I need help fixing and/or diagnosing this problem:
My colour for percentage identity isnt working!
I aligned the sequences using CLustal with defaults… then clicked on colour and percentage identity but no colour shows up and there should be considering this set of sequences have 3 T in a row across all 7 sequences.
The little circle is beside percentage identity but no colour appears…
I need help as soon as possible please!
Thanks!
Jess
Hello Jessie
On 07/02/2012 13:11, Jessie Richer wrote:
I need help fixing and/or diagnosing this problem:
My colour for percentage identity isnt working!
I aligned the sequences using CLustal with defaults… then clicked on colour and percentage identity but no colour shows up and there should be considering this set of sequences have 3 T in a row across all 7 sequences.
The little circle is beside percentage identity but no colour appears…
I need help as soon as possible please!
Could you please send me a copy of your alignment and let me know which version of Jalview you are using ? (you can see it in the dialog that pops up when you select Help->About).
Jim.
ps. if you are using a web site to align your sequences, and your sequences are all in lower case (ie ‘t’ not ‘T’), then try selecting all the seqeunces, right clicking and following the ‘Edit’ submenu to select the ‘To Upper case’ option. This might be the cause…
Hi… I managed to figure it out… had to shut down jalview and restart the computer and then the colour worked again…
Now I am waiting on the sequences to align… has said “queuing” for the last hour or so on 3 separate sets of sequences… I had this same problem last week and it turned out there was a problem with the server or something? they did eventually finish (5 hours later)… hoping it doesnt take that long today…
From: Jim Procter [foreveremain@gmail.com] on behalf of Jim Procter [jprocter@compbio.dundee.ac.uk]
Sent: February 7, 2012 9:21 AM
To: Jessie Richer
Cc: jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] help
Hello Jessie
On 07/02/2012 13:11, Jessie Richer wrote:
I need help fixing and/or diagnosing this problem:
My colour for percentage identity isnt working!
I aligned the sequences using CLustal with defaults… then clicked on colour and percentage identity but no colour shows up and there should be considering this set of sequences have 3 T in a row across all 7 sequences.
The little circle is beside percentage identity but no colour appears…
I need help as soon as possible please!
Could you please send me a copy of your alignment and let me know which version of Jalview you are using ? (you can see it in the dialog that pops up when you select Help->About).
Jim.
ps. if you are using a web site to align your sequences, and your sequences are all in lower case (ie ‘t’ not ‘T’), then try selecting all the seqeunces, right clicking and following the ‘Edit’ submenu to select the ‘To Upper case’ option. This might be the cause…
I do remember your email - but I don’t think you ever replied to my email about using a different way of starting Jalview. If you are aligning very long sequences, you should really start Jalview with more memory. You can find out how much you have or have left by selecting the ‘Show memory usage’ option under the tools menu. If you have less than 50 percent when your alignment comes back from the server, I would recommend increasing the memory allocated to jalview.
Jim.
On 07/02/2012 14:30, Jessie Richer wrote:
Hi… I managed to figure it out… had to shut down jalview and restart the computer and then the colour worked again…
Now I am waiting on the sequences to align… has said “queuing” for the last hour or so on 3 separate sets of sequences… I had this same problem last week and it turned out there was a problem with the server or something? they did eventually finish (5 hours later)… hoping it doesnt take that long today…