Re: [ccp4bb] refmac5 vs phenix refine mixed up

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Pavel, dear Garib,

how do you figure out automatically the correct flag? (I hope both
phenix and refmac will allow to manual overwrite the software's decision)

Cheers,
Tim

On 01/24/2013 07:47 PM, Pavel Afonine wrote:
> Hi,
> 
> It would be nice if default setting was the same in different 
> suites.
> 
> 
> it's a nice idea of course, but I feel it is impractical as it 
> would require changing a lot of software, both modern and legacy. 
> However, given array of flags it is algorithmically trivial to 
> figure out what is test and work flags. That's what phenix.refine 
> have been doing since its beginning (2005). And my understanding
> is that Refmac does this too. As always, there are corner cases
> here, but it's better than nothing. Plus, programs (at least 
> phenix.refine, can't speak for others) tell which flag was
> actually used, and they provide option to define the flag value to
> use.
> 
> Pavel
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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UiHvuKXg2/b3LqlbPWQpKmY=
=Awum
-END PGP SIGNATURE-

Re: [ccp4bb] off topic - legacy hardware help needed

[Adam Ralph]

You can just connect two machines together with an ethernet cable, no switches 
or
routers. However you need a crossover cable to do this. Most likely you have 
standard
cables only in the lab.


Adam 

Re: [ccp4bb] refmac5 vs phenix refine mixed up

[Garib N Murshudov]

Dear Tim

In principle if a user defines freer flag then refmac knows about that (unless 
freer flag is 0 then refmac assumes that it is default). In this case (if freer 
defined by user) then it is not altered.

regards
Garib


On 25 Jan 2013, at 09:14, Tim Gruene wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear Pavel, dear Garib,
> 
> how do you figure out automatically the correct flag? (I hope both
> phenix and refmac will allow to manual overwrite the software's decision)
> 
> Cheers,
> Tim
> 
> On 01/24/2013 07:47 PM, Pavel Afonine wrote:
>> Hi,
>> 
>> It would be nice if default setting was the same in different 
>> suites.
>> 
>> 
>> it's a nice idea of course, but I feel it is impractical as it 
>> would require changing a lot of software, both modern and legacy. 
>> However, given array of flags it is algorithmically trivial to 
>> figure out what is test and work flags. That's what phenix.refine 
>> have been doing since its beginning (2005). And my understanding
>> is that Refmac does this too. As always, there are corner cases
>> here, but it's better than nothing. Plus, programs (at least 
>> phenix.refine, can't speak for others) tell which flag was
>> actually used, and they provide option to define the flag value to
>> use.
>> 
>> Pavel
>> 
> 
> - -- 
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> 
> iD8DBQFRAkzvUxlJ7aRr7hoRAlVfAKClRD4/JLNDcOab1HjBroQYXND3bQCfegA9
> UiHvuKXg2/b3LqlbPWQpKmY=
> =Awum
> -END PGP SIGNATURE-

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] off topic - legacy hardware help needed

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Adam,

cross-over cables are only required for really old machines. For a few
years, RJ-45 plugs have been able to figure out automatically whether
they are connected to a switch or directly to another machine.

Best,
Tim

On 01/25/2013 10:40 AM, Adam Ralph wrote:
> You can just connect two machines together with an ethernet cable,
> no switches or routers. However you need a crossover cable to do
> this. Most likely you have standard cables only in the lab.
> 
> 
> Adam
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRAlfSUxlJ7aRr7hoRAln8AJ9Ry+dH1a4q4mh32A+0wJVFoRih4gCg8HGg
p8xCYBRv11m7YAx6LpXQZ1E=
=IF8v
-END PGP SIGNATURE-

Re: [ccp4bb] refmac5 vs phenix refine mixed up

[Robbie Joosten]

I noticed that Refmac has done the 1vs0 thing correct for ages, which is very 
useful because mix-ups between the work set and test set used to be quite 
common in the reflection files at the pdb (Refmac saved me a lot of extra work 
with this). Dealing with this problem is very simple as the smallest set is 
typically the test set.

Phenix however needs to deal with the CCP4 type reflection binning. Now the 
size of the sets cannot be used which means that you have find a smarter 
solution. So I wonder how this is implemented. Does Phenix use the (reasonable) 
assumption that the test set is labeled 1.00 or 0.00? Or does it also check the 
sets with other labels?

Cheers,
Robbie

Sent from my Windows Phone

From: Garib N Murshudov
Sent: 2013-01-25 10:46
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refmac5 vs phenix refine mixed up

Dear Tim

In principle if a user defines freer flag then refmac knows about that (unless 
freer flag is 0 then refmac assumes that it is default). In this case (if freer 
defined by user) then it is not altered.

regards
Garib


On 25 Jan 2013, at 09:14, Tim Gruene wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Pavel, dear Garib,
>
> how do you figure out automatically the correct flag? (I hope both
> phenix and refmac will allow to manual overwrite the software's decision)
>
> Cheers,
> Tim
>
> On 01/24/2013 07:47 PM, Pavel Afonine wrote:
>> Hi,
>>
>> It would be nice if default setting was the same in different
>> suites.
>>
>>
>> it's a nice idea of course, but I feel it is impractical as it
>> would require changing a lot of software, both modern and legacy.
>> However, given array of flags it is algorithmically trivial to
>> figure out what is test and work flags. That's what phenix.refine
>> have been doing since its beginning (2005). And my understanding
>> is that Refmac does this too. As always, there are corner cases
>> here, but it's better than nothing. Plus, programs (at least
>> phenix.refine, can't speak for others) tell which flag was
>> actually used, and they provide option to define the flag value to
>> use.
>>
>> Pavel
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFRAkzvUxlJ7aRr7hoRAlVfAKClRD4/JLNDcOab1HjBroQYXND3bQCfegA9
> UiHvuKXg2/b3LqlbPWQpKmY=
> =Awum
> -END PGP SIGNATURE-

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] A question about FFT

[Eleanor Dodson]

The FFT software tries to limit the volume to the asymmetric unit for the
spacegroup. This has to be a 3-D box, so cubic spacegroups give more peaks
than expected, but not a full list of 1260 ..
However there may not be a complete list - these S are in di-sulphide
bonds, and at limited resoluton you would not expect all the patterson
peaks to be discrete.

You could use the program vectors to generate a list of Patterson peaks
from your S coordinates, then display those in coot on the Patterson map to
see how well it predicts the sites.
Eleanor




On 25 January 2013 07:07, Wei Feng  wrote:

> Dear all,
> I have a Zn-free insulin crystal and there are 3  *disulfide bonds* in
> one asymmetry unit.*
> *
> ATOM 43  SG  CYS A   6  20.112  40.351  32.363  1.00
> 16.55   S
> ATOM 49  SG  CYS A   7  24.024  47.785  30.285  1.00
> 22.23   S
> ATOM 76  SG  CYS A  11  21.504  38.985  32.424  1.00
> 17.77   S
> ATOM167  SG  CYS A  20  16.482  31.957  26.203  1.00
> 15.38   S
> ATOM240  SG  CYS B   7  25.993  46.755  30.463  1.00
> 18.58   S
> ATOM336  SG  CYS B  19  17.764  32.878  25.093  1.00
> 15.26   S*
>
> *The space group of the crystal is < I213>.
> As we konw, there are 12 symmetry operations of the space group I213, so
> there will be
> 3*12=36  disulfide bond in the unit cell.
> And the number of the patterson peaks of these disulfide bond should be
> 36*(36-1)=1260
> But when we use FFT to calculate the patterson peaks of it, only 9 peaks
> （Peak height >6.0）are found.
>
> *ATOM  6  OW  WAT X   1  37.672   6.512  20.437  9.13
> 9.13   O
> ATOM  6  OW  WAT X   2  20.437  37.672   6.512  9.13
> 9.13   O
> ATOM  6  OW  WAT X   3   6.512  20.437  37.672  9.13
> 9.13   O
> ATOM 13  OW  WAT X   4  31.906  26.078  16.823  7.99
> 7.99   O
> ATOM 13  OW  WAT X   5  16.823  31.906  26.078  7.99
> 7.99   O
> ATOM 13  OW  WAT X   6  26.078  16.823  31.906  7.99
> 7.99   O
> ATOM  7  OW  WAT X   7  24.775  30.019   8.741  6.74
> 6.74   O
> ATOM  7  OW  WAT X   8  30.019   8.741  24.775  6.74
> 6.74   O
> ATOM  7  OW  WAT X   9   8.742  24.775  30.019  6.74
> 6.74   O
> *ATOM  8  OW  WAT X  10  25.060  34.755  10.969  4.24
> 4.24   O
> ATOM  8  OW  WAT X  11  34.755  10.969  25.060  4.24
> 4.24   O
> ATOM  8  OW  WAT X  12  10.969  25.060  34.755  4.24
> 4.24   O
> ATOM 10  OW  WAT X  13  38.803  11.242  19.278  4.04
> 4.04   O
> ATOM 10  OW  WAT X  14  11.243  19.278  38.803  4.04
> 4.04   O
> ATOM 10  OW  WAT X  15  27.561  19.278  38.803  4.04
> 4.04   O
> ATOM 10  OW  WAT X  16  38.803  27.561  19.278  4.04
> 4.04   O
> ATOM 19  OW  WAT X  17  31.656  29.083  22.684  3.83
> 3.83   O
> ATOM 19  OW  WAT X  18  22.684  31.656  29.083  3.83
> 3.83   O
> ATOM 19  OW  WAT X  19  29.083  22.684  31.656  3.83
> 3.83   O
> ATOM 17  OW  WAT X  20  29.945  29.101  21.650  3.59
> 3.59   O
> ATOM 17  OW  WAT X  21  21.650  29.945  29.101  3.59
> 3.59   O
> ATOM 17  OW  WAT X  22  29.101  21.650  29.945  3.59
> 3.59   O
> ATOM  1  OW  WAT X  23  19.402  13.112   0.000  3.53
> 3.53   O
> ATOM 24  OW  WAT X  24  34.640  34.640  34.640  3.50
> 3.50   O
> ATOM 21  OW  WAT X  25  31.626  23.245  37.418  3.37
> 3.37   O
> ATOM 21  OW  WAT X  26  37.418  31.626  23.245  3.37
> 3.37   O
> ATOM 21  OW  WAT X  27  23.245  37.418  31.626  3.37
> 3.37   O
> ATOM 20  OW  WAT X  28  23.826  29.990  26.590  3.35
> 3.35   O
> ATOM 20  OW  WAT X  29  26.590  23.826  29.990  3.35
> 3.35   O
> ATOM 20  OW  WAT X  30  29.990  26.590  23.826  3.35
> 3.35   O
> ATOM  9  OW  WAT X  31  11.321  28.206  36.494  3.33
> 3.33   O
> ATOM  9  OW  WAT X  32  28.206  36.494  11.321  3.33
> 3.33   O
> ATOM  9  OW  WAT X  33  36.494  11.321  28.206  3.33
> 3.33   O
> ATOM 23  OW  WAT X  34  33.090  30.414  36.290  3.22
> 3.22   O
> ATOM 23  OW  WAT X  35  30.414  36.290  33.090  3.22
> 3.22   O
> ATOM 23  OW  WAT X  36  36.290  33.090  30.414  3.22
> 3.22   O
> ATOM 11  OW  WAT X  37  11.962  19.803  33.965  3.21
> 3.21   O
> ATOM 11  OW  WAT X  38  33.965  11.962  19.802  3.21
> 3.21   O
> ATOM 11  OW  WAT X  39  19.803  33.965  11.962  3.21
> 3.21   O
> ATOM 14  OW  WAT X  40  37.964  18.211  35.654  3.20
> 3.20   O
> ATOM 14  OW  WAT X  41  18.211  35.654  37.964  3.20
> 3.20   O
> ATOM 14  OW  WAT X  42  35.654  3

Re: [ccp4bb] A question about FFT

[Ian Tickle]

Hi Wei

Are you saying that the highest 9 peaks in your list that you highlighted
correspond to disulphide-disulphide vectors and the rest don't?  Actually
of the 9 only 3 are independent, the other 6 are related by the 3-fold so
you need to take that into account in your calculation of the no of peaks
expected.  AFAICS on a superficial check none of the intra-asymmetric unit
vectors appear in the complete list (all the ones in the list seem to be
too far from the origin) & since you didn't specify your unit cell
dimension it's impossible to verify whether any of the inter- vectors
appear in the list.

Just to be clear: this is a SAD Patterson you're talking about, not a
native Patterson, right?  If the latter it wouldn't surprise me at all that
you don't see any S-S <=> S-S peaks.  Could you give more details of your
data processing protocol & data quality indicators? - likely that's the
source of your problem.

Cheers

-- Ian


On 25 January 2013 07:07, Wei Feng  wrote:

> Dear all,
> I have a Zn-free insulin crystal and there are 3  *disulfide bonds* in
> one asymmetry unit.*
> *
> ATOM 43  SG  CYS A   6  20.112  40.351  32.363  1.00
> 16.55   S
> ATOM 49  SG  CYS A   7  24.024  47.785  30.285  1.00
> 22.23   S
> ATOM 76  SG  CYS A  11  21.504  38.985  32.424  1.00
> 17.77   S
> ATOM167  SG  CYS A  20  16.482  31.957  26.203  1.00
> 15.38   S
> ATOM240  SG  CYS B   7  25.993  46.755  30.463  1.00
> 18.58   S
> ATOM336  SG  CYS B  19  17.764  32.878  25.093  1.00
> 15.26   S*
>
> *The space group of the crystal is < I213>.
> As we konw, there are 12 symmetry operations of the space group I213, so
> there will be
> 3*12=36  disulfide bond in the unit cell.
> And the number of the patterson peaks of these disulfide bond should be
> 36*(36-1)=1260
> But when we use FFT to calculate the patterson peaks of it, only 9 peaks
> （Peak height >6.0）are found.
>
> *ATOM  6  OW  WAT X   1  37.672   6.512  20.437  9.13
> 9.13   O
> ATOM  6  OW  WAT X   2  20.437  37.672   6.512  9.13
> 9.13   O
> ATOM  6  OW  WAT X   3   6.512  20.437  37.672  9.13
> 9.13   O
> ATOM 13  OW  WAT X   4  31.906  26.078  16.823  7.99
> 7.99   O
> ATOM 13  OW  WAT X   5  16.823  31.906  26.078  7.99
> 7.99   O
> ATOM 13  OW  WAT X   6  26.078  16.823  31.906  7.99
> 7.99   O
> ATOM  7  OW  WAT X   7  24.775  30.019   8.741  6.74
> 6.74   O
> ATOM  7  OW  WAT X   8  30.019   8.741  24.775  6.74
> 6.74   O
> ATOM  7  OW  WAT X   9   8.742  24.775  30.019  6.74
> 6.74   O
> *ATOM  8  OW  WAT X  10  25.060  34.755  10.969  4.24
> 4.24   O
> ATOM  8  OW  WAT X  11  34.755  10.969  25.060  4.24
> 4.24   O
> ATOM  8  OW  WAT X  12  10.969  25.060  34.755  4.24
> 4.24   O
> ATOM 10  OW  WAT X  13  38.803  11.242  19.278  4.04
> 4.04   O
> ATOM 10  OW  WAT X  14  11.243  19.278  38.803  4.04
> 4.04   O
> ATOM 10  OW  WAT X  15  27.561  19.278  38.803  4.04
> 4.04   O
> ATOM 10  OW  WAT X  16  38.803  27.561  19.278  4.04
> 4.04   O
> ATOM 19  OW  WAT X  17  31.656  29.083  22.684  3.83
> 3.83   O
> ATOM 19  OW  WAT X  18  22.684  31.656  29.083  3.83
> 3.83   O
> ATOM 19  OW  WAT X  19  29.083  22.684  31.656  3.83
> 3.83   O
> ATOM 17  OW  WAT X  20  29.945  29.101  21.650  3.59
> 3.59   O
> ATOM 17  OW  WAT X  21  21.650  29.945  29.101  3.59
> 3.59   O
> ATOM 17  OW  WAT X  22  29.101  21.650  29.945  3.59
> 3.59   O
> ATOM  1  OW  WAT X  23  19.402  13.112   0.000  3.53
> 3.53   O
> ATOM 24  OW  WAT X  24  34.640  34.640  34.640  3.50
> 3.50   O
> ATOM 21  OW  WAT X  25  31.626  23.245  37.418  3.37
> 3.37   O
> ATOM 21  OW  WAT X  26  37.418  31.626  23.245  3.37
> 3.37   O
> ATOM 21  OW  WAT X  27  23.245  37.418  31.626  3.37
> 3.37   O
> ATOM 20  OW  WAT X  28  23.826  29.990  26.590  3.35
> 3.35   O
> ATOM 20  OW  WAT X  29  26.590  23.826  29.990  3.35
> 3.35   O
> ATOM 20  OW  WAT X  30  29.990  26.590  23.826  3.35
> 3.35   O
> ATOM  9  OW  WAT X  31  11.321  28.206  36.494  3.33
> 3.33   O
> ATOM  9  OW  WAT X  32  28.206  36.494  11.321  3.33
> 3.33   O
> ATOM  9  OW  WAT X  33  36.494  11.321  28.206  3.33
> 3.33   O
> ATOM 23  OW  WAT X  34  33.090  30.414  36.290  3.22
> 3.22   O
> ATOM 23  OW  WAT X  35  30.414  36.290  33.090  3.22
> 3.22   O
> ATOM 23  OW  WAT X  36  36.290  33.090  30.414  3.22
> 3.22   O
> ATOM 11  OW  WAT X  37  11.962  19.803  33.965  3.21
>

Re: [ccp4bb] refmac5 vs phenix refine mixed up

[Nat Echols]

On Fri, Jan 25, 2013 at 2:24 AM, Robbie Joosten
 wrote:
> Phenix however needs to deal with the CCP4 type reflection binning. Now the
> size of the sets cannot be used which means that you have find a smarter
> solution. So I wonder how this is implemented. Does Phenix use the
> (reasonable) assumption that the test set is labeled 1.00 or 0.00? Or does
> it also check the sets with other labels?

I forget the exact rules, but the general assumption is that if you
have multiple flag values (such as 0 through 19), the test set is
marked by the lowest value.  If you have just two values, the test set
is whichever is less common.  (For SHELX files this would typically be
-1, for CNS files it would be 1, but you could just as easily swap
flag values and it would still pick the correct set.)  I'm sure
someone can figure out a way to break this (for instance, by assigning
the flags with CCP4, but using 7 instead of 0 as the test set), but in
practice nearly every file we've seen obeys these rules, and it can of
course be overridden by the user.

Anyway this is all open-source, so you can check (and re-use!) the
logic for yourself here:

http://cctbx.svn.sourceforge.net/viewvc/cctbx/trunk/iotbx/reflection_file_utils.py?revision=16491&view=markup

-Nat

[ccp4bb] RapiData: Seats are available - the deadline is in 10 days for our course on Data Collection and Structure Solving at the NSLS.

[Robert Sweet]

We will present RapiData 2013, the fifteenth offering of our popular 
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The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. 
Students could be at any level from advanced undergraduate to full professor. 
The course should accommodate 48 students total.  We encourage all students to 
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Please read the Course Announcement at http://www.bnl.gov/RapiData/.
You'll see that many experts in the field will be available for lectures
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Application tab at this site.

For the eleventh time we will hold a short lecture course on the fundamentals 
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RapiData course really requires that students have a healthy knowledge of 
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about fundamentals, this course will help. There will be a small additional fee 
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Latin American Scientists: Several scholarships are available, from the
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yrs).  Please apply for the course, and then contact R. Sweet

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In accordance with the standards of the International Union of
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Course Announcement at http://www.bnl.gov/RapiData/

=
Robert M. Sweet E-Dress: sw...@bnl.gov
Group Leader, PXRR: Macromolecular   ^ (that's L
  Crystallography Research Resource at NSLSnot 1)
  http://px.nsls.bnl.gov/
Photon Sciences and Biology Dept
Mail Stop, Bldg 463
Brookhaven Nat'l Lab.   Phones:
Upton, NY  11973631 344 3401  (Office)
U.S.A.  631 344 2741  (Facsimile)
=

Re: [ccp4bb] A question about FFT

[Ian Tickle]

Hi Wei

The explanation from looking at your FFT log file would appear to be that
what you have calculated is not a Patterson at all but an anomalous
difference Fourier, which would of course explain the lack of peaks!  The
evidence for this is that the FFT run 1) has the phase & FOM assigned, 2)
is calculated in P1 (not P-1), and 3) doesn't have an origin peak (and it's
not origin-subtracted).

With that information I think we can explain the peaks you observed:

Peak 'X 2' is due to the disulphide A20-B19.
'X 4' is from A6-A11 (with symmetry operator x, 1-y, 1/2-z).
'X 7' is from A7-B7 (same symop).

As I said, each peak appears 3 times in the list because of the 3-fold and
all the other peaks are noise.

Cheers

-- Ian


On 25 January 2013 14:58,  wrote:

> Dear Ian,
> Thank you for your detail reply.
> There are something should be clear:
> 1.The SAD Patterson vectors are calculated by I(+), Isig(+),I(-), Isig(-).
> 2. In order to submit more complete data, some information have to be
> renewed and some useful files can be found in the attachment.
> (1)The unit cell
> CRYST1   77.904   77.904   77.904  90.00  90.00  90.00 I 21 3
> (2)S-S coordinate:
> ATOM 43  SG  CYS A   6  20.158  40.510  32.477  1.00 16.55
>   S
> ATOM 49  SG  CYS A   7  24.211  47.917  30.445  1.00 22.23
>   S
> ATOM 76  SG  CYS A  11  21.536  39.121  32.557  1.00 17.77
>   S
> ATOM167  SG  CYS A  20  16.485  32.136  26.247  1.00 15.38
>   S
> ATOM240  SG  CYS B   7  26.123  46.933  30.643  1.00 18.58
>   S
> ATOM336  SG  CYS B  19  17.904  33.034  25.125  1.00 15.26
>   S
> (3)fft.pdb
> ATOM 10  OW  WAT X   1  32.611  25.754  17.013  8.54  8.54
>   O
> ATOM 10  OW  WAT X   2  17.013  32.611  25.754  8.54  8.54
>   O
> ATOM 10  OW  WAT X   3  25.755  17.013  32.611  8.54  8.54
>   O
> ATOM  5  OW  WAT X   4  21.257  38.213   6.305  7.17  7.17
>   O
> ATOM  5  OW  WAT X   5   6.305  21.257  38.213  7.17  7.17
>   O
> ATOM  5  OW  WAT X   6  38.213   6.305  21.257  7.17  7.17
>   O
> ATOM  6  OW  WAT X   7  25.414  29.923   8.402  5.30  5.30
>   O
> ATOM  6  OW  WAT X   8  29.923   8.402  25.414  5.30  5.30
>   O
> ATOM  6  OW  WAT X   9   8.402  25.414  29.923  5.30  5.30
>   O
> ATOM  1  OW  WAT X  10  26.150  11.364   2.260  3.89  3.89
>   O
> ATOM  1  OW  WAT X  11  11.364   2.260  26.150  3.89  3.89
>   O
> ATOM  1  OW  WAT X  12   2.260  26.150  11.364  3.89  3.89
>   O
> ATOM  7  OW  WAT X  13  29.944  37.250   7.974  3.72  3.72
>   O
> ATOM  7  OW  WAT X  14   7.975  29.944  37.250  3.72  3.72
>   O
> ATOM  7  OW  WAT X  15  37.250   7.974  29.944  3.72  3.72
>   O
> ATOM 12  OW  WAT X  16  22.628  20.215  27.834  3.50  3.50
>   O
> ATOM 12  OW  WAT X  17  27.834  22.628  20.215  3.50  3.50
>   O
> ATOM 12  OW  WAT X  18  20.215  27.834  22.628  3.50  3.50
>   O
> ATOM 11  OW  WAT X  19  23.336  23.420  18.588  3.39  3.39
>   O
> ATOM 11  OW  WAT X  20  23.420  18.588  23.336  3.39  3.39
>   O
> ATOM 11  OW  WAT X  21  18.588  23.336  23.420  3.39  3.39
>   O
> ATOM  3  OW  WAT X  22   9.104  17.214   5.101  3.19  3.19
>   O
> ATOM  3  OW  WAT X  23   5.101   9.104  17.214  3.19  3.19
>   O
> ATOM  3  OW  WAT X  24  17.214   5.101   9.103  3.19  3.19
>   O
> ATOM  8  OW  WAT X  25  20.507  38.952  12.372  3.19  3.19
>   O
> ATOM  9  OW  WAT X  26  22.099  14.351  35.000  3.15  3.15
>   O
> ATOM  9  OW  WAT X  27  14.351  35.000  22.099  3.15  3.15
>   O
> ATOM  9  OW  WAT X  28  35.000  22.099  14.351  3.15  3.15
>   O
> ATOM  2  OW  WAT X  29   5.038  28.656   5.496  3.12  3.12
>   O
> ATOM  2  OW  WAT X  30  28.656   5.496   5.038  3.12  3.12
>   O
> ATOM  2  OW  WAT X  31   5.496   5.038  28.656  3.12  3.12
>   O
> ATOM 13  OW  WAT X  32  33.307  37.596  24.016  3.05  3.05
>   O
> ATOM 13  OW  WAT X  33  37.596  24.016  33.307  3.05  3.05
>   O
> ATOM 13  OW  WAT X  34  24.016  33.307  37.596  3.05  3.05
>   O
> ATOM  4  OW  WAT X  35   5.606   8.131  35.777  3.04  3.04
>   O
> ATOM  4  OW  WAT X  36  35.777   5.606   8.130  3.04  3.04
>   O
> ATOM  4  OW  WAT X  37   8.131  35.777   5.606  3.04  3.04
>   O
>
> Thanks a lot!
> Wei
>
>
>
>
>
>
>
>
>
> At 2013-01-25 21:10:04,"Ian Tickle"  wrote:
>
> Hi Wei
>
> Are you saying that the highest 9 peaks in your list that you highlighted
> correspond to disulphide-disulphide vectors and the rest don't?  Actually
> of the 9 only 3 are independent, the other 6 are related by the 3-fold so
> you need to take that into account in your calculation of the no of peaks
> expected.  AFAICS on a superficial check none of the intra-asymmetric unit
> vectors appear in the complete list (all the ones in the list seem to be
> too far from the origin) & sin

[ccp4bb] CCP4 Update 015

[Ville Uski]

Dear CCP4 Users

A CCP4 update has just been released, consisting of the following
changes.

*   Ctruncate: Memory leak fixed.
*   Aimless, Pointless, Ctruncate: Documentation updated following
previous changes.

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4
Update Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0,
therefore upgrade if necessary. Please report any bugs to
c...@stfc.ac.uk

Many thanks for using CCP4.

Ville Uski
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