Re: [COOT] Coot fails to read numeric chain IDs
Kevin Cowtan wrote: Coot reads files with duplicate atom numbers just fine (at least 0.6pre-latest does). However Coot will ignore any lines beginning ATOM 1? ATOM 2? etc because those are not valid atom records. So that is the reason these are being ignored. Yes, we should say that this is handled by the mmdb library from Eugene Krissinel. The original poster could have expedited the analysis somewhat by quoting the console log which should have reproduced the problematic lines and line numbers. Paul. (p.s. back now, less out of touch)
Re: [COOT] sequencing gui
I guess you didnt give it a chain id. When sequencing the closest fragment this information is required (maybe it shouldnt, or at least it should give the appropriate warning - I will look into it at some point). B I'm trying to understand the Extensions- Dock sequence dialogue. How does it work? I've tried Place helix here Select Dock Sequence choose Helix molecule Load sequence from a file click Sequence closest fragment then I get assign-sequence-from-file2 /Users/pre/Documents/Talks/ Crystallography/LMB-2009/MapFitting/Examples/amph2.seq) iv: 0 seq.size: 1 debug pythoning and MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLSECLQEVYEPEWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDYDSARHHYESLQTAKKKDEAKIAKPVSLLEKAAPQWCQGKLQAHLVAQTNLLRNQAEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVSLEKQHGSNTFTVKAQPSDSAPEKGNKSPSPPPDGSPAATPEIRVNHEPEPASGASPGATIPKSPSQLRKGPPVKHTPSKEMKQEQILSLFDDAFVPEISVTTPSQFEAPGPFSEQASLLDLDFEPLPPVASPVKAPTPSGQSIPWDLWEPTESQAGVLPSGEPSSAEGSFAVAWPSQTAEPGPAQPAEASEVVGGTQEPGETAASEATSSSLPAVVVETFSATVNGAVEGSTTTGRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVIPFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVQ apply the sequence info here then cootaneer ERROR:: the input contains an invalid chain and/or sequence BL ERROR:: something went wrong assigning the sequence What should I have done? (Coot 0.6-pre 1 1941, OSX) Best wishes Phil
Re: [COOT] sequencing gui
OK thanks. I tried a different example, which did give me a (wrong) assignment - is there any way of picking an alternative? What partly confused me before and again was that this command assigns the sequence but doesn't build the side chains - you have to use the Fill Partial Residues command, I suppose Also if I go back to the GUI for the same molecule, it displays 2 sequences Thanks again Phil --- then cootaneer iv: 0 seq.size: 1 debug pythoning and MHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ in assign_sequence_from_string storing sequence: MHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ for chain id: A (assign-sequence-from-string2 A MHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ ) Sequence: ?KIEFT? Confidence: 0.912518 On 4 Jun 2009, at 13:37, Bernhard Lohkamp wrote: I guess you didnt give it a chain id. When sequencing the closest fragment this information is required (maybe it shouldnt, or at least it should give the appropriate warning - I will look into it at some point). B I'm trying to understand the Extensions- Dock sequence dialogue. How does it work? I've tried Place helix here Select Dock Sequence choose Helix molecule Load sequence from a file click Sequence closest fragment then I get assign-sequence-from-file2 /Users/pre/Documents/Talks/ Crystallography/LMB-2009/MapFitting/Examples/amph2.seq) iv: 0 seq.size: 1 debug pythoning and MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLSECLQEVYEPEWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDYDSARHHYESLQTAKKKDEAKIAKPVSLLEKAAPQWCQGKLQAHLVAQTNLLRNQAEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVSLEKQHGSNTFTVKAQPSDSAPEKGNKSPSPPPDGSPAATPEIRVNHEPEPASGASPGATIPKSPSQLRKGPPVKHTPSKEMKQEQILSLFDDAFVPEISVTTPSQFEAPGPFSEQASLLDLDFEPLPPVASPVKAPTPSGQSIPWDLWEPTESQAGVLPSGEPSSAEGSFAVAWPSQTAEPGPAQPAEASEVVGGTQEPGETAASEATSSSLPAVVVETFSATVNGAVEGSTTTGRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVIPFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVQ apply the sequence info here then cootaneer ERROR:: the input contains an invalid chain and/or sequence BL ERROR:: something went wrong assigning the sequence What should I have done? (Coot 0.6-pre 1 1941, OSX) Best wishes Phil
Re: [COOT] sequencing gui
Ah OK thanks Phil On 4 Jun 2009, at 15:05, Kevin Cowtan wrote: It's very unlikely to be right on anything much shorter than 12 residues. The confidence scores are a bit gung-ho. Phil Evans wrote: OK thanks. I tried a different example, which did give me a (wrong) assignment - is there any way of picking an alternative? What partly confused me before and again was that this command assigns the sequence but doesn't build the side chains - you have to use the Fill Partial Residues command, I suppose Also if I go back to the GUI for the same molecule, it displays 2 sequences Thanks again Phil --- then cootaneer iv: 0 seq.size: 1 debug pythoning and MHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ in assign_sequence_from_string storing sequence: MHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ for chain id: A (assign-sequence-from-string2 A MHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ ) Sequence: ?KIEFT? Confidence: 0.912518 On 4 Jun 2009, at 13:37, Bernhard Lohkamp wrote: I guess you didnt give it a chain id. When sequencing the closest fragment this information is required (maybe it shouldnt, or at least it should give the appropriate warning - I will look into it at some point). B I'm trying to understand the Extensions- Dock sequence dialogue. How does it work? I've tried Place helix here Select Dock Sequence choose Helix molecule Load sequence from a file click Sequence closest fragment then I get assign-sequence-from-file2 /Users/pre/Documents/Talks/ Crystallography/LMB-2009/MapFitting/Examples/amph2.seq) iv: 0 seq.size: 1 debug pythoning and MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLSECLQEVYEPEWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDYDSARHHYESLQTAKKKDEAKIAKPVSLLEKAAPQWCQGKLQAHLVAQTNLLRNQAEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVSLEKQHGSNTFTVKAQPSDSAPEKGNKSPSPPPDGSPAATPEIRVNHEPEPASGASPGATIPKSPSQLRKGPPVKHTPSKEMKQEQILSLFDDAFVPEISVTTPSQFEAPGPFSEQASLLDLDFEPLPPVASPVKAPTPSGQSIPWDLWEPTESQAGVLPSGEPSSAEGSFAVAWPSQTAEPGPAQPAEASEVVGGTQEPGETAASEATSSSLPAVVVETFSATVNGAVEGSTTTGRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVIPFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVQ apply the sequence info here then cootaneer ERROR:: the input contains an invalid chain and/or sequence BL ERROR:: something went wrong assigning the sequence What should I have done? (Coot 0.6-pre 1 1941, OSX) Best wishes Phil
Re: [COOT] sequencing gui
It's very unlikely to be right on anything much shorter than 12 residues. The confidence scores are a bit gung-ho. Phil Evans wrote: OK thanks. I tried a different example, which did give me a (wrong) assignment - is there any way of picking an alternative? What partly confused me before and again was that this command assigns the sequence but doesn't build the side chains - you have to use the Fill Partial Residues command, I suppose Also if I go back to the GUI for the same molecule, it displays 2 sequences Thanks again Phil --- then cootaneer iv: 0 seq.size: 1 debug pythoning and MHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ in assign_sequence_from_string storing sequence: MHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ for chain id: A (assign-sequence-from-string2 A MHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ) Sequence: ?KIEFT? Confidence: 0.912518 On 4 Jun 2009, at 13:37, Bernhard Lohkamp wrote: I guess you didnt give it a chain id. When sequencing the closest fragment this information is required (maybe it shouldnt, or at least it should give the appropriate warning - I will look into it at some point). B I'm trying to understand the Extensions- Dock sequence dialogue. How does it work? I've tried Place helix here Select Dock Sequence choose Helix molecule Load sequence from a file click Sequence closest fragment then I get assign-sequence-from-file2 /Users/pre/Documents/Talks/ Crystallography/LMB-2009/MapFitting/Examples/amph2.seq) iv: 0 seq.size: 1 debug pythoning and MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLSECLQEVYEPEWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDYDSARHHYESLQTAKKKDEAKIAKPVSLLEKAAPQWCQGKLQAHLVAQTNLLRNQAEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVSLEKQHGSNTFTVKAQPSDSAPEKGNKSPSPPPDGSPAATPEIRVNHEPEPASGASPGATIPKSPSQLRKGPPVKHTPSKEMKQEQILSLFDDAFVPEISVTTPSQFEAPGPFSEQASLLDLDFEPLPPVASPVKAPTPSGQSIPWDLWEPTESQAGVLPSGEPSSAEGSFAVAWPSQTAEPGPAQPAEASEVVGGTQEPGETAASEATSSSLPAVVVETFSATVNGAVEGSTTTGRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVIPFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVQ apply the sequence info here then cootaneer ERROR:: the input contains an invalid chain and/or sequence BL ERROR:: something went wrong assigning the sequence What should I have done? (Coot 0.6-pre 1 1941, OSX) Best wishes Phil
