# Difference between revisions of "Top Ten Tips"

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− | #'''Use the automated search''' | + | #'''Use the automated search'''<br/>Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs. |

− | + | #'''Search for components concurrently'''<br/>You should search for all components of the asymetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed. | |

− | #'''Search for components concurrently''' | + | #'''Search order is important'''<br/>The order in which you search for multiple solutions can affect your success in finding a solution. Components that account for the highest proportion of the scattering (highest completeness, highest sequence identity, and lowest B-factors) should be searched for first. If you are not sure which order is best, you can use the PERMUTATIONS ON keyword, which will search with all permutations of your input search components, but if you have a large number of different components be aware that this search will take a long time, especially if the signal from one of the components is not clear. |

− | + | #'''You may need to change the packing criteria'''<br/>Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look in the log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each case. In versions 1.x the default packing criterion is very strict - *no* clashes between C-alpha atoms are allowed. In versions 2.x the default packing criterion is relaxed so that the solutions with the lowest number of clashes are allowed, provided that number is 10 or less. | |

− | #'''Search order is important''' | + | #'''You may need to change the peak selection criteria'''<br/>By default, Phaser selects peaks that are between 75% and 100% of the difference between the top peak and the mean of the search for inclusion in the next round of the search (rotation or translation function). If you have many components in the asymmetric unit, the signal from the first rotation search may be very low, and you may need to decrease the cut-off for the rotation search to 70% or 65% using FINAL ROT SELECT PERCENT 65. |

− | + | #'''Beware the automated space group determination'''<br/>The space group is determined from the signal in the translation function search for the *first* model. If you have many components in the asymmetric unit, the signal from this search may be poor, and you should perform and exhaustive search in all the alternative space groups. | |

− | #'''You may need to change the packing criteria''' | + | #'''Homology models do not have 100% identity'''<br/>If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this has *not* been improved by the mutation (in fact, it has probably been made worse!). The identity you enter should thus be the same as (or less!) than that of the original sequence of your model. |

− | + | #'''Reduce the resolution if you can't find second and subsequent components'''<br/>The current algorithms have a limitation in that they do not handle the case where components of the asymmetric unit have greatly varying B-factors. This problem can be worked around by cutting the resolution to about 4 Angstroms, where the B-factor difference is less significant. | |

− | #'''You may need to change the peak selection criteria''' | + | #'''Look at the FAQ list'''<br/>If Phaser produces a strange error, or you don't understand some of the output, chances are that you are not the first person to want know what it all means. If we get asked a question three times it usually goes on the FAQ list. |

− | + | #'''Install the latest version of Phaser'''<br/>We work hard so you don't have to! | |

− | #'''Beware the automated space group determination''' | ||

− | |||

− | #'''Homology models do not have 100% identity''' | ||

− | |||

− | #'''Reduce the resolution if you can't find second and subsequent components''' | ||

− | |||

− | #'''Look at the FAQ list''' | ||

− | |||

− | #'''Install the latest version of Phaser''' | ||

− |

## Revision as of 14:11, 14 July 2009

**Use the automated search**

Don't have a quick read of the instructions and feel the need to change the defaults. If Phaser can solve your problem, it can probably solve it with the automated search using default inputs.**Search for components concurrently**

You should search for all components of the asymetric unit at the same time, and not in independent jobs. Phaser is not the same as other MR programs in this respect. Prior knowledge is used to build up a tree search. The correct solution for the first component may not be obvious until the last component is placed.**Search order is important**

The order in which you search for multiple solutions can affect your success in finding a solution. Components that account for the highest proportion of the scattering (highest completeness, highest sequence identity, and lowest B-factors) should be searched for first. If you are not sure which order is best, you can use the PERMUTATIONS ON keyword, which will search with all permutations of your input search components, but if you have a large number of different components be aware that this search will take a long time, especially if the signal from one of the components is not clear.**You may need to change the packing criteria**

Sometimes valid solutions are excluded because the number clashes is higher than the allowed default number. Look in the log and summary files to see how many high Z-score solutions Phaser is rejecting because of clashes, and how many clashes there are in each case. In versions 1.x the default packing criterion is very strict - *no* clashes between C-alpha atoms are allowed. In versions 2.x the default packing criterion is relaxed so that the solutions with the lowest number of clashes are allowed, provided that number is 10 or less.**You may need to change the peak selection criteria**

By default, Phaser selects peaks that are between 75% and 100% of the difference between the top peak and the mean of the search for inclusion in the next round of the search (rotation or translation function). If you have many components in the asymmetric unit, the signal from the first rotation search may be very low, and you may need to decrease the cut-off for the rotation search to 70% or 65% using FINAL ROT SELECT PERCENT 65.**Beware the automated space group determination**

The space group is determined from the signal in the translation function search for the *first* model. If you have many components in the asymmetric unit, the signal from this search may be poor, and you should perform and exhaustive search in all the alternative space groups.**Homology models do not have 100% identity**

If you mutate the side chains of your model so that the sequence is the same as the target structure, do not enter an identity of 100% into Phaser. The sequence identity is used to calculate the rms deviation in atomic positions between the search and target structure, and this has *not* been improved by the mutation (in fact, it has probably been made worse!). The identity you enter should thus be the same as (or less!) than that of the original sequence of your model.**Reduce the resolution if you can't find second and subsequent components**

The current algorithms have a limitation in that they do not handle the case where components of the asymmetric unit have greatly varying B-factors. This problem can be worked around by cutting the resolution to about 4 Angstroms, where the B-factor difference is less significant.**Look at the FAQ list**

If Phaser produces a strange error, or you don't understand some of the output, chances are that you are not the first person to want know what it all means. If we get asked a question three times it usually goes on the FAQ list.**Install the latest version of Phaser**

We work hard so you don't have to!