I assume that your problem is due the long names in the column named "protein". You can have org-table clip the columns to a more reasonable length by adding a row that contains e.g. <20> in the column to clip. This will clip the column to 20 characters. You can still edit the full column contents by doing ~C-c `~.

Thus add the following new row in the beginning or the end of the table:

|        |            | <20>                 |                          |        |

move to <20> and press C-c C-c.

See: http://orgmode.org/manual/Column-width-and-alignment.html

Regards,
Dov

On Thu, Apr 5, 2012 at 07:31, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
People,

I am trying to use the powerful org-table features of org-mode to solve a simple problem
I have imported a table from excel in both cvs and tab-delimited formats
and converted the region to table

the table looks like this:
##################################################################################
| Entry | Entry name | Protein names | Gene names | Length |                                                                                                                                             
| Q01284 | 2NPD_NEUCR | Nitronate monooxygenase (EC 1.13.12.16) (2-nitropropane dioxygenase) (2-NPD) (Nitroalkane oxidase) | ncd-2 G17A4.200 NCU03949 | 378 |                                            
| P05195 | 3DHQ_NEUCR | Catabolic 3-dehydroquinase (cDHQase) (EC 4.2.1.10) (3-dehydroquinate dehydratase) | qa-2 NCU06023 | 173 |                                                                        
| Q7SDX3 | 3HAO_NEUCR | 3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-hydroxyanthranilate oxygenase) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) (HAD) (Biosynthesis of nicotinic acid     
protein 1) | bna-1 NCU03282 | 180 |                                                                                                                                                                      
| P07046 | 3SHD_NEUCR | 3-dehydroshikimate dehydratase (DHS dehydratase) (DHSase) (EC 4.2.1.-) | qa-4 NCU06024 | 359 |                                                                                   
##################################################################################
but as soon as I try to align the columns, then org-table introduces a myriad of spaces where there were previously none
Why is this happening?
What am I doing wrong?

I want to use org-mode for Bioinformatics and teach students to use it as a tool, but I cannot do it unless things work seamless on my hands
 
Any help will be much appreciated

--Rodolfo Aramayo, PhD