it. profile searches 16dc9150 complex-multimer DBSCAN earlystop with maxClusterNum 04876ca2 Merge commit '97d4c6cfb57bb7f0994015580579f31a18aaf9c5' 97d4c6cf Squashed 'lib/mmseqs/' changes from 804bb2af6d..ffb05619ca 0f6bb3cc Deleted original interfaceLDDT code file 22d24ffc Separated interface retrieving and saving 7b5e7287 Implemented interfaceLDDT but naive e478a324 Saved aligned coordinates into vector but cannot use SIMD operations 75013627 Sync with master branch c86d2ce3 solved complex_db_h for monomers 50208e9b Merged commit with review 3d26d2ee commit before pull 27756597 changed order of elements in struct and class for memory e35f355f setting default parameter collides with existing default values 543db3ad createtsv with --threads 1 to make complex_db_h in order a8f0a091 The mistake was not a big problem. One stage before putting iLDDT code 3fd0dab7 Corrected targetcomplexid mistake & chain number comparison 6a94924e Corrected mistake: Saved dbKey as target complex id so far.. 3123bae1 Removed redundant loops and improved performance cdf6e786 minor, input->query e44ea30e Made Complex struct and implementation is in progress 3922544e Inactivated filter-mode param: chainNum & conformation is affected 7e3e4764 Recovery point : saved previous iLDDT implementation b6943b8e Merge branch 'steineggerlab:master' into master 6494f8a6 minor bc212bc8 FoldseekBase.cpp update (#306) 3df6bc46 solved everything 7635ea3d minor a82587c6 minor c5f59d20 Merge branch 'steineggerlab:master' ee77f9d7 Merge 4604c238 complex to multimer 25812ffa Try moving to macos 11 in azure pipelines CI ebfdc666 Revert "Fix GCC 14 warnings" 044806f3 Fix GCC 14 warnings 59d2a253 Fix pymol mmcif files breaking gemmi (upstreamed here project-gemmi/gemmi#325) e06bc508 octant 1da321c2 not done, but added vector check e8469df0 Update filtercomplex.cpp 5b10e67f Update filtercomplex.cpp cb0a43ec minor b31f2ada reset 8bc07703 reset cb277387 [MAYBE SOLVED} chainTM c411e323 DbKey to AlnId/DbId 01a39259 Check if no aligned chain exists 693d723d res.Len seems right 3855d2e8 Look at this. ChainTM goes higher than 1 a8f6588f simple 09b4e410 Solved Multithreading fe0c9383 [TODO] multithreading segfault e4abea41 Revert "maybe solved chain TM" 27f9ac86 maybe solved chain TM 0430e9e5 Calculate chain TM everytime a78bbd5d Set default param as set4final when computing chaintmscore e333ad48 Made few comments reviewing filtercomplex.cpp 8f2ab715 simplify building complex header cf28e076 parsing problem solved 55b5338c memcpy error solve 6f3ac2b6 parsing with pdb d02373d8 parsing 961b8cf0 removing extension a2ea4743 make filtcov.tsv not db 0bc9d97d minor f3a9c22b minor 36490d18 minor change 77936ab3 handling monomer & calculate chainTM if complexTM satisfied a0b426ef Merge branch 'steineggerlab:master' into master 79ad721c Solved weird chain TM-score behavior 81fbfd99 Implemented per-chain-tm but tmscore is suspicious e44034e6 Implemented realloc function in Coordinate.h 6ef9dc7b modified complex header 94da95c4 complex header make 5e47a2ac still 99251fd6 complexheader, but still issue exists 4e7c3624 Revised code of filter complex a27efde9 tmthreshold parameter 52f0459a TODO maybe TMthreshold c1294530 both tm for all cov modes 7367a247 assID, query, target, coverage(1 or 2), tm(1 or 2) ff5a8e5f filtercomplex tmp coverage.tsv 73c2aa7a Merge branch 'steineggerlab:master' into master 369842e2 Solved argument list too long issue 4329b254 Finalized rmdb 81ac5ef5 Generates comment about rep complex in fastafile b7a27454 easy-cc description b25de75f remove tmp files 4ceb9ada Completed to output rep seqs fasta file 560c6e49 temporary Result2repseq d16ac100 tmp remove 7e5bd089 changed tmp dir 86f5fe9e colsed easycc 412b51d0 header file fa875fdf making complex header file fe9865cb small changes 819a75a8 add description 06945aed Parameters 7d34bcbb default parameters e3defcd4 separated buildCmplDb from filtercomplex 83100b8e Solved complexsearch parameter not applied problem 607c14fc Success command run 9b183905 share status 7e054b6f [DONE] Build successed. [TODO] Default Parameter setting 6ac16224 finally make works c3a7c959 [TODO] Solve conflicts during make 8dd17b24 Organized shell scripts a36b8c7e git conflicts 6db40b57 tmp LocalParameters.cpp dd34d670 still build failed aebd3fd8 small changes b9d73150 .cpp files 02a89148 easycc and cc .sh dbd9b076 To Complexclusterworkflow f7b9508e Changes 03c635e5 Changed ComplexCluster into FilterComplex ec234b1d revised parameters for filtercomplex 39b2f062 renamed complexcluster.sh to filtercomplex.sh and finalized 47cfb386 share status 40a0e719 to share status 413faeeb Add filtercomplex parameter for coverage 8667be3d [TODO] Build failed. check localparameters, workflowfiles, etc. 3782b550 Made workflow file e15a2241 [IN PROGRESS] separated complexcluster and easycomplexcluster but need to organize 84c5279f FoldSeelBase.cpp should be changed though, easy-complexcluster output instruction 017ad0fe Updated LocalParameter files 83a46549 clustered results to flatfiles 38b60958 data/CMakeLists update 46611c48 CMakeLists update 51d29b8c Changed complexcluster.sh to easycomplexcluster.sh 69876616 Merge branch 'master' of https://github.com/rachelse/foldseek b5c45c37 minor modification ef00e785 [IN PROGRESS] Draft state complexcluster.sh 5ac175fd erased default -c 0.8 aaf1a6b1 complexclust.sh e52c527a cleaned code b7bc37fc -c default 0.8 d81811f9 TODO: select highest aligned alignments among same complex-complex & what if user wants to use -c 0.0? 5adeb999 no errors, not debugged yet 03860d19 has error, but for sharing status. Coverge criteria 47c37e08 Merge branch 'steineggerlab:master' into master 35c5914a Merge branch 'steineggerlab:master' into master bb7ec93b First version for complex filter git-subtree-dir: lib/foldseek git-subtree-split: 3310337471fc46880c245508af6a23adcb192cee
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I found that Foldseek does not extract any chains from PyMol exported mmCIF files. Tracking the issue down to gemmi seems to be due to gemmi requiring
auth_seq_idto be present, but PyMol not saving it.I tested the PR within Foldseek and everything works as expected.
I also attached a mmCIF file exported from PyMol that has the issue.
pymol_wo_auth_seq_id.cif.txt