Re: [ccp4bb] A grumble

2019-11-10 Thread Ivan Shabalin 

Dear All,

I would like to add my 5 cents to partly answer Eugene's questions about 
the script, and to follow up on Eleonor's mentioning of Zbsyzek and the 
rules for placing macromolecular structures in the crystal lattice.


For the last couple of years, we have been routinely using the ACHESYM 
server  for standardized placement of macromolecular models in the unit 
cell cell (http://achesym.ibch.poznan.pl/) for all structure before 
depositing them. It works great.


The following paper describes the server.

Kowiel, M., Jaskolski, M. & Dauter, Z. (2014). ACHESYM: an algorithm and 
server for standardized placement of macromolecular models in the unit 
cell. Acta Cryst. D70, doi:10.1107/S1399004714024572.


Dauter Z. On optimal placement of molecules in the unit cell. Acta 
Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):872-8. doi: 
10.1107/S0907444913002722. Epub 2013 Apr 19.


Ivan

With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/

On 11/10/19 06:49, Eugene Osipov wrote:

Dear Eleanor,
 From PDB files I see that  the structures were solved by molecular 
replacement using pdbid 1gci as a starting model. It is hard to say 
definitely without the linked paper but may be the depositors made the 
same error that I did some time ago: they solved both structures using 
molecular replacement instead of running rigid body refinement for 
follow up structure.
Actually, the issue with different origins is pretty common in pdb. For 
example, I searched pdb for isomorphous lysozyme structures in P43212 
with unit cell dimensions a=b=78.5-79.3 and c=36.5-37.3 and have found 
121 structures. I picked 6 random structures and only 2 of them have the 
same origin.
By the way, may be someone has a script to move several isomorphous 
structures to the same origin and rename chains according to reference 
structure?



пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk 
>:


I have just downloaded two isomorphous coordinates from the pdb
5arb and 5arc  deposited by the same team


Tried to compare and they are on different origins.

I know it doesnt affect the crystallography
It is easily corrected

BUT it seems bad practice to me

Eleanor





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--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O



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Re: [ccp4bb] A grumble

2019-11-10 Thread Eleanor Dodson 
Especially Frank..

Of course the grumble does not mean either deposition is "wrong" - both are
completely valid..
However at deposition there are certain tidying functions which may help
people who want to use the structures.

I absolutely agree with Zbysek (as always!) - it helps if structures are
moved close to origin.There is nothing wrong with symmetry links at 1.5-x
,-1/2+y, -2-z   but it is neater if the links were between 1/2-x,1/2+y, -z
; - which is more likely  if the original deposition was in an asymmetric
unit near the origin..

And as Eugene said; they doubtless solved both structures by MR, instead of
starting refinement of the isomorphous structure 2 from the coordinates of
structure 1.

No real problem - just a grumble!
Eleanor

On Sun, 10 Nov 2019 at 17:08, Martin Noble 
wrote:

> So does the CCP4 program csymmatch
> Best wishes,
> Martin
>
>
> On 10 Nov 2019, at 16:55, R. D. Oeffner  wrote:
>
> The program phenix.famos (or phenix.find_alt_orig_sym_mate) does exactly
> that for a pair of pdb files.
>
> Robert
>
> *From:* Eugene Osipov
> *Sent:* Sunday, November 10, 2019 11:49 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] A grumble
> By the way, may be someone has a script to move several isomorphous
> structures to the same origin and rename chains according to reference
> structure?
>
>
> пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
>
>> I have just downloaded two isomorphous coordinates from the pdb
>> 5arb and 5arc  deposited by the same team
>>
>>
>> Tried to compare and they are on different origins.
>>
>> I know it doesnt affect the crystallography
>> It is easily corrected
>>
>> BUT it seems bad practice to me
>>
>> Eleanor
>>
>>
>>
>> --
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
> Evgenii Osipov
> Laboratory for Biocrystallography,
> Department of Pharmaceutical Sciences,
> KU Leuven O
>
> --
> To unsubscribe from the CCP4BB list, click the following link:
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>
> --
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>
>
>
> --
>
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>



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Re: [ccp4bb] A grumble

2019-11-10 Thread Martin Noble 
So does the CCP4 program csymmatch
Best wishes,
Martin


On 10 Nov 2019, at 16:55, R. D. Oeffner 
mailto:rd...@cam.ac.uk>> wrote:

The program phenix.famos (or phenix.find_alt_orig_sym_mate) does exactly that 
for a pair of pdb files.

Robert

From: Eugene Osipov
Sent: Sunday, November 10, 2019 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A grumble
By the way, may be someone has a script to move several isomorphous structures 
to the same origin and rename chains according to reference structure?


пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
I have just downloaded two isomorphous coordinates from the pdb
5arb and 5arc  deposited by the same team


Tried to compare and they are on different origins.

I know it doesnt affect the crystallography
It is easily corrected

BUT it seems bad practice to me

Eleanor




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


--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O


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Re: [ccp4bb] A grumble

2019-11-10 Thread R. D. Oeffner 
The program phenix.famos (or phenix.find_alt_orig_sym_mate) does exactly that 
for a pair of pdb files.

Robert

From: Eugene Osipov 
Sent: Sunday, November 10, 2019 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] A grumble
By the way, may be someone has a script to move several isomorphous structures 
to the same origin and rename chains according to reference structure?


пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:

  I have just downloaded two isomorphous coordinates from the pdb
  5arb and 5arc  deposited by the same team 



  Tried to compare and they are on different origins.

  I know it doesnt affect the crystallography
  It is easily corrected

  BUT it seems bad practice to me 


  Eleanor





--

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-- 

Evgenii Osipov
Laboratory for Biocrystallography, 
Department of Pharmaceutical Sciences, 
KU Leuven O




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Re: [ccp4bb] A grumble

2019-11-10 Thread Hinrichs, Winfried 
There was a paper/comment in Acta Cryst  by Zbigniew Dauter "the
asymmetric unit should be close to the origin". 




The uncomfortable source is most probably that the result of a
molecular replacement is sometimes an asymmetric unit "elsewhere" ,
origin shifts etc. 









Nice weekend



Winfried Hinrichs

--
Dr. rer. nat. Winfried Hinrichs
Professor and Chair of Biochemistry, Emeritus

University of Greifswald
Institute for Biochemistry
Felix-Hausdorff-Str. 4
D-17487 Greifswald, Germany

E-mail winfried.hinri...@uni-greifswald.de

http://orcid.org/-0002-0435-4565
--





Am Sonntag, den 10-11-2019 um 12:55 schrieb Frank Von Delft:


Eleanor, whom are you grumbling at? If it's at the depositors, here's
a counter-grumble:

How would a depositor even know 



* know that it's "wrong"

* know what definition of "wrong" to work towards

* know that someone somewhere will care about this particular
"wrongness"
* know that visualisation or analysis software does not elegantly
deal with this - it is after all 2019 already
If I had to prioritise wrongnesses, I'd put top of the list that it is
not as absolutely trivial as possible to get data into the public
domain. Which means working hard (even harder!) to remove all arcane
things from the ecosystem.




Frank











On 10/11/2019 11:49, Eugene Osipov wrote:






Dear Eleanor,



>From PDB files I see that the structures were solved by molecular
replacement using pdbid 1gci as a starting model. It is hard to say
definitely without the linked paper but may be the depositors made the
same error that I did some time ago: they solved both structures using
molecular replacement instead of running rigid body refinement for
follow up structure.




Actually, the issue with different origins is pretty common in pdb.
For example, I searched pdb for isomorphous lysozyme structures in
P43212 with unit cell dimensions a=b=78.5-79.3 and c=36.5-37.3 and
have found 121 structures. I picked 6 random structures and only 2 of
them have the same origin.



Bythe way, may be someone has a script to move several isomorphous
structures to the same origin and rename chains according to reference
structure?

















пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson :










I have just downloaded two isomorphous coordinates from the pdb



5arb and 5arc deposited by the same team 














Tried to compare and they are on different origins.








I know it doesnt affect the crystallography



It is easily corrected








BUT it seems bad practice to me 









Eleanor


















-


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-- 


























Evgenii Osipov



Laboratory for Biocrystallography,



Department of Pharmaceutical Sciences,



KU Leuven O



























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Re: [ccp4bb] A grumble

2019-11-10 Thread Frank Von Delft 
Eleanor, whom are you grumbling at?  If it's at the depositors, here's a 
counter-grumble:

How would a depositor even know

  *   know that it's "wrong"
  *   know what definition of "wrong" to work towards
  *   know that someone somewhere will care about this particular "wrongness"
  *   know that visualisation or analysis software does not elegantly deal with 
this - it is after all 2019 already

If I had to prioritise wrongnesses, I'd put top of the list that it is not as 
absolutely trivial as possible to get data into the public domain.  Which means 
working hard (even harder!) to remove all arcane things from the ecosystem.

Frank



On 10/11/2019 11:49, Eugene Osipov wrote:
Dear Eleanor,
From PDB files I see that  the structures were solved by molecular replacement 
using pdbid 1gci as a starting model. It is hard to say definitely without the 
linked paper but may be the depositors made the same error that I did some time 
ago: they solved both structures using molecular replacement instead of running 
rigid body refinement for follow up structure.
Actually, the issue with different origins is pretty common in pdb. For 
example, I searched pdb for isomorphous lysozyme structures in P43212 with unit 
cell dimensions a=b=78.5-79.3 and c=36.5-37.3 and have found 121 structures. I 
picked 6 random structures and only 2 of them have the same origin.
By the way, may be someone has a script to move several isomorphous structures 
to the same origin and rename chains according to reference structure?


пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
I have just downloaded two isomorphous coordinates from the pdb
5arb and 5arc  deposited by the same team


Tried to compare and they are on different origins.

I know it doesnt affect the crystallography
It is easily corrected

BUT it seems bad practice to me

Eleanor





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


--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O



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Re: [ccp4bb] A grumble

2019-11-10 Thread Eugene Osipov 
Dear Eleanor,
>From PDB files I see that  the structures were solved by molecular
replacement using pdbid 1gci as a starting model. It is hard to say
definitely without the linked paper but may be the depositors made the same
error that I did some time ago: they solved both structures using molecular
replacement instead of running rigid body refinement for follow up
structure.
Actually, the issue with different origins is pretty common in pdb. For
example, I searched pdb for isomorphous lysozyme structures in P43212 with
unit cell dimensions a=b=78.5-79.3 and c=36.5-37.3 and have found 121
structures. I picked 6 random structures and only 2 of them have the same
origin.
By the way, may be someone has a script to move several isomorphous
structures to the same origin and rename chains according to reference
structure?


пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:

> I have just downloaded two isomorphous coordinates from the pdb
> 5arb and 5arc  deposited by the same team
>
>
> Tried to compare and they are on different origins.
>
> I know it doesnt affect the crystallography
> It is easily corrected
>
> BUT it seems bad practice to me
>
> Eleanor
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O



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