Re: [ccp4bb] map rotation

[Jan Abendroth]

Thanks, Eleanor!
what i really want to do with this script is to compare ligand binding
sites from many structures in several space groups. So, I want to move
coordinates and density onto one reference molecule. Since we ran into
issues, I used this dimer structure as a simple test case.

The script you outlined, only recreates the same density w/o any rotation.

mapmask \

mapin AB_full-cell.ccp4 \

xyzin B.pdb \

mskout B.msk \

<< eof

border 5

eof


maprot \

mapin AB_full-cell.ccp4 \

mskin B.msk \

mapout B_rot.map \

<< eof

MODE to

AVER

rota euler 152.440   110.24328.112

TRANS  -42.212 5.510   -57.243

end

eof


Btw, I had to remove the rota euler 0 0 0 / trans 0 0 0 lines. Maprot
complained about too many operators.

The odd thing -to me- is that when I shift a map around molecule B or the
dimer (mapmask with border 5) with a small amount ( euler 1 0 0  or trans
0.5 0.5 0.5) the map does not look jagged at the edges of the molecule,
while it does when I rotate the full amount to match B on A:

maprot  \

wrkin  AB-5.map \

mapout AB_rot.map \

 << eof

CELL xtal 61.0100   142.360068.280090.97.198090.

GRID xtal 100 228 112

MODE to

AVER

rota euler  1 0 0

TRANS   0 0 0

end

eof

Cheers,
Jan

On Mon, Mar 25, 2019 at 3:49 AM Eleanor Dodson 
wrote:

> Hmm - I find maprot extremely confusing, but remember a wrkmap does not
> use any symmetry so maybe that is why some is lost.
>
> I would have done this, but I havent tested it. And the documentation is
> SERIOUSLY confusing!!
>
> Do I understand you want to ADD the density for mol B to that of Mol A
>
>
> mapmask mapin whole-cell.map
> xyzin A.pdb
> mskout A-mol.msk
>
> Then
> maprot
> mapin whole-cell.map
> mskin A-mol.msk ! only density withing this mask
> is interesting
> mapout A-mol.map
>
> MODE to
>
> AVER
>
> rota euler 0 0 0! to pick up mol A density
>
> trans 0 0 0
>
>
> rota euler 152.440   110.24328.112   ! to rotate map by B to A
> rotation
>
> TRANS  -42.212 5.510   -57.243
>
> end
>
>
>
>
>
> On Mon, 25 Mar 2019 at 04:58, Jan Abendroth 
> wrote:
>
>> Hi all,
>> thanks for the feedback. Suggestions like coot or pymol won't work for us
>> well, since we will have to do this with dozens of structures/maps.So, I'd
>> rather have this scripted.
>>
>> Still running into some issues that I think relate to maprot.
>> My understanding is that I first have to create a map covering molecule B
>> that I want to map on A. Checking the extend of the map in chimera confirms
>> that this worked:
>>
>>
>> mapmask \
>>
>> mapin 2mol_2mFo-DFc.map \
>>
>> xyzin 2mol_B.pdb \
>>
>> mapout 2mol_2mFo-DFc_B.map \
>>
>> << eof
>>
>> border 5
>>
>> eof
>>
>>
>> Next, I need to rotate/translate the map in maprot. Since in maprot,
>> mapin requires a map that covers the unit cell, I use wrkin and 'mode to'
>> as below. In this script, the cell and grid values are the same mapdump
>> provides me for the map. The rotation and translation are from superpose,
>> RMSD of that superposition is 0.5Å.
>>
>>
>> maprot  \
>>
>> wrkin  2mol_2mFo-DFc_B.map \
>>
>> mapout 2mol_2FoFc_rot.map \
>>
>>  << eof
>>
>> CELL xtal 61.0100   142.360068.280090.97.198090.
>>
>> GRID xtal 100 228 112
>>
>> MODE to
>>
>> AVER
>>
>> rota euler 152.440   110.24328.112
>>
>> TRANS  -42.212 5.510   -57.243
>>
>> eof
>>
>>
>> The issue now is that the superposed map for the center of molecule A
>> looks great. Towards the edges of the molecule it gets weaker, does not
>> match up with the molecule or stops entirely. Again, molecule and maps
>> between A and B, as visualized in Coot by NCS hopping, are very similar.
>>
>>
>> I am still quite puzzled by what is happening. I guess I am missing
>> something in maprot. Any input would be appreciated. This is public
>> data, so I would be happy to share the data.
>>
>>
>> Cheers,
>>
>> Jan
>>
>>
>>
>> On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth 
>> wrote:
>>
>>> Hi all,
>>> this should be easy, scripting the rotation of a map.
>>> Purpose for this is: Superimpose several structures of the same protein
>>> that crystallized in different space groups, and then drag the maps along.
>>> As a simple test, I took a dimeric protein and try to superimpose
>>> molecule B along with the map on molecule A.
>>>
>>> The execution should be straightforward:
>>> a) take a map that covers the unit cell (fft),
>>> b) generate a mask around molecule B (mapmask),
>>> c) apply rotation/translation that I obtain from superimposing molecule
>>> B on molecule A.
>>>
>>> The issue is that the obtained map covers both molecule A and B (not a
>>> big deal), more importantly, it cuts of certain areas on both molecules.
>>> Molecule A and B have low RMSDs (0.5Å).
>>>
>>> I must be missing something fairly obvious, have not been able to see
>>> what. Feedback would be much appreciated. Scripts are below.
>>>
>>> Thanks!
>>> Jan
>>>
>>> mapmask

Re: [ccp4bb] Refinement

[Holton, James M]

In coot, select.

Validate > Difference Map Peaks > Find Peaks Above 4 r.m.s.d > [Find Peaks]

What do you see?

Always remember, the real-space representation of your Rwork is the Fo-Fc map.  
The biggest peak or valley in this map is usually dominating your Rwork/Rfree.  
If you feel your Rwork/Rfree are too high, it is best to think of something 
sensible to put into your biggest Fo-Fc peak.  If you have a big, negative 
feature in the middle of nowhere, try adjusting your bulk solvent parameters in 
refinement.

It is also a good idea to look at your data quality stats.  If I/sig(I) is 5, 
then I wouldn't expect Rwork/Rfree to ever drop below ~20%.  This is because 
the error in the data is already about 20%.  If your model fits better than 
that, it is probably modelling noise.

If you have no difference features to speak of and your Rwork/Rfree are still 
high, it can be a good thing to prune back your model to include only the atoms 
you are really sure about.  That is, well-ordered main chain, and maybe a few 
strong side chains like disulfides and obvious aromatics.  Refine this heavily 
pruned-model to convergence.  Don't worry about the R factors being high, they 
are supposed to be high when large parts of the model are missing.  By 
"convergence" I mean until the atoms stop moving.  R factors leveling off is 
not "convergence".  If your atoms are still wandering about and changing B 
factors, then run the refinement one more time.  Wait for things to settle.  
This is kind of like running a column, you want to wait until everything has 
equilibrated before you inject something new.  This kind of equilibration is 
the only way to know that the rise or fall in R you see is due to the change 
you just made, as opposed to an after-effect of something you did a few dozen 
cycles ago.  Once that is done, look at the top feature in your Fo-Fc 
difference map.  This tallest peak is the least likely thing in your unit cell 
to be wrong.  Build in this feature.  Then re-refine to convergence again.  
This can take a while, but it is the best way to ensure that you avoid model 
bias of any kind.  Building just one feature at a time is the most conservative 
strategy.  If you're in more of a hurry, you might consider anything above 6 
sigmas to be "safe", but 5 is pushing it, and 4 is dangerous unless there is 
nothing else left in the map.

Happy Building!

-James Holton
MAD Scientist

On 3/23/2019 9:17 PM, StrBio wrote:
ALL.

I have data at 2.4 A in P21 sp gr, helical protein.
Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics 
oither Rfactor (by Phenix). Refmac quit same.
Should I deposit it or look better data?
Any suggestion?





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Re: [ccp4bb] 12th CCP4/APS Crystallographic School in the US

[Xu, Qingping]

Just a friendly reminder that the registration for the upcoming CCP4/APS School 
will close on Apr 15th, 2019. Please apply if you plan to attend.

Thanks.

Charles, Garib and Qingping


On 1/3/19 8:09 AM, Qingping Xu wrote:

Dear Colleagues,

We are pleased to announce the 12th annual CCP4 crystallographic school “From 
data collection to structure refinement and beyond” will be held on June 17-24, 
2019 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near 
Chicago, Illinois, USA. All details can be found at the school website: 
http://www.ccp4.ac.uk/schools/APS-2019/index.php.

Dates: June 17 through 24, 2019

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near 
Chicago), Illinois, USA

The school comprises two parts: data collection workshop and crystallographic 
computing workshop. Data collection workshop includes beamline training, data 
collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M 
and Eiger 16M detectors respectively, and data processing. For data collection, 
only the participants' crystals will be used. Crystallographic computation 
workshop will feature many modern crystallographic software packages taught by 
authors and other experts. The daily schedule will be organized in three 
sections – lectures, tutorials, and hands-on (interactive trouble-shooting of 
the technical difficulties the participants face in their projects). We have 
had considerable success resolving these problems in past years, attested by 
resulting publications (see 
http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, 
contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career 
faculty, along with commercial/industrial researchers are encouraged to apply. 
Only 20 applicants will be selected for participation. Participants of the 
workshop are strongly encouraged to bring their own problem data sets or 
crystals so the problems can be addressed during data collection and/or 
computation workshops.

Application: Application deadline is April 15th, 2019. To apply, visit 
https://www.ccp4.ac.uk/schools/APS-2019/application.php.

Fees: The registration for application is free but there is $500 participation 
fee for the selected academic students and $950 for the industrial researchers. 
The link for the on-line payments and instructions will be provided once the 
selection process is completed. The students will be responsible for their 
transportation and lodging. The workshop organizers can assist in making the 
lodging reservations at the Argonne Guest House. The workshop will cover all 
other expenses (including meals).

We hope to see you at the school.

Charles, Garib and Qingping



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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

[Wim Burmeister]

  
  
Hello,
I rather think the model has a problem. 
Are there large domains which are invisible in the structure ?
Is it possible that the data are twinned ?
Did you use TLS refinement to account for anisotropy ?
Just cutting the resolution will probably not help, unless there is
a serious problem in data quality.
Best
Wim

On 25/03/2019 13:31, Sharan Karade
  wrote:


  
As I understand helical assembly, the data some time is
  anisotropic (any one or two a*,b* or c* has more diffraction
  than other), which may be responsible for your high Rfactors.
  You can crop the data to the resolution using softwares.


Regards
Sharan
  
  
On Mon, Mar 25, 2019, 8:17
  AM Andreas Förster 
  wrote:


  
Yeah, good stuff:
  
  
  http://www.auspex.de/
  
  
  
  All best.
  
  
  
  
  Andreas
  
  
  
  

  
  
  
On Mon, Mar 25, 2019
  at 10:45 AM CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
  wrote:


  
Even if you can't see them, it may be
  worthwhile investigating with Auspex (Parkhurst,
  Thorn, Winter & Waterman - sorry, I can't
  remember the reference off-hand). There's an easy
  to use webserver somewhere that runs it...
  
  Harry
  --
  Dr
  Harry Powell


  On 25 Mar 2019, at 09:03, herman.schreu...@sanofi.com
  wrote:
  


  

  Dear
  ???,
  Do
  you have any ice rings (even hardly
  visible ones) in your diffraction data?
  Best,
  Herman

   
  Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
  Im Auftrag von StrBio
  Gesendet: Sonntag, 24. März 2019
  05:17
  An: CCP4BB@JISCMAIL.AC.UK
  Betreff: [EXTERNAL] [ccp4bb]
  Refinement
   
  

  ALL.


   


  I have data at 2.4 A
in P21 sp gr, helical protein. 


  Refined to Rwork 29
Rfree 34 with nice density map and all
nice statistics oither Rfactor (by
Phenix). Refmac quit same.
  


  Should I deposit it
or look better data?


  Any suggestion?


   


    

  
   
  

  
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Re: [ccp4bb] map rotation

[Paul Emsley]

On 25/03/19 04:57, Jan Abendroth wrote:
>
> thanks for the feedback. Suggestions like coot or pymol won't work for
> us well, since we will have to do this with dozens of
> structures/maps.So, I'd rather have this scripted.
>

Do you think that Coot cannot be scripted? It can. See Section 6.20 of
the manual.

Regards,

Paul.



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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

[Sharan Karade]

As I understand helical assembly, the data some time is anisotropic (any
one or two a*,b* or c* has more diffraction than other), which may be
responsible for your high Rfactors. You can crop the data to the resolution
using softwares.

Regards
Sharan

On Mon, Mar 25, 2019, 8:17 AM Andreas Förster  wrote:

> Yeah, good stuff:
>
> http://www.auspex.de/
>
> All best.
>
>
> Andreas
>
>
>
> On Mon, Mar 25, 2019 at 10:45 AM CCP4BB <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Even if you can't see them, it may be worthwhile investigating with
>> Auspex (Parkhurst, Thorn, Winter & Waterman - sorry, I can't remember the
>> reference off-hand). There's an easy to use webserver somewhere that runs
>> it...
>>
>> Harry
>> --
>> Dr Harry Powell
>>
>> On 25 Mar 2019, at 09:03, herman.schreu...@sanofi.com wrote:
>>
>> Dear ???,
>>
>> Do you have any ice rings (even hardly visible ones) in your diffraction
>> data?
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
>> ] *Im Auftrag von *StrBio
>> *Gesendet:* Sonntag, 24. März 2019 05:17
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] [ccp4bb] Refinement
>>
>>
>>
>> ALL.
>>
>>
>>
>> I have data at 2.4 A in P21 sp gr, helical protein.
>>
>> Refined to Rwork 29 Rfree 34 with nice density map and all nice
>> statistics oither Rfactor (by Phenix). Refmac quit same.
>>
>> Should I deposit it or look better data?
>>
>> Any suggestion?
>>
>>
>>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>> 
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>
> --
>
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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

[Andreas Förster]

Yeah, good stuff:

http://www.auspex.de/

All best.


Andreas



On Mon, Mar 25, 2019 at 10:45 AM CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Even if you can't see them, it may be worthwhile investigating with Auspex
> (Parkhurst, Thorn, Winter & Waterman - sorry, I can't remember the
> reference off-hand). There's an easy to use webserver somewhere that runs
> it...
>
> Harry
> --
> Dr Harry Powell
>
> On 25 Mar 2019, at 09:03, herman.schreu...@sanofi.com wrote:
>
> Dear ???,
>
> Do you have any ice rings (even hardly visible ones) in your diffraction
> data?
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] *Im Auftrag von *StrBio
> *Gesendet:* Sonntag, 24. März 2019 05:17
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] Refinement
>
>
>
> ALL.
>
>
>
> I have data at 2.4 A in P21 sp gr, helical protein.
>
> Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics
> oither Rfactor (by Phenix). Refmac quit same.
>
> Should I deposit it or look better data?
>
> Any suggestion?
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
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>
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Re: [ccp4bb] map rotation

[Eleanor Dodson]

Hmm - I find maprot extremely confusing, but remember a wrkmap does not use
any symmetry so maybe that is why some is lost.

I would have done this, but I havent tested it. And the documentation is
SERIOUSLY confusing!!

Do I understand you want to ADD the density for mol B to that of Mol A


mapmask mapin whole-cell.map
xyzin A.pdb
mskout A-mol.msk

Then
maprot
mapin whole-cell.map
mskin A-mol.msk ! only density withing this mask is
interesting
mapout A-mol.map

MODE to

AVER

rota euler 0 0 0! to pick up mol A density

trans 0 0 0


rota euler 152.440   110.24328.112   ! to rotate map by B to A rotation

TRANS  -42.212 5.510   -57.243

end





On Mon, 25 Mar 2019 at 04:58, Jan Abendroth  wrote:

> Hi all,
> thanks for the feedback. Suggestions like coot or pymol won't work for us
> well, since we will have to do this with dozens of structures/maps.So, I'd
> rather have this scripted.
>
> Still running into some issues that I think relate to maprot.
> My understanding is that I first have to create a map covering molecule B
> that I want to map on A. Checking the extend of the map in chimera confirms
> that this worked:
>
>
> mapmask \
>
> mapin 2mol_2mFo-DFc.map \
>
> xyzin 2mol_B.pdb \
>
> mapout 2mol_2mFo-DFc_B.map \
>
> << eof
>
> border 5
>
> eof
>
>
> Next, I need to rotate/translate the map in maprot. Since in maprot, mapin
> requires a map that covers the unit cell, I use wrkin and 'mode to' as
> below. In this script, the cell and grid values are the same mapdump
> provides me for the map. The rotation and translation are from superpose,
> RMSD of that superposition is 0.5Å.
>
>
> maprot  \
>
> wrkin  2mol_2mFo-DFc_B.map \
>
> mapout 2mol_2FoFc_rot.map \
>
>  << eof
>
> CELL xtal 61.0100   142.360068.280090.97.198090.
>
> GRID xtal 100 228 112
>
> MODE to
>
> AVER
>
> rota euler 152.440   110.24328.112
>
> TRANS  -42.212 5.510   -57.243
>
> eof
>
>
> The issue now is that the superposed map for the center of molecule A
> looks great. Towards the edges of the molecule it gets weaker, does not
> match up with the molecule or stops entirely. Again, molecule and maps
> between A and B, as visualized in Coot by NCS hopping, are very similar.
>
>
> I am still quite puzzled by what is happening. I guess I am missing
> something in maprot. Any input would be appreciated. This is public data,
> so I would be happy to share the data.
>
>
> Cheers,
>
> Jan
>
>
>
> On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth 
> wrote:
>
>> Hi all,
>> this should be easy, scripting the rotation of a map.
>> Purpose for this is: Superimpose several structures of the same protein
>> that crystallized in different space groups, and then drag the maps along.
>> As a simple test, I took a dimeric protein and try to superimpose
>> molecule B along with the map on molecule A.
>>
>> The execution should be straightforward:
>> a) take a map that covers the unit cell (fft),
>> b) generate a mask around molecule B (mapmask),
>> c) apply rotation/translation that I obtain from superimposing molecule B
>> on molecule A.
>>
>> The issue is that the obtained map covers both molecule A and B (not a
>> big deal), more importantly, it cuts of certain areas on both molecules.
>> Molecule A and B have low RMSDs (0.5Å).
>>
>> I must be missing something fairly obvious, have not been able to see
>> what. Feedback would be much appreciated. Scripts are below.
>>
>> Thanks!
>> Jan
>>
>> mapmask \
>>
>> mapin 2mol_2mFo-DFc.map \
>>
>> xyzin 2mol_B.pdb \
>>
>> mskout 2mol_2mFo-DFc_2mol_B.msk \
>>
>> << eof
>>
>> border 2
>>
>> eof
>>
>>
>> maprot  \
>>
>> mapin  2mol_2mFo-DFc.map \
>>
>> mskin 2mol_2mFo-DFc_2mol_B.msk \
>>
>> wrkout 2mol_2mFo-DFc_rot.map \
>>
>>  << eof
>>
>> MODE from
>>
>> AVER
>>
>> ROTA euler  152.440   110.24328.112
>>
>> TRANS -42.212 5.510   -57.243
>>
>> eof
>> --
>> Jan Abendroth
>> Seattle / Bainbridge Island, WA, USA
>> home: Jan.Abendroth_at_gmail.com
>>
>>
>
> --
> Jan Abendroth
> Emerald Biostructures
> Seattle / Bainbridge Island, WA, USA
> home: Jan.Abendroth_at_gmail.com
> work: JAbendroth_at_embios.com
> http://www.emeraldbiostructures.com
>
> --
>
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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

[CCP4BB]

Even if you can't see them, it may be worthwhile investigating with Auspex 
(Parkhurst, Thorn, Winter & Waterman - sorry, I can't remember the reference 
off-hand). There's an easy to use webserver somewhere that runs it...

Harry
--
Dr Harry Powell

> On 25 Mar 2019, at 09:03, herman.schreu...@sanofi.com wrote:
> 
> Dear ???,
> Do you have any ice rings (even hardly visible ones) in your diffraction data?
> Best,
> Herman
>  
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von StrBio
> Gesendet: Sonntag, 24. März 2019 05:17
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] [ccp4bb] Refinement
>  
> ALL.
>  
> I have data at 2.4 A in P21 sp gr, helical protein.
> Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics 
> oither Rfactor (by Phenix). Refmac quit same.
> Should I deposit it or look better data?
> Any suggestion?
>  
>  
>  
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> 
> 
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[ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

[Herman . Schreuder]

Dear ???,
Do you have any ice rings (even hardly visible ones) in your diffraction data?
Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von StrBio
Gesendet: Sonntag, 24. März 2019 05:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Refinement

ALL.

I have data at 2.4 A in P21 sp gr, helical protein.
Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics 
oither Rfactor (by Phenix). Refmac quit same.
Should I deposit it or look better data?
Any suggestion?





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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1



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