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Hi, I am new to using alphafold for prediction, i tried today with a reasonable size model ( 400 AA ) of a kinase domain. i opted to use 'high RAM " available on colab pro and after running for an few hours , the job stops without any
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
Hi,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
I am new to using alphafold for prediction, i tried today with a reasonable size model ( 400 AA ) of a kinase domain. i opted to use 'high RAM " available on colab pro and after running for an few hours , the job stops without any error, the colab notebook
had disconnected due to inactivity and it did not generate any models.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
please share with me your experience of using alphafold from within chimerax , helpful tips to get the job to finish .</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
here is the output ( output on google colab):<br>
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<div class="stream output-id-144" style="display: inline; color: rgb(33, 33, 33); font-family: Roboto, Noto, sans-serif; font-size: 14px; background-color: rgb(255, 255, 255);">
<div class="output_subarea output_text" style="display:inline">
<pre style="margin-bottom:0px;margin-top:0px;display:inline">Sequence length 401
Have Colab GPU runtime
Installing HMMER for computing sequence alignments
Installing matplotlib to plot sequence alignment coverage
Installing AlphaFold
Installing OpenMM for structure energy minimization
Finding fastest mirror for sequence databases using united states
Searching sequence databases (147 Gbytes).
Search will take 29 minutes or more.
Searching uniref90 sequence database, 59 Gbytes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
Searching smallbfd sequence database, 17 Gbytes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
Searching mgnify sequence database, 71 Gbytes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
61 62 63 64 65 66 67 68 69 70 71
Computing multiple sequence alignment
327620 similar sequences found (311112 uniref90, 16008 smallbfd, 500 mgnify)
</pre>
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<div class="output_subarea output_image"><img style="max-width: 100%; vertical-align: bottom; background-color: white;" class="w-742 h-224" size="21205" contenttype="image/png" data-outlook-trace="F:1|T:1" src="cid:4e178c51-cd4c-4958-b2e8-fa714cbfcd07"></div>
</div>
<div class="stream output-id-146" style="display: inline; color: rgb(33, 33, 33); font-family: Roboto, Noto, sans-serif; font-size: 14px; background-color: rgb(255, 255, 255);">
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<pre style="margin-bottom:0px;margin-top:0px;display:inline">Computing structures using 5 AlphaFold parameter sets:
model_1</pre>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
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<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
thanks a lot again for all your support,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
best</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
amith</div>
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