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On 19 Sep 2016, at 19:01, CCP4BB automatic digest system 
> wrote:

There are 10 messages totaling 22446 lines in this issue.

Topics of the day:

 1. Problem of diffraction patterns (2)
 2. How to determine the number of occurrences of a particular type of amino
acid on the surface of a protein
 3. Teaching models and cognition w/ xtallography as example, high school lvl
(2)
 4. multiple similar solutions in phaser (4)
 5. Job Posting - Research Fellow in Protein Crystallography - Portsmouth, UK
(BBSRC/NSF)

--

Date:Mon, 19 Sep 2016 16:37:15 +0800
From:"xiaoron...@cau.edu.cn" 
>
Subject: Problem of diffraction patterns

Dear all:
We have got two crystals in crystallization solution(crystal growth for more 
than a month):
11.25% PEG8000  0.625 M NaCl   0.15 M MgCl2   75 mM Tris-HCl pH8.5   33 mM Na/K 
phosphate pH6.2final pH7.09
When we mounted the crystal to diffraction test, the diffract pattern is as 
follow picture shows:
The diffraction result is opened with HKL2000, the right section is magnified 
view of left black box.
It seems that there are a badly diffraction at about 9~12 Å.
Is there anyone knows why? Can we discern this is the crystal of protein or 
salt from the diffraction pattern?
If it is a protein crystal, have any suggestions for subsequent optimization of 
this protein crystals?

Best,
Xiaorong Li


xiaoron...@cau.edu.cn

--

Date:Mon, 19 Sep 2016 10:05:23 +0100
From:Klaus Fütterer 
Subject: Re: Problem of diffraction patterns

Dear Xiarong,

You appear to have diffraction from a salt crystal ( the highly intense spots 
at high resolution) mixed with something that may be protein (speckles of 
difraction spots at 9 - 12 Å), plus some diffraction from ice (rings from 3.7 Å 
outwards).

Klaus


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On 19 Sep 2016, at 09:37, xiaoron...@cau.edu.cn  wrote:

Dear all:
We have got two crystals in crystallization solution(crystal growth for more 
than a month):
11.25% PEG8000  0.625 M NaCl   0.15 M MgCl2   75 mM Tris-HCl pH8.5   33 mM Na/K 
phosphate pH6.2final pH7.09
When we mounted the crystal to diffraction test, the diffract pattern is as 
follow picture shows:

The diffraction result is opened with HKL2000, the right section is magnified 
view of left black box.
It seems that there are a badly diffraction at about 9~12 Å.
Is there anyone knows why? Can we discern this is the crystal of protein or 
salt from the diffraction pattern?
If it is a protein crystal, have any suggestions for subsequent optimization of 
this protein crystals?

Best,
Xiaorong Li
xiaoron...@cau.edu.cn 

--

Date:Mon, 19 Sep 2016 12:14:10 +0200
From:Gert Vriend 
Subject: Re: How to determine the number of occurrences of a particular type of 
amino acid on the surface of a protein

Hai Joel,

At the CMBI we maintain a series of protein structure (PDB-file based)
facilities at http://swift.cmbi.ru.nl/gv/facilities/. Robbie mentioned
the PDBFINDER2 already. One of the not so often used facilities is a
collection of 'lists' in which we performed some calculation or the
other over all PDB files.

Greetings
Gert

On 18-9-2016 16:08, Joel Sussman wrote:
  18-Sep-2016
Is there a simple way to determine (calculate) the number of occurrences of a 
particular type of amino acid on the surface of a protein,
e.g. How many Tyr are on the surface of a particular protein?
Any help, most appreciated.
Thanks
Joel

Prof. Joel L. Sussman  
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309  

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-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CCP4BB 
automatic digest system
Sent: 27 September 2012 00:00
To: CCP4BB@JISCMAIL.AC.UK
Subject: CCP4BB Digest - 26 Sep 2012 (#2012-272)

There are 4 messages totaling 193 lines in this issue.

Topics of the day:

  1. Maprot question.
  2. map sharpening
  3. Refmac- solvent mask (2)

--

Date:Wed, 26 Sep 2012 15:21:44 +0100
From:Eleanor Dodson eleanor.dod...@york.ac.uk
Subject: Re: Maprot question.

You could use COOT to do the map rotation - then the parameters seem to work

The conventions should be the same. I thought but I can't really speak for COOT.
If you look at the CCP4 documentation for MAPROT, and use the Superpose 
molecules GUI task to fit A to B using lsqkab - that gives you a matrix which 
should be OK for MAPROT. Check it against the COOt output Eleanor

There is
On 26 Sep 2012, at 01:19, Niu Tou wrote:

 Dear Colleagues,
  
 Does anybody know if the definition of rotation parameters in Maprot are 
 different from that of Coot? I used Coot to superimpose a model A to model B, 
 to get a new model A* and rotation parameters (Euler angles and 
 translations), howerver when I used these parameters to move the original map 
 with Maprot, the new map did not fit with model A*. I tried the 3x3 matrix 
 and translations, it did not work either. I wonder if there is any different 
 from these two prgrams? 
  
 Thanks!
 Niu 

--

Date:Wed, 26 Sep 2012 17:45:11 +0100
From:Andreas Förster docandr...@gmail.com
Subject: map sharpening

Dear all,

a follow-up to yesterday's question about map sharpening.  The problem was that 
the sharpened maps aren't displayed in coot, but this is not coot's fault, as 
can be seen from the output:

regular map:

making conventional map from MTZ filename unsharp.mtz using FWT PHWT Number of 
OBSERVED reflections: 34725
INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid 
sampling...Nuvw = ( 128, 128, 384)
INFO:: 0.086 seconds to read MTZ file
INFO:: 0.002 seconds to initialize map
INFO:: 0.305 seconds for FFT
INFO:: 0.013 seconds for statistics
   Map mean:  -1.4987e-06
   Map sigma: ... 0.0957995
   Map maximum: . 0.629714
   Map minimum: . -0.606727
INFO:: 0.026 seconds for contour map
INFO:: 0.432 seconds in total

sharpened map:
(as above, except:)

   Map mean:  0
   Map sigma: ... 0
   Map maximum: . 0
   Map minimum: . 0


These mtz files are generated identically, zero rounds of refinement in Refmac 
5.7 (from ccp4 6.3.0) with sharpening disabled or enabled (B value = 5, 20, 60, 
200).  There are no features in the sharpened maps.  Why?

When I don't specify a B value for map sharpening, it is calculated to
61 and the resulting map displays just fine.


Andreas




On 25/09/2012 11:52, Robert Nicholls wrote:
 Hi Andreas,

 In your case, it sounds like a reasonable strategy would be to use external 
 restraints for a few rounds of refinement (as you have done), but then 
 release them and instead use jelly-body restraints. This two-stage process 
 will help to initially hold your model in a sensible conformation using 
 external restraints, but then gently release the structure in order to reduce 
 further bias in later rounds. The immediate subsequent use of jelly-body 
 restraints after external restraints will ensure that the model won't deviate 
 too far from that sensible conformation, unless the data suggests otherwise.

 Of course, if certain regions lose their sensible conformations in subsequent 
 rounds of refinement, you can continue to use external restraints just in 
 these regions.

 I substantially rebuilt a surface loop that I don't want to restrain by the 
 model.


 In this case, I would recommend re-generating the external restraints, this 
 time telling ProSMART not to generate restraints for these particular 
 residues/regions. This can be done using the -restrain and -restrain_rm 
 keywords, as described in the documentation (let me know off-board if you 
 want help with this).

 If you enable map sharpening then the single output MTZ file should be the 
 sharpened map… I'm not sure why you are finding that the map is not 
 displayed… do you see any difference between enabling/disabling map 
 sharpening?

 Cheers,
 Rob



-- 
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 Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
 http://www.msf.bio.ic.ac.uk

--

Date:Wed, 26 Sep 2012 11:45:52 -0700
From:Kiran Kulkarni dr.kirankulka...@yahoo.com
Subject: Refmac- solvent mask

Dear CCP4 users,

Is it possible to specify a solvent mask to the refmac ?

Many thanks in advance for your time and help.

Regards,
-Ki

--

Date:Wed, 26 

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