<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Just to follow up on the Python question here, a model can have multiple sequences (one per chain), so your code should be:<div class=""><br class=""></div><div class="">from chimera import openModels<br class="">all_mods = chimera.openModels.list(modelTypes=[chimera.Molecule])<br class="">with open('output.fasta', 'w') as ofh:<br class=""> for mod in all_mods:</div><div class=""> for seq in mod.sequences():</div><div class=""> ofh.write('>%s.%s\n%s' % (mod.name, seq.chainID, seq)</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">What you were trying to use, mod.sequence, is a method that takes a chain ID as an argument and returns the Sequence object corresponding to that chain ID (e.g. mod.sequence(‘A’) returns the Sequence for chain A).</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 10, 2018, at 4:48 AM, Healey, Joe <<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="caret-color: rgb(0, 0, 0); font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Chimera Team,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I've been experiencing issues with the "Align Chains" tools that connect to Clustal and Muscle - I think ostensibly this might be because the servers are no longer available or something.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I'm happy to make the alignments myself, but to do this I'd like to try and simply export the sequences of all open models to a fasta file or similar. I know this can be done manually sequence-by-sequence thtrough the GUI.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Could you tell me what the python (or chimera syntax) would be to do this if it's possible?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I'm envisaging something to the effect of this, but I can't quite get what I need back in terms of the sequence (it returns a `bound object'?):</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">```</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">from chimera import openModels</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">all_mods = <span class="">chimera.openModels.list(modelTypes=[chimera.Molecule])</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">with open('output.fasta', 'w') as ofh:</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""> for mod in all_mods:</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""> ofh.write(<span class="">'>%s\n%s' % (mod.name, mod.sequence)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">```</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">Joe Healey<br style="font-size: 10pt;" class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><span style="text-decoration: underline;" class=""> </span><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><span style="font-size: 10pt;" class="">M.Sc. B.Sc. (Hons) MRSB</span><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><span style="font-size: 10pt;" class=""></span><div class=""><span style="font-size: 10pt;" class="">PhD Student</span></div><div class=""><span style="font-size: 10pt;" class="">MOAC CDT, Senate House</span></div><div class=""><span style="font-size: 10pt;" class="">University of Warwick<br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">Coventry<br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">CV47AL<br class="">Mob: +44 (0) 7536 042620 | </span><span style="font-size: 10pt;" class="">Email:<span class="Apple-converted-space"> </span><a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a></span></div><div class=""><span style="font-size: 10pt;" class=""><br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">Jointly working in:<br class=""></span></div><div class=""><span style="font-size: 10pt;" class=""><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP" class="">Waterfield Lab</a><span class="Apple-converted-space"> </span>(<span style="font-family: Calibri, Arial, Helvetica, sans-serif; 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