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<p>Hi Eric,</p>
<p><br>
</p>
<p>That is perfect thanks very much. I think I'm at the last hurdle now more or less. I can pull the RMSD out of the loop, having ended up with the code below:</p>
<p><br>
</p>
<p></p>
<div><span class="Apple-tab-span" style="white-space:pre"></span># Get reference structure from PDB</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>chimera.openModels.open(top_hit,type="PDB")</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>print("Opened reference structure: " + top_hit)</div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span># Open model structures</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>for model_path in model_list:</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>chimera.openModels.open(model_path,type="PDB")</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>print("Opened: " + os.path.basename(model_path))</div>
<div><br>
</div>
<div> <span class="Apple-tab-span" style="white-space:pre"> </span>if args.rmsd is not None:</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>rmsd_file = args.rmsd</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>else:</div>
<div> <span class="Apple-tab-span" style="white-space:pre"> </span>rmsd_file = '{0}{1}.tsv'.format(locus_dir,basename)</div>
<div><br>
</div>
<div> <span class="Apple-tab-span" style="white-space:pre"> </span>with open(rmsd_file, "a") as rmsd_output_file:</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>all_models = chimera.openModels.list(modelTypes=[chimera.Molecule])</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>ref = all_models[0]</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>sims = all_models[1:]</div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST,[ref, sims],defaults[MATRIX],\</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>"nw",defaults[GAP_OPEN],defaults[GAP_EXTEND]):</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>print(str(atoms1) + "\t" + str(atoms2) + "\t" + str(rmsd))</div>
<div> <span class="Apple-tab-span" style="white-space:pre"> </span>rmsd_output_file.write(<span style="font-family: Calibri, Arial, Helvetica, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">str(atoms1)
+ "\t" + str(atoms2) + "\t" + str(rmsd)</span>)</div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>rmsd_output_file.close()</div>
<br>
<p></p>
<p>The final hurdle seems to be can I access the model name rather than the atomspec for the output of each iteration of match? My current output looks like this:</p>
<p><br>
</p>
<p>.....(abridged)...</p>
<p></p>
<div> <_molecule.Atom object at 0x3a9c288> <_molecule.Atom object at 0x3a9c3c8></div>
<div> <_molecule.Atom object at 0x3a9c530> <_molecule.Atom object at 0x3a9c620></div>
<div> <_molecule.Atom object at 0x3a9c6e8>]<span class="Apple-tab-span" style="white-space:pre">
</span>3.06267824307</div>
<br>
<p></p>
<p>Which is pretty close. I assume I'd need something like: chimera.Atom.name() or Molecule.name() to access that element of the class , but that's just throwing me back this error:</p>
<p><br>
</p>
<p></p>
<div> File "strucfit.py", line 198, in main</div>
<div> ref_name = chimera.Atom.name(atoms1)</div>
<div>TypeError: 'getset_descriptor' object is not callable</div>
<br>
<p></p>
<p>I'm hoping to get the final output to be a tab separated list of:</p>
<p><br>
</p>
<p>referenceName \t modelName \t RMSD</p>
<p><br>
</p>
<p><br>
</p>
<p>Final step then I promise I'll leave you be!!</p>
<p><br>
</p>
<p>Joe</p>
<p><br>
</p>
<p><br>
</p>
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Joe Healey<br style="font-size:10pt">
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> 21 September 2016 21:47:20<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers</font>
<div> </div>
</div>
<div>Hi Joe,
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>I guess the first thing is that since you are using the default chain pairing (i.e. best pair in both) you want to call match() with CP_BEST rather than CP_SPECIFIC_SPECIFIC. Then you
can pass in structures instead of chains. Of course, you still need to get the structures (rather than just their ID numbers). Assuming the ref structure is opened first, the following code will get the structures:</div>
<div class=""><br class="">
</div>
<div class="">models = chimera.openModels.list(modelTypes=[chimera.Molecule])</div>
<div class="">ref = models[0]</div>
<div class="">sims = models[1:]</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""># No iteration is the default, so just omit the ‘iterate’ keyword. ‘rmsd’ and ‘fullRmsd’ will be the same when there's no iteration.</div>
</div>
<div class="">for simAtoms, refAtoms, rmsd, fullRmsd in match(CP_BEST, [ref, sims], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]):</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span># One set of simAtoms/refAtoms/rmsds per sim structure</div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>…output RMSD…</div>
<div class=""><br class="">
</div>
<div class="">—Eric</div>
<div class=""><br class="">
</div>
<div class="">P.S. You’ll need to import CP_BEST instead of CP_SPECIFIC_SPECIFIC</div>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On Sep 21, 2016, at 11:47 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" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks for clarifying Eric. That is what I had assumed the code to be doing, but I guess I'm trying to be a bit more naive than that in not having to specify the chains/atoms. I'll explain a little
more of what I'm trying to do in the hope that makes it a bit more understandable:</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">As per the original question, I have several hundred protein simulation models. I'm running the HHSuite of tools to identify their nearest published structures, and then I want to get the RMSDs of the
'reference' structure, vs each of my simulations (for any given protein, there are up to 5 simulated PDBs). So far everything works, I parse in the top hit no problem, and can retrieve my models and open everything in chimera programmatically.</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=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">If we assume in the preceeding code, a variable is populated with the PDB ID of the nearest hit and stored in "top_hit". Next the script trawls my folders of all the simulations, finds them based on
a "basename" which is just the locus tag for the corresponding gene (also defined earlier in the code):</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div class=""> # Acquire the protein simulations<br class="">
<br class="">
model_list = []<br class="">
for root, dirnames, filenames in os.walk(directory):<br class="">
for filename in fnmatch.filter(filenames, '*.pdb'):<br class="">
if filename.startswith(basename):<br class="">
model_list.append(os.path.join(root, filename))<br class="">
<br class="">
print("---------------------------")<br class="">
print("Found the following models:")<br class="">
for model_path in model_list:<br class="">
print(model_path)<br class="">
<br class="">
locus_dir = os.path.dirname(model_path)<br class="">
<br class="">
# Get reference structure from PDB<br class="">
reference = chimera.openModels.open(top_hit,type="PDB")<br class="">
print("Opened reference structure: " + top_hit)<br class="">
<br class="">
# Open model structures<br class="">
for model_path in model_list:<br class="">
chimera.openModels.open(model_path,type="PDB")<br class="">
print("Opened: " + model_path)<br class="">
<br class="">
<br class="">
rmsd_file = '{0}{1}.tsv'.format(locus_dir,basename)<br class="">
<br class="">
with open(rmsd_file, "a") as rmsd_output_file:<br class="">
for j in len(model_list): # For every model retrieved above, match it to the reference structure and obtain an RMSD for it<br class="">
rc('matchmaker #{0} #{1} alg nw iter false'.format(reference,j))<br class="">
< capture RMSD somehow ><br class="">
rmsd_output_file.write(reference + "\t" + j + "\t" + rmsd)</div>
<br class="">
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">So where I'm still stuck is that when I execute the mmaker command within chimera in it's own syntax, I can specify the models and not the atoms with the #0 #1 notations. The command runs and chimera
picks the best atoms for me (this is also desirable because when I run this unattended on many structures, I don't know which chain within those chimera might match best). I want to emulate that behaviour exactly. So unless I'm very much mistaken, chimera
should take the 2 models, fit them as best it can, and return the RMSD.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">In short, whatever the MatchMaker.match() equivalent syntax of the relatively 'naive' <span style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 16px;" class="">rc('matchmaker
#{0} #{1} alg nw iter false'.format(reference,j)) command is what I need I think?</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 16px;" class=""><br class="">
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 16px;" class="">Hope
that's clear,</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 16px;" class=""><br class="">
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Joe Healey<br style="font-size: 10pt;" class="">
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<span style="font-size: 10pt;" class="">M.Sc. B.Sc. (Hons)</span><br class="">
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<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>
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</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>
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<div class=""><span style="font-size: 10pt;" class="">Jointly working in:<br class="">
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<div class=""><span style="font-size: 10pt;" class="">Twitter:<span class="Apple-converted-space"> </span><a href="https://twitter.com/JRJHealey" id="LPNoLP" class="">@JRJHealey</a> | </span><span style="font-size: 10pt;" class="">Website:<span class="Apple-converted-space"> </span></span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" id="LPNoLP" style="font-size: 10pt;" class="">MOAC
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>21 September 2016 18:54:26<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Healey, Joe<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> BB<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers</font>
<div class=""> </div>
</div>
<div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
When the matching is CP_SPECIFIC_SPECIFIC, the arguments have to be chains, not structures. This is what this part of the original commented-out code was doing:
<div class=""><br class="">
</div>
<div class="">
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>s1, s2 = openModels.list(modelTypes=[Molecule])<br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>c1, c2 = s1.sequence('A'), s2.sequence('A’)</div>
<div class=""><br class="">
</div>
<div class="">c1/c2 were the specific chains (namely, the ‘A’ chains) that would be used in the ‘match’ call:</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],<br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span> "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],<br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>iterate=defaults[ITER_CUTOFF])[0]</div>
</div>
<div class=""><br class="">
</div>
<div class="">Maybe if you sent me the part of your script that was trying to make the ‘match’ call I could help you sort this out. ‘runCommand’ is a generic command that just treats the string as if it were typed at the command line (and therefore it could
contain multiple commands strung together with ‘;’) and does not return any value.</div>
<div class=""><br class="">
</div>
<div class="">—Eric</div>
<div class=""><br class="">
</div>
<div class="">
<blockquote type="cite" class="">
<div class="">On Sep 21, 2016, at 8:01 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="">
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">Thanks Eric,</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">I still can't wrap my head around calling the module directly, so string synthesis and the runCommand will have to do.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">I'm now getting errors from it such as:</div>
<p class="" style="margin-top: 0px; margin-bottom: 0px;"></p>
<div class=""> return proteinMatrix == chain.hasProtein()</div>
<div class="">AttributeError: '_molecule.Molecule' object has no attribute 'hasProtein'</div>
<br class="">
<p class="" style="margin-top: 0px; margin-bottom: 0px;"></p>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Which I don't know what to do with, but the runcommand syntax does what I want - I just can't emulate it exactly in full python.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">This means my hopefully final question is how exactly do you extract the RMSD from it if using chimera syntax wrapped in runCommand? Just doing:</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">result = runCommand('mmaker #{0} #{1} alg nw iter false'.format(reference, model)')</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">leaves "result" as None. I was hoping it would behave like your multiple variable assignment in:</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">"atoms1, atoms2, rmsd = match(......)"</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Allowing me to then pull out the number.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">All help much appreciated,</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Joe</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
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<span class="" style="font-size: 10pt;">M.Sc. B.Sc. (Hons)</span><br class="">
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<span class="" style="font-size: 10pt;"></span>
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<div class=""><span class="" style="font-size: 10pt;">Jointly working in:<br class="">
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<div class=""><span class="" style="font-size: 10pt;"><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 class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">WMS </span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">Microbiology
and Infecti</span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">on Un</span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">it)</span></span></div>
<div class=""><span class="" style="font-size: 10pt;">and the <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP" class="">Gibson Lab</a> (Warwick Chemistry)<br class="">
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<font face="Calibri, sans-serif" class="" style="font-size: 11pt;"><b class="">From:</b><span class="Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>21 September 2016 00:20:41<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Healey, Joe<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: Chimera-users Digest, Vol 161, Issue 19</font>
<div class=""> </div>
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<div class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
As you’ve noticed, the back end of your script pretty much has the exact code you need, just commented out. The function called in that code. MatchMaker.match(), is the function that the mmaker command ultimately calls (there’s an intermediate “cmdMatch” function
that does some argument parsing). You already do the correct imports at the top of your script (“from MatchMaker import match, …”). I think you just need to adapt the commented-out code into the script’s workflow.
<div class=""><br class="">
</div>
<div class="">—Eric</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Sep 20, 2016, at 3:16 PM, 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="">
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like:</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<p class="" style="margin-top: 0px; margin-bottom: 0px;"></p>
<div class=""> chimera.openModels.open(top_hit, type="PDB")<br class="">
<br class="">
# Open model structures<br class="">
for model_path in model_list:<br class="">
chimera.openModels.open(model_path,type="PDB")<br class="">
print("Opened: " + model_path)<br class="">
<br class="">
rmsd_file = '{0}.tsv'.format(rmsd)<br class="">
with open(rmsd_file, "a") as rmsd_output_file:<br class="">
for j in len(model_list):</div>
<div class=""> match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j)<br class="">
runCommand(match_cmd)</div>
<div class=""><br class="">
</div>
<div class=""># <somewhere in here retrieve the rmsd and append to a result file></div>
<div class=""><br class="">
</div>
<div class="">or the other option would be to do the above but avoiding the string synthesis step with something like:</div>
<div class="">chimera.module.mmaker()</div>
<div class=""><br class="">
</div>
<div class="">If the module can be accessed directly? If so which module is the mmaker function within?</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index?</div>
<div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;">
<br class="">
</div>
<div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;">
Looking at your Match script the rmsd was the 3rd value of the tuple in the line:
<div class="">atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0]</div>
<p class="" style="margin-top: 0px; margin-bottom: 0px;"></p>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Would the same be true for mmaker?</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">(Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones)</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Thanks again for all your help</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
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Joe Healey<br class="" style="font-size: 10pt;">
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<span class="" style="text-decoration: underline;"> </span><br class="">
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<span class="" style="font-size: 10pt;">M.Sc. B.Sc. (Hons)</span><br class="">
</div>
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<span class="" style="font-size: 10pt;"></span>
<div class=""><span class="" style="font-size: 10pt;">PhD Student</span></div>
<div class=""><span class="" style="font-size: 10pt;">MOAC CDT, Senate House</span></div>
<div class=""><span class="" style="font-size: 10pt;">University of Warwick<br class="">
</span></div>
<div class=""><span class="" style="font-size: 10pt;">Coventry<br class="">
</span></div>
<div class=""><span class="" style="font-size: 10pt;">CV47AL<br class="">
Mob: +44 (0) 7536 042620 | </span><span class="" style="font-size: 10pt;">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 class="" style="font-size: 10pt;"><br class="">
</span></div>
<div class=""><span class="" style="font-size: 10pt;">Jointly working in:<br class="">
</span></div>
<div class=""><span class="" style="font-size: 10pt;"><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 class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">WMS </span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">Microbiology
and Infecti</span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">on Un</span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">it)</span></span></div>
<div class=""><span class="" style="font-size: 10pt;">and the <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP" class="">Gibson Lab</a> (Warwick Chemistry)<br class="">
</span></div>
<div class=""><span class="" style="font-size: 10pt;"><br class="">
</span></div>
<div class=""><span class="" style="font-size: 10pt;">Twitter:<span class="Apple-converted-space"> </span><a href="https://twitter.com/JRJHealey" id="LPNoLP" class="">@JRJHealey</a> | </span><span class="" style="font-size: 10pt;">Website:<span class="Apple-converted-space"> </span></span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" id="LPNoLP" class="" style="font-size: 10pt;">MOAC
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<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Chimera-users Digest, Vol 161, Issue 19</font>
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1. Re: Recursive structure matching and acquisition of<br class="">
descriptive numbers (Eric Pettersen)<br class="">
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<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Tue, 20 Sep 2016 11:30:38 -0700<br class="">
From: Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class="">
To: "Healey, Joe" <<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>><br class="">
Cc: "<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span>BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class="">
Subject: Re: [Chimera-users] Recursive structure matching and<br class="">
acquisition of descriptive numbers<br class="">
Message-ID: <<a href="mailto:30002D29-1B25-4596-8868-EB3370B72E42@cgl.ucsf.edu" class="">30002D29-1B25-4596-8868-EB3370B72E42@cgl.ucsf.edu</a>><br class="">
Content-Type: text/plain; charset="windows-1252"<br class="">
<br class="">
Hi Joe,<br class="">
I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when
you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here:<br class="">
<br class="">
<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options</a><<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options</a>><br class="">
<br class="">
I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though.<br class="">
<br class="">
?Eric<br class="">
<br class="">
<br class="">
> On Sep 20, 2016, at 5:07 AM, Healey, Joe <<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>> wrote:<br class="">
><span class="Apple-converted-space"> </span><br class="">
> Hi again,<br class="">
><span class="Apple-converted-space"> </span><br class="">
> I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information.<br class="">
><span class="Apple-converted-space"> </span><br class="">
> Is there are resource with more information on the commandline implementation of match anywhere other than the link below?<br class="">
><span class="Apple-converted-space"> </span><br class="">
><span class="Apple-converted-space"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options</a><<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options</a>><br class="">
><span class="Apple-converted-space"> </span><br class="">
> I took a look at Eric's suggestion of the match.py script here:<span class="Apple-converted-space"> </span><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a><span class="Apple-converted-space"> </span><<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a>><br class="">
><span class="Apple-converted-space"> </span><br class="">
> But I can't quite unwrap the options specified in the command for my uses.<br class="">
><span class="Apple-converted-space"> </span><br class="">
> Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed?<br class="">
><span class="Apple-converted-space"> </span><br class="">
> I've put the semi-complete script in pastebin here<span class="Apple-converted-space"> </span><a href="http://pastebin.com/6k9cew55" class="">http://pastebin.com/6k9cew55</a><span class="Apple-converted-space"> </span><<a href="http://pastebin.com/6k9cew55" class="">http://pastebin.com/6k9cew55</a>>
incase it gives you some indication of what I'm attempting to do.<br class="">
><span class="Apple-converted-space"> </span><br class="">
> Many thanks<br class="">
><span class="Apple-converted-space"> </span><br class="">
><span class="Apple-converted-space"> </span><br class="">
> Joe Healey<br class="">
><span class="Apple-converted-space"> </span><br class="">
> <span class="Apple-converted-space"> </span><br class="">
> M.Sc. B.Sc. (Hons)<br class="">
> PhD Student<br class="">
> MOAC CDT, Senate House<br class="">
> University of Warwick<br class="">
> Coventry<br class="">
> CV47AL<br class="">
> Mob: +44 (0) 7536 042620 | 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 class="Apple-converted-space"> </span><<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>><br class="">
><span class="Apple-converted-space"> </span><br class="">
> Jointly working in:<br class="">
> Waterfield Lab <<a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" class="">http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/</a>> (WMS Microbiology and Infection Unit)<br class="">
> and the Gibson Lab <<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" class="">http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/</a>> (Warwick Chemistry)<br class="">
><span class="Apple-converted-space"> </span><br class="">
> Twitter: @JRJHealey <<a href="https://twitter.com/JRJHealey" class="">https://twitter.com/JRJHealey</a>> | Website: MOAC Page <<a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" class="">http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey</a>><br class="">
> From: Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:gregc@cgl.ucsf.edu" class="">mailto:gregc@cgl.ucsf.edu</a>>><br class="">
> Sent: 08 September 2016 22:43:55<br class="">
> To: Healey, Joe;<span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:chimera-users@cgl.ucsf.edu" class="">mailto:chimera-users@cgl.ucsf.edu</a>>
BB<br class="">
> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers<br class="">
> <span class="Apple-converted-space"> </span><br class="">
> chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares.<br class="">
><span class="Apple-converted-space"> </span><br class="">
> -- Greg<br class="">
><span class="Apple-converted-space"> </span><br class="">
> On 09/08/2016 11:53 AM, Healey, Joe wrote:<br class="">
>> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server
where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin.<br class="">
>><span class="Apple-converted-space"> </span><br class="">
>> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either<br class="">
>><span class="Apple-converted-space"> </span><br class="">
>><span class="Apple-converted-space"> </span><br class="">
>> Joe Healey<br class="">
>><span class="Apple-converted-space"> </span><br class="">
>> <span class="Apple-converted-space"> </span><br class="">
>> M.Sc. B.Sc. (Hons)<br class="">
>> PhD Student<br class="">
>> MOAC CDT, Senate House<br class="">
>> University of Warwick<br class="">
>> Coventry<br class="">
>> CV47AL<br class="">
>> Mob: +44 (0) 7536 042620 | 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 class="Apple-converted-space"> </span><<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>><br class="">
>><span class="Apple-converted-space"> </span><br class="">
>> Jointly working in:<br class="">
>> Waterfield Lab <<a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" class="">http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/</a>> (WMS Microbiology and Infection Unit)<br class="">
>> and the Gibson Lab <<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" class="">http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/</a>> (Warwick Chemistry)<br class="">
>><span class="Apple-converted-space"> </span><br class="">
>> Twitter: @JRJHealey <<a href="https://twitter.com/JRJHealey" class="">https://twitter.com/JRJHealey</a>> | Website: MOAC Page <<a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" class="">http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey</a>><br class="">
>> From: Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a>> <<a href="mailto:gregc@cgl.ucsf.edu" class="">mailto:gregc@cgl.ucsf.edu</a>><br class="">
>> Sent: 07 September 2016 19:49:19<br class="">
>> To: Healey, Joe;<span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:chimera-users@cgl.ucsf.edu" class="">mailto:chimera-users@cgl.ucsf.edu</a>>
BB<br class="">
>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers<br class="">
>> <span class="Apple-converted-space"> </span><br class="">
>> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,<a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b" class="">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b</a><<a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b" class="">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b</a>>,
for how to install other software into Chimera. Other parts of the FAQ may help you too.<br class="">
>><span class="Apple-converted-space"> </span><br class="">
>> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject,<span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html" class="">http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html</a><span class="Apple-converted-space"> </span><<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html" class="">http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html</a>>,
and came up with pychimera,<span class="Apple-converted-space"> </span><a href="https://pypi.python.org/pypi/pychimera" class="">https://pypi.python.org/pypi/pychimera</a><span class="Apple-converted-space"> </span><<a href="https://pypi.python.org/pypi/pychimera" class="">https://pypi.python.org/pypi/pychimera</a>>.
I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you.<br class="">
>><span class="Apple-converted-space"> </span><br class="">
>> HTH,<br class="">
>><span class="Apple-converted-space"> </span><br class="">
>> Greg<br class="">
>><span class="Apple-converted-space"> </span><br class="">
>> On 09/07/2016 07:36 AM, Healey, Joe wrote:<br class="">
>>> Hi Eric,<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however.<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather
than a python interpreter calling chimera modules in?<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!).<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'.<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script.<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> Do you have any advice about how best to proceed?<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> Many thanks,<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> Joe Healey<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> <span class="Apple-converted-space"> </span><br class="">
>>> M.Sc. B.Sc. (Hons)<br class="">
>>> PhD Student<br class="">
>>> MOAC CDT, Senate House<br class="">
>>> University of Warwick<br class="">
>>> Coventry<br class="">
>>> CV47AL<br class="">
>>> Mob: +44 (0) 7536 042620 | 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 class="Apple-converted-space"> </span><<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>><br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> Jointly working in:<br class="">
>>> Waterfield Lab <<a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" class="">http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/</a>> (WMS Microbiology and Infection Unit)<br class="">
>>> and the Gibson Lab <<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" class="">http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/</a>> (Warwick Chemistry)<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> Twitter: @JRJHealey <<a href="https://twitter.com/JRJHealey" class="">https://twitter.com/JRJHealey</a>> | Website: MOAC Page <<a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" class="">http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey</a>><br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> From: Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> <<a href="mailto:pett@cgl.ucsf.edu" class="">mailto:pett@cgl.ucsf.edu</a>><br class="">
>>> Sent: 31 August 2016 18:23<br class="">
>>> To: Healey, Joe<br class="">
>>> Cc:<span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:chimera-users@cgl.ucsf.edu" class="">mailto:chimera-users@cgl.ucsf.edu</a>><br class="">
>>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers<br class="">
>>> <span class="Apple-converted-space"> </span><br class="">
>>> Hi Joe,<br class="">
>>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just
change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs?<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>><span class="Apple-converted-space"> </span><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a><span class="Apple-converted-space"> </span><<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a>><br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> ?Eric<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> Eric Pettersen<br class="">
>>> UCSF Computer Graphics Lab<br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe <<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a><span class="Apple-converted-space"> </span><<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>>>
wrote:<br class="">
>>>><span class="Apple-converted-space"> </span><br class="">
>>>> Hi,<br class="">
>>>><span class="Apple-converted-space"> </span><br class="">
>>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins.<br class="">
>>>><span class="Apple-converted-space"> </span><br class="">
>>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog
and then run the matchmaker algorithm.<br class="">
>>>><span class="Apple-converted-space"> </span><br class="">
>>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log?<br class="">
>>>><span class="Apple-converted-space"> </span><br class="">
>>>> Thanks<br class="">
>>>><span class="Apple-converted-space"> </span><br class="">
>>>> Joe Healey<br class="">
>>>><span class="Apple-converted-space"> </span><br class="">
>>>> <span class="Apple-converted-space"> </span><br class="">
>>>> M.Sc. B.Sc. (Hons)<br class="">
>>>> PhD Student<br class="">
>>>> MOAC CDT, Senate House<br class="">
>>>> University of Warwick<br class="">
>>>> Coventry<br class="">
>>>> CV47AL<br class="">
>>>> Mob: +44 (0) 7536 042620 | 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 class="Apple-converted-space"> </span><<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>><br class="">
>>>><span class="Apple-converted-space"> </span><br class="">
>>>> Jointly working in:<br class="">
>>>> Waterfield Lab <<a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" class="">http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/</a>> (WMS Microbiology and Infection Unit)<br class="">
>>>> and the Gibson Lab <<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" class="">http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/</a>> (Warwick Chemistry)<br class="">
>>>><span class="Apple-converted-space"> </span><br class="">
>>>> Twitter: @JRJHealey <<a href="https://twitter.com/JRJHealey" class="">https://twitter.com/JRJHealey</a>> | Website: MOAC Page <<a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" class="">http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey</a>>_______________________________________________<br class="">
>>>> Chimera-users mailing list:<span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:Chimera-users@cgl.ucsf.edu" class="">mailto:Chimera-users@cgl.ucsf.edu</a>><br class="">
>>>> Manage subscription:<span class="Apple-converted-space"> </span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>><br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>><span class="Apple-converted-space"> </span><br class="">
>>> _______________________________________________<br class="">
>>> Chimera-users mailing list:<span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:Chimera-users@cgl.ucsf.edu" class="">mailto:Chimera-users@cgl.ucsf.edu</a>><br class="">
>>> Manage subscription:<span class="Apple-converted-space"> </span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>><br class="">
>><span class="Apple-converted-space"> </span><br class="">
><span class="Apple-converted-space"> </span><br class="">
><span class="Apple-converted-space"> </span><br class="">
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