ConSurfDB vs. ConSurf: Difference between revisions

Line 50:

#Go to [http://consurf.tau.ac.il consurf.tau.ac.il], the ConSurf Server (distinct from ConSurf-DB).

~~#If you are offered a choice between the new version and the old one, choose the new version.~~

#Fill out the form. When you get to the section ''Choose parameters to build the Multiple Sequence Alignment (MSA)'', be sure to check '''Let me select the sequences for the analysis manually out of Blast results'''. The other options in this section can be left at their default settings.

#Fill out the form. When you get to the section ''Choose parameters to build the Multiple Sequence Alignment (MSA)'', be sure to check '''Let me select the sequences for the analysis manually out of Blast results~~'''.~~

~~#Under ''Maximum Homologs to collect'', change 50 to '''all~~'''. The other options in this section can be left at their default settings.

#Enter your email address and click the ''Submit'' button.

#After a few minutes, a ~~red~~ message will appear "~~Please choose which sequences you want to use for ConSurf calculation~~"~~. However, this message '''may appear low on the page, out of view''', so scroll down periodically to check for it~~. The job cannot continue until you select the sequences.

#After a few minutes, a green message will appear SELECT SEQUENCES. The job cannot continue until you select the sequences.

#Scan the names of the proteins in the list that has checkboxes, under the header "Sequences producing significant alignments:". Find the first case where the function of the protein is not the same as the protein of interest (or the function is unclear). Usually you will want to exclude sequences for proteins of different functions.

#Scroll to the bottom of the page and put the number of the last sequence having the same function as the protein of interest in the box "Select the first [ .... ] sequences". Then click on the "Update selection" button.

ConSurfDB vs. ConSurf: Difference between revisions

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@@ Line 50: / Line 50: @@
 #Go to [http://consurf.tau.ac.il consurf.tau.ac.il], the ConSurf Server (distinct from ConSurf-DB).
-#If you are offered a choice between the new version and the old one, choose the new version.
+#Fill out the form. When you get to the section ''Choose parameters to build the Multiple Sequence Alignment (MSA)'', be sure to check '''Let me select the sequences for the analysis manually out of Blast results'''. The other options in this section can be left at their default settings.
-#Fill out the form. When you get to the section ''Choose parameters to build the Multiple Sequence Alignment (MSA)'', be sure to check '''Let me select the sequences for the analysis manually out of Blast results'''.
-#Under ''Maximum Homologs to collect'', change 50 to '''all'''. The other options in this section can be left at their default settings.
 #Enter your email address and click the ''Submit'' button.
-#After a few minutes, a red message will appear "Please choose which sequences you want to use for ConSurf calculation". However, this message '''may appear low on the page, out of view''', so scroll down periodically to check for it. The job cannot continue until you select the sequences.
+#After a few minutes, a <font color="#00d000"><b>green</b></font> message will appear <font color="#00d000"><b>SELECT SEQUENCES</b></font>. The job cannot continue until you select the sequences.
 #Scan the names of the proteins in the list that has checkboxes, under the header "Sequences producing significant alignments:". Find the first case where the function of the protein is not the same as the protein of interest (or the function is unclear). Usually you will want to exclude sequences for proteins of different functions.
 #Scroll to the bottom of the page and put the number of the last sequence having the same function as the protein of interest in the box "Select the first [ .... ] sequences". Then click on the "Update selection" button.