ConSurfDB vs. ConSurf: Difference between revisions

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

#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.

#Look at 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. 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.

#Just below the large red line Please choose which sequences you want to use for ConSurf calculation is a form. 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.

#~~Scroll back~~ to the ~~top and~~ make sure that only the desired sequences are checked. (Of course you may check or uncheck individual sequences if you wish.)

## ConSurf will not accept >500 sequences. 200-250 sequences are plenty. More simply load the server unnecessarily. If the number of the last sequence having the same function as the query protein is higher than 250, use the radio buttons labeled "only every 2nd, 3rd, ..." to reduce the total number of sequences selected.

#When you are satisfied, scroll ~~back~~ to the bottom of the ~~sequences list~~ and click the ''Submit'' button.

#Examine the list of sequences to make sure that only the desired sequences are checked. (Of course you may check or uncheck individual sequences if you wish.)

#When you are satisfied, scroll to the very bottom of the page and click the ''Submit'' button.

The results of this "one function" job will usually enable you to identify more functional sites than did the ConSurf-DB result built into Proteopedia.

ConSurfDB vs. ConSurf: Difference between revisions

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@@ Line 53: / Line 53: @@
 #Enter your email address and click the ''Submit'' button.
 #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.
+#Look at 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. 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.
+#Just below the large red line <font color="red">Please choose which sequences you want to use for ConSurf calculation</font> is a form. 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.
-#Scroll back to the top and make sure that only the desired sequences are checked. (Of course you may check or uncheck individual sequences if you wish.)
+## ConSurf will not accept >500 sequences. 200-250 sequences are plenty. More simply load the server unnecessarily. If the number of the last sequence having the same function as the query protein is higher than 250, use the radio buttons labeled "only every 2nd, 3rd, ..." to reduce the total number of sequences selected.
-#When you are satisfied, scroll back to the bottom of the sequences list and click the ''Submit'' button.
+#Examine the list of sequences to make sure that only the desired sequences are checked. (Of course you may check or uncheck individual sequences if you wish.)
+#When you are satisfied, scroll to the very bottom of the page and click the ''Submit'' button.
 The results of this "one function" job will usually enable you to identify more functional sites than did the ConSurf-DB result built into Proteopedia.