from:"Richard Gildea"

Re: [ccp4bb] shadow at the edge

2017-04-27 Thread Richard Gildea

Dear Abhishek,

This looks very like the goniometer shadowing we have seen from the mini Kappa 
goniometer on I04 at DLS. DIALS (and xia2) now support dynamic shadow masking, 
although a model for the goniometer shadowing needs to be coded in the detector 
"format class" in order for it to work. We have done this work for the DLS I04 
format class - if you let me know (off list) the location of your data on disk 
at Diamond I can try to help you process the data taking into account the 
goniometer shadowing.

Thanks,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Dr A.A. Jalan 
[aa...@cam.ac.uk]
Sent: 27 April 2017 21:49
To: ccp4bb
Subject: [ccp4bb] shadow at the edge


Dear all,

The attached diffraction image has a shadow at the right edge. It moves from 
the top to the bottom right corner. I was wondering if anyone knows what it 
could be and whether it would affect data processing?

Thank you

Abhishek







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Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-10 Thread Richard Gildea

The documentation you linked to is out of date (our fault), the new DIALS 
homepage is:

http://dials.github.io

The precise behaviour of the dials.index parameter filter_ice is described more 
explicitly in the current documentation:

http://dials.github.io/documentation/programs/dials_index.html

max_cell_estimation
.expert_level = 1
  {
filter_ice = True
  .help = "Filter out reflections at typical ice ring resolutions before"
  "max_cell estimation."
  .type = bool
  }

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Richard Gildea 
[richard.gil...@diamond.ac.uk]
Sent: 10 December 2016 17:56
To: ccp4bb
Subject: Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; 
CCfit...) in certain resolution bin

Dear Eugene,

This is only in dials.index, and even then it is only in the initial maximum 
cell estimation that reflections from ice rings are excluded by default. They 
are included in the basis vector determination and further refinement. If you 
wish to exclude ice ring reflections from all steps of indexing you need to 
filter ice rings in dials.find_spots.

For dials.integrate see:

http://dials.github.io/documentation/programs/dials_integrate.html

The parameter filter.ice_rings=false by default.

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: Eugene Osipov [e.m.osi...@gmail.com]
Sent: 10 December 2016 17:21
To: Gildea, Richard (DLSLtd,RAL,LSCI)
Cc: ccp4bb
Subject: Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; 
CCfit...) in certain resolution bin

Dear RIchard,
It is probably my problems with understanding.
>From this page:
http://dials.sourceforge.net/documentation/programs/dials_index.html

I understood that :

filter_ice = True

is default parameter and by default DIALS will not consider spots at typical 
ice resolutions. Or it is only true before refinement procedure?

2016-12-10 18:05 GMT+03:00 
<richard.gil...@diamond.ac.uk<mailto:richard.gil...@diamond.ac.uk>>:
"E.g. DIALS by default do not process reflections near ice rings,"

I'm not sure where you got this information from, but this is not correct - by 
default DIALS will process all reflections.

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] 
on behalf of Eugene Osipov [e.m.osi...@gmail.com<mailto:e.m.osi...@gmail.com>]
Sent: 10 December 2016 13:39
To: ccp4bb
Subject: Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; 
CCfit...) in certain resolution bin

E.g. DIALS by default do not process reflections near ice rings,

2016-12-09 21:05 GMT+03:00 Phil Evans 
<p...@mrc-lmb.cam.ac.uk<mailto:p...@mrc-lmb.cam.ac.uk><mailto:p...@mrc-lmb.cam.ac.uk<mailto:p...@mrc-lmb.cam.ac.uk>>>:
For some reason there is no data in that resolution bin

Phil

> On 9 Dec 2016, at 17:30, Xiao Lei 
> <xiaolei...@gmail.com<mailto:xiaolei...@gmail.com><mailto:xiaolei...@gmail.com<mailto:xiaolei...@gmail.com>>>
>  wrote:
>
> Hi All,
>
> I have an x ray diffraction dataset of protein and dna complex processed with 
> pointless and I am trying to get the resolution cut for this data, the result 
> is below, I do not know why in the N=23 (Dmid=3.68) bin, there is no 
> statistic of CC(1/2), N_cc, CCfit, etc?  The program just put a "-" sign into 
> it.  I guess if this means something bad probably I have to cut the 
> resolution to 3.7A.
>
> $TABLE: Mn(I/sigI) and CC(1/2) [in P1] vs. resolution:
> $GRAPHS:Resolution estimate 3.89A:0.000213587|0.0981986x0|1:2,4,6,7,9:
>  $$
>   N  1/d^2Dmid CC(1/2)   N_CC   CCfit  Mn(I/sigI)  N (I/sigI)/10   $$ 
> $$
>   1  0.0018  23.27   0.939 51   0.990   92.43142   9.243
>   2  0.0051  13.99   0.993210   0.987   72.33607   7.233
>   3  0.0084  10.92   0.984323   0.984   61.77937   6.177
>   4  0.0116   9.27   0.974344   0.981   54.77   1030   5.477
>   5  0.0149   8.19   0.969486   0.976   29.98   1412   2.998
>   6  0.0182   7.42   0.961491   0.971   13.24   1459   1.324
>   7  0.0214   6.83   0.879535   0.9648.75   1558   0.875
>   8  0.0247   6.36   0.885597   0.9566.70

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-10 Thread Richard Gildea

"E.g. DIALS by default do not process reflections near ice rings,"

I'm not sure where you got this information from, but this is not correct - by 
default DIALS will process all reflections.

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eugene Osipov 
[e.m.osi...@gmail.com]
Sent: 10 December 2016 13:39
To: ccp4bb
Subject: Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; 
CCfit...) in certain resolution bin

E.g. DIALS by default do not process reflections near ice rings,

2016-12-09 21:05 GMT+03:00 Phil Evans 
<p...@mrc-lmb.cam.ac.uk<mailto:p...@mrc-lmb.cam.ac.uk>>:
For some reason there is no data in that resolution bin

Phil

> On 9 Dec 2016, at 17:30, Xiao Lei 
> <xiaolei...@gmail.com<mailto:xiaolei...@gmail.com>> wrote:
>
> Hi All,
>
> I have an x ray diffraction dataset of protein and dna complex processed with 
> pointless and I am trying to get the resolution cut for this data, the result 
> is below, I do not know why in the N=23 (Dmid=3.68) bin, there is no 
> statistic of CC(1/2), N_cc, CCfit, etc?  The program just put a "-" sign into 
> it.  I guess if this means something bad probably I have to cut the 
> resolution to 3.7A.
>
> $TABLE: Mn(I/sigI) and CC(1/2) [in P1] vs. resolution:
> $GRAPHS:Resolution estimate 3.89A:0.000213587|0.0981986x0|1:2,4,6,7,9:
>  $$
>   N  1/d^2Dmid CC(1/2)   N_CC   CCfit  Mn(I/sigI)  N (I/sigI)/10   $$ 
> $$
>   1  0.0018  23.27   0.939 51   0.990   92.43142   9.243
>   2  0.0051  13.99   0.993210   0.987   72.33607   7.233
>   3  0.0084  10.92   0.984323   0.984   61.77937   6.177
>   4  0.0116   9.27   0.974344   0.981   54.77   1030   5.477
>   5  0.0149   8.19   0.969486   0.976   29.98   1412   2.998
>   6  0.0182   7.42   0.961491   0.971   13.24   1459   1.324
>   7  0.0214   6.83   0.879535   0.9648.75   1558   0.875
>   8  0.0247   6.36   0.885597   0.9566.70   1755   0.670
>   9  0.0280   5.98   0.939693   0.9477.16   2003   0.716
>  10  0.0312   5.66   0.807697   0.9354.97   2042   0.497
>  11  0.0345   5.38   0.815757   0.9215.53   2195   0.553
>  12  0.0378   5.15   0.910878   0.9046.08   2547   0.608
>  13  0.0410   4.94   0.913890   0.8847.49   2582   0.749
>  14  0.0443   4.75   0.906934   0.8617.42   2710   0.742
>  15  0.0476   4.58   0.824976   0.8345.06   2695   0.506
>  16  0.0508   4.44   0.812   1010   0.8025.32   2859   0.532
>  17  0.0541   4.30   0.843   1099   0.7675.25   3126   0.525
>  18  0.0574   4.17   0.862   1030   0.7274.49   2790   0.449
>  19  0.0606   4.06   0.752   1115   0.6833.04   2927   0.304
>  20  0.0639   3.96   0.675439   0.6362.53   1117   0.253
>  21  0.0672   3.86   0.139176   0.5861.64393   0.164
>  22  0.0704   3.77   0.734   1082   0.5342.65   2641   0.265
>  23  0.0737   3.68- -----
>  24  0.0770   3.60   0.489681   0.4292.20   1633   0.220
>  25  0.0802   3.53   0.358   1430   0.3781.85   3248   0.185
>  26  0.0835   3.46  -0.428 12   0.3301.38 22   0.138
>  27  0.0868   3.39   0.390663   0.2851.73   1404   0.173
>  28  0.0900   3.33   0.128   1443   0.2441.39   2946   0.139
>  29  0.0933   3.27   0.149   1372   0.2071.37   2835   0.137
>  30  0.0966   3.22   0.183   1578   0.1751.40   3202   0.140
>
> Thanks ahead.



--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com<mailto:e.m.osi...@gmail.com>

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please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any dama

Re: [ccp4bb] Spot Integration Vs Fitting

2016-02-10 Thread Richard Gildea

Dear Jacob,

DIALS and MOSFLM each output both of the intensities you describe (although 
DIALS does 3D profile fitting whereas MOSFLM does 2D profile fitting). The 
first, Isum, are the summation integrated intensities, the second, Iprf, are 
the profile-fitted intensities. The scaling program AIMLESS (by default) 
combines the two values by calculating a weighted mean that varies smoothly 
from Iprf for the weak reflections to Isum for the strong reflections (it turns 
out that summation integrated intensities are often better than the 
profile-fitted intensities for strong data). See the AIMLESS documentation or 
Phil Evan’s scaling papers for more details:

http://www.ccp4.ac.uk/html/aimless.html#intensities

http://journals.iucr.org/d/issues/2013/07/00/ba5190/index.html#SEC2

Cheers,

Richard

On 10 Feb 2016, at 17:09, Keller, Jacob 
> wrote:

Let me clarify: I was not asking whether there is such a thing as profile 
fitting, 3D or otherwise. I thought, however, that profiles used for making a 
mask through which to integrate the actual counts, and those numbers were the 
intensities. Not true? Are the derived mathematical profile estimates/fits 
themselves output as the measurements?

A difference practically between the two is whether fine phi slicing would 
reduce error by allowing multiple measurements of the Gaussian for each spot. 
In terms of fitting, it would be much better to sample the Gaussian ten times 
at different phi than once (back to the observation:parameter ratio question--a 
ratio of ten is better than one). Thus with fitting, one could consider each 
spot, if measured 10 times, to have a sort of multiplicity of its own.

JPK

-Original Message-
From: graeme.win...@diamond.ac.uk 
[mailto:graeme.win...@diamond.ac.uk]
Sent: Wednesday, February 10, 2016 9:38 AM
To: Keller, Jacob; ccp4bb@jiscmail.ac.uk
Subject: RE: Spot Integration Vs Fitting

Dear Jacob

There is a strong tradition of profile fitting in integration - for 3D profile 
fitting I would feel that this is the best place to start:

http://scripts.iucr.org/cgi-bin/paper?S0021889888007903

(Kabsch, 1988)

This was about processing data from a multiwire detector which behaved a lot 
like the pixel array detectors of today re: fine slicing & big (ish) pixels

The assumption of a Gaussian form is however a dangerous one, as we are 
certainly seeing "fine structure" in spots these days.

I am certain you will get many other references pointed your way, going back to 
e.g. Diamond 1969 on the profile fitting for point detector data

Best wishes Graeme


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
Sent: 10 February 2016 14:24
To: ccp4bb
Subject: [ccp4bb] Spot Integration Vs Fitting

Dear Crystallographers,

As I understand it, all integration software uses measured intensities rather 
than fits thereof. Wouldn't it be better in the case of (very) fine phi slicing 
to start using 3D gaussian fits to the spots, perhaps even with outlier 
rejection? I would think a fit to, say, 10 samples of a Gaussian would be more 
precise than summing the intensities.

Perhaps a lot of datasets have non-Gaussian distribution?

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

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please notify us of receipt by returning the e-mail and do not use, copy, 
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the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
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Re: [ccp4bb] Writing .xplor or CCP4 maps from raw data

2013-10-08 Thread Richard Gildea

Hi Anthony,

You can achieve this easily using the cctbx. I assume that your 3D grid of 
floating points is a numpy array - if so you will have to convert this to a 
cctbx flex array as shown in the simple example below. The cctbx can also has 
the functionality to write out xplor maps - if needed I can dig out an example 
for this too:

import numpy
from scitbx.array_family import flex
from iotbx.ccp4_map import write_ccp4_map
from cctbx import sgtbx
from cctbx import uctbx

a = numpy.random.rand(10,10,10)
b = flex.double(a.astype(numpy.float64))

write_ccp4_map(
  file_name=random.map,
  unit_cell=uctbx.unit_cell((1,1,1,90,90,90)),
  space_group=sgtbx.space_group_info(P1).group(),
  gridding_first=(0,0,0),
  gridding_last=tuple(b.all()),
  map_data=b,
  labels=flex.std_string([iotbx.ccp4_map.tst]))

Cheers,

Richard

On 8 Oct 2013, at 10:32, Anthony Bradley 
anthony.brad...@worc.ox.ac.ukmailto:anthony.brad...@worc.ox.ac.uk
 wrote:

Hi all,

I would like to write CCP4 or .xplor maps of a potential field I have derived 
myself.

I am using python and have a 3D grid of floating points. I would like to write 
these out as a ccp4 or .xplor map.

Does anybody have any suggestions of functions that might be able to help me 
with this?

Best wishes,

Anthony




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please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.

Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.

Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Richard Gildea

The cctbx provides comprehensive tools for handling mmcif files (and indeed all 
types of cif files - it is not fussy), freely available under the BSD-style 
cctbx licence.

Cheers,

Richard

On 7 Aug 2013, at 19:16, Jeffrey, Philip D. pjeff...@princeton.edu wrote:

 Are all the APIs open source ?  I was under the impression that CCP4 had 
 moved away from that, which might justifiably reduce interest in any 
 limited-availability API.
 
 Phil Jeffrey
 Princeton
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Stroud 
 [xtald...@gmail.com]
 Sent: Wednesday, August 07, 2013 1:51 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] mmCIF as working format?
 
 On Aug 5, 2013, at 4:33 AM, Eugene Krissinel wrote:
 I just hope that one day we all will be discussing a sort of universal API 
 to read/write structural information instead of referencing to raw formats, 
 and routines to query MX data, which would be more appropriate than grep 
 (would many SB students/postdocs use grep these days? but many if them would 
 need to inspect files somehow). This, in essence, is similar to discussing 
 read/write primitives in C/C++/Fortran rather than I/O functions of BIOS and 
 HDD/BUS commands that they drive.
 
 I just want to reinforce this point by quoting it verbatim and also emphasize 
 that it was not lost on some of us.
 
 In the long term, the MM structure community should perhaps get its 
 inspiration from SQL, which focuses on the scope of data and the semantics 
 its manipulation, rather than how the data is encoded beneath the surface.
 
 James

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please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
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Re: [ccp4bb] CCP4 Update victim of own success

2013-04-11 Thread Richard Gildea

Perhaps there needs to be a separate update manager to manage updates to
the update manager:

[image: Inline images 1]

(from http://xkcd.com/1197/)

Cheers,

Richard

--

Richard Gildea

Software Developer
Physical Biosciences Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
Mail Stop 64R0121
Berkeley
CA 94720-8118


On 11 April 2013 05:17, eugene.krissi...@stfc.ac.uk wrote:

 Sorry that this was unclear. We assume that updater is used primarily from
 ccp4i, where nothing changed (and why it should be used from command line
 at all ?:)). The name was changed because it is reserved in Windows, which
 caused lots of troubles. Now it will stay as is.

 Eugene

 On 11 Apr 2013, at 05:16, James Stroud wrote:


 On Apr 10, 2013, at 9:30 PM, eugene.krissi...@stfc.ac.ukmailto:
 eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.ukmailto:
 eugene.krissi...@stfc.ac.uk wrote:

 No, it got renamed to ccp4um :) That should have been written in update
 descriptions, was it not?


 There was only one mention of ccp4um that I could find in all update
 descriptions that I found (6.3.0-020). I only figured out what information
 was trying to be communicated because of your message (see attachment).

 James


 um-what.png



 On 11 Apr 2013, at 03:54, James Stroud wrote:

 Hello All,

 I downloaded a crispy new version of CCP4 and ran update until the update
 update script disappeared. Is the reason that CCP4 has reached its final
 update?

 James




 --
 Scanned by iCritical.

Re: [ccp4bb] Off-topic: Best Scripting Language

2012-09-13 Thread Richard Gildea

In my opinion, the Python equivalent of your pseudo-code is fairly close to
how you would write the instructions logically. But then maybe not everyone
thinks in the same way that I do :-)

for x in range(1, 10):
  if age_of_person(x)  50:
print name_of_person(x), is an old man (or woman)

Of course you would have to define the functions age_of_person() and
name_of_person() in order for this to work, or you could write it in a more
object-oriented method so you have a Person object which has attributes
name, age, gender, etc. and the code would be even more readable.

for person in list_of_people:
  if person.age  50:
print person.name, is an old , person.gender

Disclaimer: I mainly write in Python, so obviously am naturally biased
towards Python, however I have yet to see another widely used language that
is as readable or intuitive to learn (to me).

Cheers,

Richard

--

Richard Gildea

Software Developer
Physical Biosciences Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
Mail Stop 64R0121
Berkeley
CA 94720-8118



On 13 September 2012 10:02, Patrick Shaw Stewart patr...@douglas.co.ukwrote:


 Like most computer users and many scientists I don't write scripts to
 organize or analyse my data unless I get desperate.  I've used both Python
 and Perl a few years ago, but it would take quite a lot of time and effort
 and staring at on-line tutorials to get back into either of them right now.
  So I end up using massive Excel files that kind of work, but are a pain.
  I've noticed that quite a few structural biologists have the same problem.

 I've never understood why there can't be a simple programming language
 that is completely self-explanatory bercause it uses English sentences.
  Our robot scripting language uses syntax like

 Dispense 0.5 * DropVol ul to TargetWells using ProteinSyringe

 That is pretty obvious.


 So why can't I have a language where I can write


 Carry_out_a_sequence_where

  x is 1 to 10

 with_step_size 1 :

 if
 age of person(x) is_greater_than 50
  then
 print name of person(x) is an old man (or woman) .

 Repeat_for_next x .


 ?


 I don't care if it's efficient (anything is efficient compared to Excel)
 or if it's easy to write big programs in.  All I care about is that it's
 easy to get going.

 Later on I can learn to write simply Sequence instead of
 Carry_out_a_sequence_where.  I could click a button that would make the
 replacement to make my code more compact and readable to a trained eye.
  And of course  is_greater_than  could be written as   .

 Any intelligent school-child could understand it too, which would be
 fantastic here in the UK where kids aren't taught to program any more.

 Does such a language exist?





 On 13 September 2012 17:08, James Stroud xtald...@gmail.com wrote:


 On Sep 13, 2012, at 3:24 AM, Tim Gruene wrote:

 I have the impression that
 python programmers spend a lot of effort in trying to convince others
 that python is a good choice. Why bother rather than let people make
 their own decision?


 Someone asked.

 Plus, python programmers put no more effort than any other programmer.
 It's just that python has more advocates (for good reason) so the apparent
 effort is amplified.

 Don't hate us because our preferred programming language is beautiful.

 James

   --
 James Stroud

 http://www.jamesstroud.com




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  Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
  Directors: Peter Baldock, Patrick Shaw Stewart

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Re: [ccp4bb] IUCr checkCIF server.

2012-08-21 Thread Richard Gildea

Hi,

The interface for uploading both structure factor and model files can be
found here:

http://journals.iucr.org/services/cif/checking/checkfull.html

Checkcif is mainly intended for checking the structural details of small
molecule CIF files - I have no idea what it will make of mmcif-format PDB
files (the mmcif dictionary differs significantly from the core CIF
dictionary which is used for small molecules), or indeed whether any
checkcif output would be meaningful for a macromolecule.

Cheers,

Richard

--

Richard Gildea

Software Developer
Physical Biosciences Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
Mail Stop 64R0121
Berkeley
CA 94720-8118



On 21 August 2012 11:02, Niu Tou niutou2...@gmail.com wrote:

 Dear Collegues,
 Does anybody know how to use the server http://checkcif.iucr.org/? I have
 downloaded structure factor and structure model cif files of a structure
 from PDB. However it looks this server only accept one single file, it does
 not work if these two files are uploaded separately. My question is: do I
 need to combine these two cif files into one? How to do that? Thanks!

 Niu

Re: [ccp4bb] Anybody knows why SSRL is unaccessible ?

2012-04-14 Thread Richard Gildea

They were hit by a lightning strike on Thursday evening which took out
their power:

https://slacportal.slac.stanford.edu/sites/esh/emergency/Pages/default.aspx

Cheers,

Richard
On Apr 14, 2012 9:28 AM, Bosch, Juergen jubo...@jhsph.edu wrote:

 neither the websites nor ssh works to any of the machines.
 Did they fall into a black hole ?
 e.g. http://www-ssrl.slac.stanford.edu

 Jürgen

 ..
 Jürgen Bosch
 Johns Hopkins University
 Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Office: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-2926
 http://web.mac.com/bosch_lab/

Re: [ccp4bb] shadow at the edge

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Re: [ccp4bb] Spot Integration Vs Fitting

Re: [ccp4bb] Writing .xplor or CCP4 maps from raw data

Re: [ccp4bb] mmCIF as working format?

Re: [ccp4bb] CCP4 Update victim of own success

Re: [ccp4bb] Off-topic: Best Scripting Language

Re: [ccp4bb] IUCr checkCIF server.

Re: [ccp4bb] Anybody knows why SSRL is unaccessible ?

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