difference map for cryo-EM (cryo-EM map minus model map)

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Re: [phenixbb] phenix.erraser and...

Pavel Afonine

3 Dec 2016 3 Dec '16

3:54 a.m.

For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map): Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps. One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of: (F_obs, Phase_obs) - (F_calc, Phase_calc). The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved. I'm not sure which one of the two is better. Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography). Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed. To use: phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9 which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 . If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb. In future (once fully tested) this will be integrated into phenix.real_space_refine. The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome! All the best, Pavel

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Simone Pellegrino

14 Mar 14 Mar

3:42 p.m.

New subject: difference map for cryo-EM (cryo-EM map minus model map)

Dear Pavel, I am trying to obtain a difference map for the recent pdb ID: 5umd. I took the map deposited as emd_8576 and tried to obtain the difference map as you suggest. Unfortunately I have several blobs appearing but nothing where the ligand (an antibiotic binding the ribosome) was (I removed it from the initial pdb prior running the script). Also I find that it is difficult to interpret the two maps coming as output. Many thanks for your comments on this. Best Simone 2016-12-03 4:54 GMT+01:00 Pavel Afonine :

...

For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map):

Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps.

One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of:

(F_obs, Phase_obs) - (F_calc, Phase_calc).

The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved.

I'm not sure which one of the two is better.

Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography).

Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed.

To use:

phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9

which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 .

If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb.

In future (once fully tested) this will be integrated into phenix.real_space_refine.

The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome!

All the best, Pavel

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France

Pavel Afonine

5:55 p.m.

Hi Simone, what's the ligand id (chain name, residue name and number)? Once I have it I will get pdb and map files off the data based and run the program and see what's happening. Pavel On 3/14/17 08:42, Simone Pellegrino wrote:

...

Dear Pavel,

I am trying to obtain a difference map for the recent pdb ID: 5umd. I took the map deposited as emd_8576 and tried to obtain the difference map as you suggest. Unfortunately I have several blobs appearing but nothing where the ligand (an antibiotic binding the ribosome) was (I removed it from the initial pdb prior running the script). Also I find that it is difficult to interpret the two maps coming as output.

Many thanks for your comments on this. Best Simone

2016-12-03 4:54 GMT+01:00 Pavel Afonine mailto:[email protected]>:

For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map):

Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps.

One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of:

(F_obs, Phase_obs) - (F_calc, Phase_calc).

The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved.

I'm not sure which one of the two is better.

Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography).

Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed.

To use:

phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9

which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 .

If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb.

In future (once fully tested) this will be integrated into phenix.real_space_refine.

The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome!

All the best, Pavel

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France

Pavel Afonine

6:30 p.m.

Hi Simome, I get a very nice difference density for the ligand: http://cci.lbl.gov/~afonine/tmp/coot.png Command I used: phenix.real_space_diff_map 5umd_box.pdb 5umd_box.ccp4 resolution=3.2 Make sure to use map_model_difference_1.ccp4 as it seems to be better than the seconds map and also load it into Coot as a difference map. So.. all seems to work fine for me. Pavel On 3/14/17 08:42, Simone Pellegrino wrote:

...

Dear Pavel,

I am trying to obtain a difference map for the recent pdb ID: 5umd. I took the map deposited as emd_8576 and tried to obtain the difference map as you suggest. Unfortunately I have several blobs appearing but nothing where the ligand (an antibiotic binding the ribosome) was (I removed it from the initial pdb prior running the script). Also I find that it is difficult to interpret the two maps coming as output.

Many thanks for your comments on this. Best Simone

2016-12-03 4:54 GMT+01:00 Pavel Afonine mailto:[email protected]>:

For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map):

Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps.

One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of:

(F_obs, Phase_obs) - (F_calc, Phase_calc).

The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved.

I'm not sure which one of the two is better.

Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography).

Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed.

To use:

phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9

which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 .

If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb.

In future (once fully tested) this will be integrated into phenix.real_space_refine.

The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome!

All the best, Pavel

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France

Simone Pellegrino

16 Mar 16 Mar

12:56 p.m.

New subject: difference map for cryo-EM (cryo-EM map minus model map)

Hi Pavel, thanks for your mail. I first tried to run as a difference map in Coot (I was not doing so before, my mistake) but I still do not obtain th same as you. Could you please tell me how you get the ccp4 file? Do you go from the deposited .map file to .mtz and then from this to .ccp4 format using phenix? Many thanks for the help Best Simone 2017-03-14 19:30 GMT+01:00 Pavel Afonine :

...

Hi Simome,

I get a very nice difference density for the ligand:

http://cci.lbl.gov/~afonine/tmp/coot.png

Command I used:

phenix.real_space_diff_map 5umd_box.pdb 5umd_box.ccp4 resolution=3.2

Make sure to use map_model_difference_1.ccp4 as it seems to be better than the seconds map and also load it into Coot as a difference map.

So.. all seems to work fine for me.

Pavel

On 3/14/17 08:42, Simone Pellegrino wrote:

Dear Pavel,

I am trying to obtain a difference map for the recent pdb ID: 5umd. I took the map deposited as emd_8576 and tried to obtain the difference map as you suggest. Unfortunately I have several blobs appearing but nothing where the ligand (an antibiotic binding the ribosome) was (I removed it from the initial pdb prior running the script). Also I find that it is difficult to interpret the two maps coming as output.

Many thanks for your comments on this. Best Simone

2016-12-03 4:54 GMT+01:00 Pavel Afonine :

...
For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map):

Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps.

One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of:

(F_obs, Phase_obs) - (F_calc, Phase_calc).

The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved.

I'm not sure which one of the two is better.

Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography).

Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed.

To use:

phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9

which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 .

If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb.

In future (once fully tested) this will be integrated into phenix.real_space_refine.

The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome!

All the best, Pavel

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France

Pavel Afonine

1:33 p.m.

New subject: difference map for cryo-EM (cryo-EM map minus model map)

Hi Simone, the file (emd_8576) you get form EMDB is in ccp4 format (little nuances aside, essentially it’s all the same -- .ccp4, .map, .mrc), and then just use the command I quoted earlier. Pavel

...

On Mar 16, 2017, at 05:56, Simone Pellegrino wrote:

Hi Pavel,

thanks for your mail. I first tried to run as a difference map in Coot (I was not doing so before, my mistake) but I still do not obtain th same as you. Could you please tell me how you get the ccp4 file? Do you go from the deposited .map file to .mtz and then from this to .ccp4 format using phenix?

Many thanks for the help

Best Simone

2017-03-14 19:30 GMT+01:00 Pavel Afonine mailto:[email protected]>: Hi Simome,

I get a very nice difference density for the ligand:

http://cci.lbl.gov/~afonine/tmp/coot.png http://cci.lbl.gov/~afonine/tmp/coot.png

Command I used:

phenix.real_space_diff_map 5umd_box.pdb 5umd_box.ccp4 resolution=3.2

Make sure to use map_model_difference_1.ccp4 as it seems to be better than the seconds map and also load it into Coot as a difference map.

So.. all seems to work fine for me.

Pavel

On 3/14/17 08:42, Simone Pellegrino wrote:

...
Dear Pavel,

I am trying to obtain a difference map for the recent pdb ID: 5umd. I took the map deposited as emd_8576 and tried to obtain the difference map as you suggest. Unfortunately I have several blobs appearing but nothing where the ligand (an antibiotic binding the ribosome) was (I removed it from the initial pdb prior running the script). Also I find that it is difficult to interpret the two maps coming as output.

Many thanks for your comments on this. Best Simone

2016-12-03 4:54 GMT+01:00 Pavel Afonine mailto:[email protected]>: For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map):

Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps.

One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of:

(F_obs, Phase_obs) - (F_calc, Phase_calc).

The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved.

I'm not sure which one of the two is better.

Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography).

Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed.

To use:

phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9

which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 .

If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb.

In future (once fully tested) this will be integrated into phenix.real_space_refine.

The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome!

All the best, Pavel

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France

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