Re: [ccp4bb] baverage: no tables were found in this file

[Tim Gruene]

Dear Bing,

can you post the exact command you were using, please? Also please check
with a different PDB file. In case you are using baverage from the
command line, can you make sure you are actually using the program from
ccp4 by typing 'which baverage' at the command prompt?

Regards.
Tim

On 06/02/2014 10:16 PM, Wang, Bing wrote:
> 
> Hi CCP4,
> 
> Recently when I input my pdb file and run the baverage in the ccp4 suit to 
> check the temperature factor, it always tell me "No tables were fund in this 
> file." Could you tell me how to fix this problem? Or is there another 
> software instead of baverage I could use to check the temperature factor?
> 
> Thanks!
> 
> Bing
> 

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

GPG Key ID = A46BEE1A



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] baverage: no tables were found in this file

[Mark J van Raaij]

This also occurred to me once where the file path had a space,(/Google Drive/), 
when I moved the file somewhere else it worked. I was using baverage from the 
CCP4i GUI.

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 3 Jun 2014, at 09:20, Tim Gruene wrote:

> Dear Bing,
> 
> can you post the exact command you were using, please? Also please check
> with a different PDB file. In case you are using baverage from the
> command line, can you make sure you are actually using the program from
> ccp4 by typing 'which baverage' at the command prompt?
> 
> Regards.
> Tim
> 
> On 06/02/2014 10:16 PM, Wang, Bing wrote:
>> 
>> Hi CCP4,
>> 
>> Recently when I input my pdb file and run the baverage in the ccp4 suit to 
>> check the temperature factor, it always tell me "No tables were fund in this 
>> file." Could you tell me how to fix this problem? Or is there another 
>> software instead of baverage I could use to check the temperature factor?
>> 
>> Thanks!
>> 
>> Bing
>> 
> 
> -- 
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 

[ccp4bb] Publishing raw data

[Graeme Winter]

Hi Folks,

Colleague of mine here at Diamond just pointed out a neat EU funded way of
publishing raw data which generates a digital object identifier as part of
the process:

http://zenodo.org

Worked through it myself to see if it "works" and apparently it does:

doi:10.5281/zenodo.10271

Thought that this may be of some interest to the community... (the service,
not the data!)

Cheerio, Graeme

[ccp4bb] Fwd: [ccp4bb] phaser issue MR

[Almudena Ponce Salvatierra]

Dear all,

thank you for your suggestions, I finally fix the problem as follows. I'll
write a summary here for future reference.

1) Phaser run 1#

- I provide different ensembles
- I get a solution in which some of them have been placed

2) Phaser run 2# ERROR

- I provide the ensembles that were not placed in the previous run and
REMOVE THE ONES THAT HAD BEEN PLACED
- I provide the .sol file
- The program gives the error I sent yesterday

3) Phaser run 3# it works again

Since you said what happened was that Phaser was not finding something and
the .sol file contained information about the ensembles that I removed...

- I provided again all the ensembles I gave in run 1#
- I provide de .sol file (I understand it will fix the solution of the
ensembles from run 1#)
- It runs

So, this was my fix :-) I hear many times the sentence "fix a solution",
but then whenever I asked someone (before yesterday), each person refers to
it in an ambiguous way! some say you need to provide phaser with the pdb
from the solution you want to fix, some say that you need to provide the
.sol file from what you want to fix and then provide only one new ensemble
at the time... maybe it would be useful to have some script/example online
of the command line itself, so that one knows what to input exactly. Maybe
each one's way of explaining the same thing can lead to misunderstandings
at the end.

Best wishes,

Have a nice day.

Almudena


-- Forwarded message --
From: Almudena Ponce Salvatierra 
Date: 2014-06-03 9:49 GMT+02:00
Subject: Re: [ccp4bb] phaser issue MR
To: Airlie McCoy 


Dear Airlie,

don't worry, actually it was you who gave me the clue when you told me what
the error was standing for. I will try to be a clear as possible:

1) Phaser run 1#

- I provide different ensembles
- I get a solution in which some of them have been placed

2) Phaser run 2# ERROR

- I provide the ensembles that were not placed in the previous run and
REMOVE THE ONES THAT HAD BEEN PLACED
- I provide the .sol file
- The program gives the error I sent yesterday

3) Phaser run 3# it works again

Since you said what happened was that Phaser was not finding something and
the .sol file contained information about the ensembles that I removed...

- I provided again all the ensembles I gave in run 1#
- I provide de .sol file (I understand it will fix the solution of the
ensembles from run 1#)
- It runs

So, this was my fix :-) I hear many times the sentence "fix a solution",
but then whenever I asked someone (before yesterday), each person refers to
it in an ambiguous way! some say you need to provide phaser with the pdb
from the solution you want to fix, some say that you need to provide the
.sol file from what you want to fix and then provide only one new ensemble
at the time... maybe it would be useful to have some script/example online
of the command line itself, so that one knows what to input exactly. Maybe
each one's way of explaining the same thing can lead to misunderstandings
at the end.

I have another question, if you don't mind. How good does the TFZ score get
in one of this "iterative Molecular replacement routines"? I am now above 5
(5.4) which I know is "unlikely" but I need to take into account that I
start with fragments that maybe are not exactly as they are in the
structure (I mean in reality) and also that the model is incomplete,
meaning that even though I have now most of it places there are still some
regions that are not connected, some others with empty electron density...
What would you recommend in this case?

I also have the following warinings:

- Best model and data are insufficient to reach half expected LLG target:
placement of one/first ensemble will be very difficult.

- Search request requires more scattering than defined in composition.
Composition increased to accomodate search components.

Thank you very much for your time and consideration.

Best wishes,

Almudena.



2014-06-02 22:33 GMT+02:00 Airlie McCoy :

Hi Almundena, Apologies, I had not had a chance to look at it... what was
> your fix? Airlie
>
>
> On Jun 2 2014, Almudena Ponce Salvatierra wrote:
>
>  Dear Airlie,
>>
>> I already solved the problem.
>>
>> Thank you very much anyway.
>>
>> Best wishes,
>>
>> Almudena
>>
>>
>> 2014-06-02 15:43 GMT+02:00 Almudena Ponce Salvatierra <
>> maps.fa...@gmail.com>
>> :
>>
>>  Sorry, Airlie, the input is this one,
>>>
>>> ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT
>>>
>>>
>>> $TEXT:Script: $$ Baubles Markup $$
>>>
>>> #---PHASER COMMAND SCRIPT GENERATED BY CCP4I---
>>>
>>> TITLE start
>>>
>>> MODE MR_AUTO
>>>
>>> ROOT "/data/almudena/ccp4/iterativeMR/may_attempt/epmrsol/epmr_24"
>>>
>>>  #---DEFINE DATA---
>>>
>>> HKLIN "/data/almudena/ccp4/iterativeMR/epmr/forccp4_itMR.mtz"
>>>
>>> LABIN  F=FP SIGF=SIGFP
>>>
>>> SGALTERNATIVE SELECT HAND
>>>
>>> #---DEFINE ENSEMBLES---
>>>
>>> ENSEMBLE loop &
>>>
>>> PDB 
>>> "/data/almudena/ccp4/iterativeMR/epmr/epmr_start_6bp/4ntloop-coot-0.pdb"
>>> 

[ccp4bb] R-merge,R-meas > 1 in outermost resolution shell

[sreetama das]

Dear All,
  What are reasonable values of Rmerge in the outermost resolution 
shell? 


Some of the recent discussions suggest using data up to those shells where 
 ~2 and CC1/2 = 0.5.
But I am getting Rmerge & Rmeas > 1 in the outermost shell for those values of 
 and CC1/2.
Reducing the resolution
 cut-off while data reduction & scaling (aimless) reduces the R-values, but I 
am not sure how much I should reduce the resolution (if at all). 

Following are the results from the aimless log file:
At a resolution cut-off of 1.62A:
   Overall  InnerShell  OuterShell
Low resolution limit   42.12 42.12  1.65
High resolution limit   1.62  8.87  1.62

Rmerge  (within
 I+/I-) 0.071 0.019 1.325
Rmerge  (all I+ and I-)    0.074 0.020 1.381
Rmeas (within I+/I-)   0.078 0.021 1.446
Rmeas (all I+ & I-)    0.077 0.022 1.441
Rpim (within
 I+/I-)    0.031 0.009 0.575
Rpim (all I+ & I-) 0.022 0.007 0.410
Rmerge in top intensity bin    0.031    - - 
Total number of observations  311022  1839 14876
Total number
 unique    25311   184  1212
Mean((I)/sd(I)) 19.2  52.7   2.0
Mn(I) half-set correlation CC(1/2) 1.000 1.000 0.740
Completeness   100.0  99.4
 100.0
Multiplicity    12.3  10.0  12.3

If I take improved resolution cut-off (1.6A, 1.57A), the  and CC1/2 
in the outermost shell are lower, and the R-merge,meas,pim are higher. No 
resolution cut-off was used while integrating the data (imosflm), only a mask 
for the beam stop was used.


looking forward to your suggestions,
thanking you,
sreetama

Re: [ccp4bb] R-merge,R-meas > 1 in outermost resolution shell

[Tim Gruene]

Dear sreetama,

I have published data with Rmerge > 5 in the outer resolution shell and
could reason this the way Phil Evans explained to you yesterday.

Best regards,
Tim

On 06/03/2014 11:19 AM, sreetama das wrote:
> Dear All,
>   What are reasonable values of Rmerge in the outermost 
> resolution shell? 
> 
> 
> Some of the recent discussions suggest using data up to those shells where 
>  ~2 and CC1/2 = 0.5.
> But I am getting Rmerge & Rmeas > 1 in the outermost shell for those values 
> of  and CC1/2.
> Reducing the resolution
>  cut-off while data reduction & scaling (aimless) reduces the R-values, but I 
> am not sure how much I should reduce the resolution (if at all). 
> 
> Following are the results from the aimless log file:
> At a resolution cut-off of 1.62A:
>Overall  InnerShell  OuterShell
> Low resolution limit   42.12 42.12  1.65
> High resolution limit   1.62  8.87  1.62
> 
> Rmerge  (within
>  I+/I-) 0.071 0.019 1.325
> Rmerge  (all I+ and I-)0.074 0.020 1.381
> Rmeas (within I+/I-)   0.078 0.021 1.446
> Rmeas (all I+ & I-)0.077 0.022 1.441
> Rpim (within
>  I+/I-)0.031 0.009 0.575
> Rpim (all I+ & I-) 0.022 0.007 0.410
> Rmerge in top intensity bin0.031- - 
> Total number of observations  311022  1839 14876
> Total number
>  unique25311   184  1212
> Mean((I)/sd(I)) 19.2  52.7   2.0
> Mn(I) half-set correlation CC(1/2) 1.000 1.000 0.740
> Completeness   100.0  99.4
>  100.0
> Multiplicity12.3  10.0  12.3
> 
> If I take improved resolution cut-off (1.6A, 1.57A), the  and CC1/2 
> in the outermost shell are lower, and the R-merge,meas,pim are higher. No 
> resolution cut-off was used while integrating the data (imosflm), only a mask 
> for the beam stop was used.
> 
> 
> looking forward to your suggestions,
> thanking you,
> sreetama
> 

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

GPG Key ID = A46BEE1A



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] [ccp4bb] phaser issue MR

[Randy Read]

Dear Almudena,

We actually have a tutorial that goes through the process of defining a 
solution step by step: 
http://www.phaser.cimr.cam.ac.uk/index.php/MR_using_keyword_input.

The .sol file is a small text file that just contains the description of how a 
defined ensemble should be rotated and translated.  If you look at that file, 
you’ll see that it doesn’t contain the ENSEMBLE definitions, so those still 
have to be provided in the script that refers to the .sol file.

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

On 3 Jun 2014, at 09:55, Almudena Ponce Salvatierra  
wrote:

> Dear all, 
> 
> thank you for your suggestions, I finally fix the problem as follows. I'll 
> write a summary here for future reference. 
> 
> 1) Phaser run 1# 
> 
> - I provide different ensembles
> - I get a solution in which some of them have been placed
> 
> 2) Phaser run 2# ERROR
> 
> - I provide the ensembles that were not placed in the previous run and REMOVE 
> THE ONES THAT HAD BEEN PLACED
> - I provide the .sol file
> - The program gives the error I sent yesterday
> 
> 3) Phaser run 3# it works again
> 
> Since you said what happened was that Phaser was not finding something and 
> the .sol file contained information about the ensembles that I removed...
> 
> - I provided again all the ensembles I gave in run 1#
> - I provide de .sol file (I understand it will fix the solution of the 
> ensembles from run 1#)
> - It runs
> 
> So, this was my fix :-) I hear many times the sentence "fix a solution", but 
> then whenever I asked someone (before yesterday), each person refers to it in 
> an ambiguous way! some say you need to provide phaser with the pdb from the 
> solution you want to fix, some say that you need to provide the .sol file 
> from what you want to fix and then provide only one new ensemble at the 
> time... maybe it would be useful to have some script/example online of the 
> command line itself, so that one knows what to input exactly. Maybe each 
> one's way of explaining the same thing can lead to misunderstandings at the 
> end.
> 
> Best wishes, 
> 
> Have a nice day.
> 
> Almudena
> 
> 
> -- Forwarded message --
> From: Almudena Ponce Salvatierra 
> Date: 2014-06-03 9:49 GMT+02:00
> Subject: Re: [ccp4bb] phaser issue MR
> To: Airlie McCoy 
> 
> 
> Dear Airlie, 
> 
> don't worry, actually it was you who gave me the clue when you told me what 
> the error was standing for. I will try to be a clear as possible:
> 
> 1) Phaser run 1# 
> 
> - I provide different ensembles
> - I get a solution in which some of them have been placed
> 
> 2) Phaser run 2# ERROR
> 
> - I provide the ensembles that were not placed in the previous run and REMOVE 
> THE ONES THAT HAD BEEN PLACED
> - I provide the .sol file
> - The program gives the error I sent yesterday
> 
> 3) Phaser run 3# it works again
> 
> Since you said what happened was that Phaser was not finding something and 
> the .sol file contained information about the ensembles that I removed...
> 
> - I provided again all the ensembles I gave in run 1#
> - I provide de .sol file (I understand it will fix the solution of the 
> ensembles from run 1#)
> - It runs
> 
> So, this was my fix :-) I hear many times the sentence "fix a solution", but 
> then whenever I asked someone (before yesterday), each person refers to it in 
> an ambiguous way! some say you need to provide phaser with the pdb from the 
> solution you want to fix, some say that you need to provide the .sol file 
> from what you want to fix and then provide only one new ensemble at the 
> time... maybe it would be useful to have some script/example online of the 
> command line itself, so that one knows what to input exactly. Maybe each 
> one's way of explaining the same thing can lead to misunderstandings at the 
> end.
> 
> I have another question, if you don't mind. How good does the TFZ score get 
> in one of this "iterative Molecular replacement routines"? I am now above 5 
> (5.4) which I know is "unlikely" but I need to take into account that I start 
> with fragments that maybe are not exactly as they are in the structure (I 
> mean in reality) and also that the model is incomplete, meaning that even 
> though I have now most of it places there are still some regions that are not 
> connected, some others with empty electron density... What would you 
> recommend in this case? 
> 
> I also have the following warinings:
> 
> - Best model and data are insufficient to reach half expected LLG target: 
> placement of one/first ensemble will be very difficult. 
> 
> - Search request requires more scattering than define

Re: [ccp4bb] experimental phasing at low resolution

[Kay Diederichs]

Hi Vijay,

I think your data may be good enough to solve the substructure and get phases, 
but
1) you should be using the latest versions of SHELXC SHELXD SHELXE - it seems 
you are using SHELXD-2006/3 .
2) you could try more cycles (100 is on the low side)
3) you might want to try searching for less sites 
4) the files you attach show runs in space group P6322, not P3 which you 
suggest in your posting?

My personal opinion is that SHELXD is great for finding the sites, but at this 
resolution you want to refine the sites, and calculate phases with other 
programs/pipelines, like Phaser/Crank/Crunch.

best,

Kay

On Tue, 3 Jun 2014 16:37:58 +0800, vijay srivastava  
wrote:

>Dear All,
Does anyone know of a facility
that provides amino acid analysis for determination of SeMet
incorporation in a recombinant protein?
We're looking for some advice
about how to proceed with a structure we're working on.� Our
protein is 350 amino acids (10 methionine are present) and naturally binds 
magnesium.� We
have a SeMet data set at peak that goes down to  5.4 angstroms.�
We tried to find the heavy atom position with Shelxcde program. The
log file is given as below.

Resl.   Inf - 8.0 - 6.0 - 5.6 - 5.4 -
5.2 - 5.0 - 4.8 - 4.6 - 4.4 - 4.2 - 3.98 
N(data) 529   643   24129
0 0 0 0 0 0 0 
63.5  19.5  10.6 
10.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0 
%Complete  94.1  98.9  99.2  18.0  
0.0   0.0   0.0   0.0   0.0   0.0   0.0 
   3.06  1.24  1.07 1.21 

I am also attaching the .lst and .res file and
from that we were considering that only one selenomethionine
position.We have one monomer per AU
(-unfortunately, MR is not working for this project). The space group
is P3 .� We also have a native set down to 3.4 angstroms.�
While we understand that we may need more phasing information  we're
wondering if anyone might have some other suggestions or insights
about how we can move forward given the data that we currently have. 
Can we extend the phases with our native data set. Thanks in advance
for any advice.

regards

�
Vijay

Re: [ccp4bb] experimental phasing at low resolution

[vijay srivastava]

Dear Kay ,

I have used SG P6322 for run and P3 is the typo error.


regards 
Vijay


On Tuesday, 3 June 2014 3:53 PM, Kay Diederichs 
 wrote:
 


Hi Vijay,

I think your data may be good enough to solve the substructure and get phases, 
but
1) you should be using the latest versions of SHELXC SHELXD SHELXE - it seems 
you are using SHELXD-2006/3 .
2) you could try more cycles (100 is on the low side)
3) you might want to try searching for less sites 
4) the files you attach show runs in space group P6322, not P3 which you 
suggest in your posting?

My personal opinion is that SHELXD is great for finding the sites, but at this 
resolution you want to refine the sites, and calculate phases with other 
programs/pipelines, like Phaser/Crank/Crunch.

best,

Kay

On Tue, 3 Jun 2014 16:37:58 +0800, vijay srivastava  
wrote:

>Dear All,
Does anyone know of a facility
that provides amino acid analysis for determination of SeMet
incorporation in a recombinant protein?
We're looking for some advice
about how to proceed with a structure we're working on.� Our
protein is 350 amino acids (10 methionine are present) and naturally binds 
magnesium.� We
have a SeMet data set at peak that goes down to  5.4 angstroms.�
We tried to find the heavy atom position with Shelxcde program. The
log file is given as below.

Resl.   Inf - 8.0 - 6.0 - 5.6 - 5.4 -
5.2 - 5.0 - 4.8 - 4.6 - 4.4 - 4.2 - 3.98 
N(data)     529   643   241    29    
0     0     0     0     0     0     0 
    63.5  19.5  10.6 
10.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0 
%Complete  94.1  98.9  99.2  18.0  
0.0   0.0   0.0   0.0   0.0   0.0   0.0 
   3.06  1.24  1.07 1.21 

I am also attaching the .lst and .res file and
from that we were considering that only one selenomethionine
position.We have one monomer per AU
(-unfortunately, MR is not working for this project). The space group
is P3 .� We also have a native set down to 3.4 angstroms.�
While we understand that we may need more phasing information  we're
wondering if anyone might have some other suggestions or insights
about how we can move forward given the data that we currently have. 
Can we extend the phases with our native data set. Thanks in advance
for any advice.

regards

�
Vijay

Re: [ccp4bb] experimental phasing at low resolution

[Bert Van-Den-Berg]

First, I wouldn't worry about the extent of SeMet incorporation. If you have 
followed an established protocol (either using  an auxotroph or regular strain) 
the incorporation should be fine.

For your SeMet data, what is the redundancy and resolution? In my experience it 
is often very hard to find Se sites and solve the structure for low resolution 
data (lower than 3 A). Most often the data is just not good enough to pick out 
the weak signal, and, like in your case, you get "useful" anomalous signal to 
5-6 A resolution. However, you should also try different programs like SOLVE 
and AUTOSOL within phenix. Also, given that you have a high symmetry space 
group, it may be possible to remove some data and still have sufficient 
redundancy; check carefully if you have radiation damage and cut off data 
accordingly.
For phase extension you first need to have decent phases...

Good luck, bert


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of vijay srivastava 
[vijaytec...@yahoo.co.in]
Sent: Tuesday, June 03, 2014 9:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] experimental phasing at low resolution

Dear All,
Does anyone know of a facility that provides amino acid analysis for 
determination of SeMet incorporation in a recombinant protein?
We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 350 amino acids (10 methionine are present) and 
naturally binds magnesium.  We have a SeMet data set at peak that goes down to 
5.4 angstroms.  We tried to find the heavy atom position with Shelxcde program. 
The log file is given as below.

Resl. Inf - 8.0 - 6.0 - 5.6 - 5.4 - 5.2 - 5.0 - 4.8 - 4.6 - 4.4 - 4.2 - 3.98
N(data) 529 643 241 29 0 0 0 0 0 0 0
 63.5 19.5 10.6 10.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
%Complete 94.1 98.9 99.2 18.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
 3.06 1.24 1.07 1.21

I am also attaching the .lst and .res file and from that we were considering 
that only one selenomethionine position.We have one monomer per AU 
(-unfortunately, MR is not working for this project). The space group is P3 .  
We also have a native set down to 3.4 angstroms.  While we understand that we 
may need more phasing information we're wondering if anyone might have some 
other suggestions or insights about how we can move forward given the data that 
we currently have. Can we extend the phases with our native data set. Thanks in 
advance for any advice.

regards

Vijay

Re: [ccp4bb] experimental phasing at low resolution

[MARTYN SYMMONS]

Don't forget that your SeMet has real differences from your native - the S to 
Se brings in 18 extra electrons (less obviously if there is lower 
incorporation). But that mean if your native is isomorphous enough (you didn't 
say) then you possibly have 'ordinary' isomorphous differences to work with. 
You could then work in the anomalous as a sort of SIRAS solution.  
SeMet as isomorphous has been used previously in many structure solutions.
All the best
  Martyn

Martyn Symmons
Cambridge 



 From: vijay srivastava 
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Tuesday, 3 June 2014, 9:37
Subject: [ccp4bb] experimental phasing at low resolution
 


Dear All,
Does anyone know of a facility
that provides amino acid analysis for determination of SeMet
incorporation in a recombinant protein?
We're looking for some advice
about how to proceed with a structure we're working on.  Our
protein is 350 amino acids (10 methionine are present) and naturally binds 
magnesium.  We
have a SeMet data set at peak that goes down to  5.4 angstroms. 
We tried to find the heavy atom position with Shelxcde program. The
log file is given as below.

Resl.   Inf - 8.0 - 6.0 - 5.6 - 5.4 -
5.2 - 5.0 - 4.8 - 4.6 - 4.4 - 4.2 - 3.98 
N(data) 529   643   24129
0 0 0 0 0 0 0 
63.5  19.5  10.6 
10.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0 
%Complete  94.1  98.9  99.2  18.0  
0.0   0.0   0.0   0.0   0.0   0.0   0.0 
   3.06  1.24  1.07 1.21 

I am also attaching the .lst and .res file and
from that we were considering that only one selenomethionine
position.We have one monomer per AU
(-unfortunately, MR is not working for this project). The space group
is P3 .  We also have a native set down to 3.4 angstroms. 
While we understand that we may need more phasing information  we're
wondering if anyone might have some other suggestions or insights
about how we can move forward given the data that we currently have. 
Can we extend the phases with our native data set. Thanks in advance
for any advice.

regards

 
Vijay

Re: [ccp4bb] baverage: no tables were found in this file

[Eugene Krissinel]

I take this chance to to confirm once more, as publicly as possible, that file 
paths with spaces are discouraged in today's CCP4. This inconvenience 
originates from ancient times in computing when good half of CCP4 was written 
and when spaces were disallowed on file system nodes.

Please take a notice of this fact as CCP4 core still receives (albeit 
infrequent) bug reports, where surprising behaviour is due to using file paths 
with white spaces.

Fixing this has proved to be a hard problem, purely because of technical 
choices made quite a number of years ago. But good news are that this 
limitation will be removed in new CCP4 Gui under development.

Eugene

On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:

> This also occurred to me once where the file path had a space,(/Google 
> Drive/), when I moved the file somewhere else it worked. I was using baverage 
> from the CCP4i GUI.
> 
> Mark J van Raaij
> Lab 20B
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.cnb.csic.es/~mjvanraaij
> 
> 
> 
> 
> 
> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
> 
>> Dear Bing,
>> 
>> can you post the exact command you were using, please? Also please check
>> with a different PDB file. In case you are using baverage from the
>> command line, can you make sure you are actually using the program from
>> ccp4 by typing 'which baverage' at the command prompt?
>> 
>> Regards.
>> Tim
>> 
>> On 06/02/2014 10:16 PM, Wang, Bing wrote:
>>> 
>>> Hi CCP4,
>>> 
>>> Recently when I input my pdb file and run the baverage in the ccp4 suit to 
>>> check the temperature factor, it always tell me "No tables were fund in 
>>> this file." Could you tell me how to fix this problem? Or is there another 
>>> software instead of baverage I could use to check the temperature factor?
>>> 
>>> Thanks!
>>> 
>>> Bing
>>> 
>> 
>> -- 
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>> 
>> GPG Key ID = A46BEE1A
>> 


-- 
Scanned by iCritical.

Re: [ccp4bb] baverage: no tables were found in this file

[Felix Frolow]

Possibility to have file names with the spaces is a curse put on the community 
by Microsoft, and it will be a big mistake to introduce this to CCP4 (my 
opinion).
I guess there are much more important things new CCP4 GUI should deal with. If 
CCP4 GUI will start to go this way,
file names with spaces will become file names with spaces and multilingual, in 
some these languages writing is going in the different direction.
In my introduction to UNIX, I teach in the beginning of practical protein 
crystallography my first demand from student is to forget about spaces in the 
fie names and the life will be much easier.
No fix is needed for that, concentrate on more important problems :-)
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Jun 3, 2014, at 14:47 , Eugene Krissinel  wrote:

> I take this chance to to confirm once more, as publicly as possible, that 
> file paths with spaces are discouraged in today's CCP4. This inconvenience 
> originates from ancient times in computing when good half of CCP4 was written 
> and when spaces were disallowed on file system nodes.
> 
> Please take a notice of this fact as CCP4 core still receives (albeit 
> infrequent) bug reports, where surprising behaviour is due to using file 
> paths with white spaces.
> 
> Fixing this has proved to be a hard problem, purely because of technical 
> choices made quite a number of years ago. But good news are that this 
> limitation will be removed in new CCP4 Gui under development.
> 
> Eugene
> 
> On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
> 
>> This also occurred to me once where the file path had a space,(/Google 
>> Drive/), when I moved the file somewhere else it worked. I was using 
>> baverage from the CCP4i GUI.
>> 
>> Mark J van Raaij
>> Lab 20B
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> c/Darwin 3
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616
>> http://www.cnb.csic.es/~mjvanraaij
>> 
>> 
>> 
>> 
>> 
>> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
>> 
>>> Dear Bing,
>>> 
>>> can you post the exact command you were using, please? Also please check
>>> with a different PDB file. In case you are using baverage from the
>>> command line, can you make sure you are actually using the program from
>>> ccp4 by typing 'which baverage' at the command prompt?
>>> 
>>> Regards.
>>> Tim
>>> 
>>> On 06/02/2014 10:16 PM, Wang, Bing wrote:
 
 Hi CCP4,
 
 Recently when I input my pdb file and run the baverage in the ccp4 suit to 
 check the temperature factor, it always tell me "No tables were fund in 
 this file." Could you tell me how to fix this problem? Or is there another 
 software instead of baverage I could use to check the temperature factor?
 
 Thanks!
 
 Bing
 
>>> 
>>> -- 
>>> Dr Tim Gruene
>>> Institut fuer anorganische Chemie
>>> Tammannstr. 4
>>> D-37077 Goettingen
>>> 
>>> GPG Key ID = A46BEE1A
>>> 
> 
> 
> -- 
> Scanned by iCritical.
> 

Re: [ccp4bb] baverage: no tables were found in this file

[Mark J van Raaij]

completely agree with avoiding spaces in paths and file names, but Google Drive 
is very handy for sharing files, so every once in a while I forget to move a 
file someone shares with me before running Unix programs on it and get strange 
errors. Depending on how awake one is at the time finding out the source can be 
time-consuming...Google should really remove the space!

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:

> I take this chance to to confirm once more, as publicly as possible, that 
> file paths with spaces are discouraged in today's CCP4. This inconvenience 
> originates from ancient times in computing when good half of CCP4 was written 
> and when spaces were disallowed on file system nodes.
> 
> Please take a notice of this fact as CCP4 core still receives (albeit 
> infrequent) bug reports, where surprising behaviour is due to using file 
> paths with white spaces.
> 
> Fixing this has proved to be a hard problem, purely because of technical 
> choices made quite a number of years ago. But good news are that this 
> limitation will be removed in new CCP4 Gui under development.
> 
> Eugene
> 
> On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
> 
>> This also occurred to me once where the file path had a space,(/Google 
>> Drive/), when I moved the file somewhere else it worked. I was using 
>> baverage from the CCP4i GUI.
>> 
>> Mark J van Raaij
>> Lab 20B
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> c/Darwin 3
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616
>> http://www.cnb.csic.es/~mjvanraaij
>> 
>> 
>> 
>> 
>> 
>> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
>> 
>>> Dear Bing,
>>> 
>>> can you post the exact command you were using, please? Also please check
>>> with a different PDB file. In case you are using baverage from the
>>> command line, can you make sure you are actually using the program from
>>> ccp4 by typing 'which baverage' at the command prompt?
>>> 
>>> Regards.
>>> Tim
>>> 
>>> On 06/02/2014 10:16 PM, Wang, Bing wrote:
 
 Hi CCP4,
 
 Recently when I input my pdb file and run the baverage in the ccp4 suit to 
 check the temperature factor, it always tell me "No tables were fund in 
 this file." Could you tell me how to fix this problem? Or is there another 
 software instead of baverage I could use to check the temperature factor?
 
 Thanks!
 
 Bing
 
>>> 
>>> -- 
>>> Dr Tim Gruene
>>> Institut fuer anorganische Chemie
>>> Tammannstr. 4
>>> D-37077 Goettingen
>>> 
>>> GPG Key ID = A46BEE1A
>>> 
> 
> 
> -- 
> Scanned by iCritical.
> 

Re: [ccp4bb] baverage: no tables were found in this file

[Harry Powell]

Hi Felix

Couldn't agree more, particularly when non-native anglophones have to contend 
with limiting themselves to ASCII  characters in their filenames anyway (e.g. 
Spanish users have to carefully rename the OSX unnamed folder (carpeta sin 
título) to something without an accent...)

On 3 Jun 2014, at 12:58, Felix Frolow wrote:

> Possibility to have file names with the spaces is a curse put on the 
> community by Microsoft, and it will be a big mistake to introduce this to 
> CCP4 (my opinion).
> I guess there are much more important things new CCP4 GUI should deal with. 
> If CCP4 GUI will start to go this way,
> file names with spaces will become file names with spaces and multilingual, 
> in some these languages writing is going in the different direction.
> In my introduction to UNIX, I teach in the beginning of practical protein 
> crystallography my first demand from student is to forget about spaces in the 
> fie names and the life will be much easier.
> No fix is needed for that, concentrate on more important problems :-)
> Dr Felix Frolow   
> Professor of Structural Biology and Biotechnology, Department of Molecular 
> Microbiology and Biotechnology
> Tel Aviv University 69978, Israel
> 
> Acta Crystallographica F, co-editor
> 
> e-mail: mbfro...@post.tau.ac.il
> Tel:  ++972-3640-8723
> Fax: ++972-3640-9407
> Cellular: 0547 459 608
> 
> On Jun 3, 2014, at 14:47 , Eugene Krissinel  
> wrote:
> 
>> I take this chance to to confirm once more, as publicly as possible, that 
>> file paths with spaces are discouraged in today's CCP4. This inconvenience 
>> originates from ancient times in computing when good half of CCP4 was 
>> written and when spaces were disallowed on file system nodes.
>> 
>> Please take a notice of this fact as CCP4 core still receives (albeit 
>> infrequent) bug reports, where surprising behaviour is due to using file 
>> paths with white spaces.
>> 
>> Fixing this has proved to be a hard problem, purely because of technical 
>> choices made quite a number of years ago. But good news are that this 
>> limitation will be removed in new CCP4 Gui under development.
>> 
>> Eugene
>> 
>> On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
>> 
>>> This also occurred to me once where the file path had a space,(/Google 
>>> Drive/), when I moved the file somewhere else it worked. I was using 
>>> baverage from the CCP4i GUI.
>>> 
>>> Mark J van Raaij
>>> Lab 20B
>>> Dpto de Estructura de Macromoleculas
>>> Centro Nacional de Biotecnologia - CSIC
>>> c/Darwin 3
>>> E-28049 Madrid, Spain
>>> tel. (+34) 91 585 4616
>>> http://www.cnb.csic.es/~mjvanraaij
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
>>> 
 Dear Bing,
 
 can you post the exact command you were using, please? Also please check
 with a different PDB file. In case you are using baverage from the
 command line, can you make sure you are actually using the program from
 ccp4 by typing 'which baverage' at the command prompt?
 
 Regards.
 Tim
 
 On 06/02/2014 10:16 PM, Wang, Bing wrote:
> 
> Hi CCP4,
> 
> Recently when I input my pdb file and run the baverage in the ccp4 suit 
> to check the temperature factor, it always tell me "No tables were fund 
> in this file." Could you tell me how to fix this problem? Or is there 
> another software instead of baverage I could use to check the temperature 
> factor?
> 
> Thanks!
> 
> Bing
> 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
>> 
>> 
>> -- 
>> Scanned by iCritical.
>> 
> 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

Re: [ccp4bb] baverage: no tables were found in this file

[Harry Powell]

I'm wondering if GUI2 will cope with accents as well as spaces (e.g. in the 
Spanish "carpeta sin título" which is the default new folder on Macs)?

Discipline. That's what we need...

On 3 Jun 2014, at 13:03, Mark J van Raaij wrote:

> completely agree with avoiding spaces in paths and file names, but Google 
> Drive is very handy for sharing files, so every once in a while I forget to 
> move a file someone shares with me before running Unix programs on it and get 
> strange errors. Depending on how awake one is at the time finding out the 
> source can be time-consuming...Google should really remove the space!
> 
> Mark J van Raaij
> Lab 20B
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.cnb.csic.es/~mjvanraaij
> 
> 
> 
> 
> 
> On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:
> 
>> I take this chance to to confirm once more, as publicly as possible, that 
>> file paths with spaces are discouraged in today's CCP4. This inconvenience 
>> originates from ancient times in computing when good half of CCP4 was 
>> written and when spaces were disallowed on file system nodes.
>> 
>> Please take a notice of this fact as CCP4 core still receives (albeit 
>> infrequent) bug reports, where surprising behaviour is due to using file 
>> paths with white spaces.
>> 
>> Fixing this has proved to be a hard problem, purely because of technical 
>> choices made quite a number of years ago. But good news are that this 
>> limitation will be removed in new CCP4 Gui under development.
>> 
>> Eugene
>> 
>> On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
>> 
>>> This also occurred to me once where the file path had a space,(/Google 
>>> Drive/), when I moved the file somewhere else it worked. I was using 
>>> baverage from the CCP4i GUI.
>>> 
>>> Mark J van Raaij
>>> Lab 20B
>>> Dpto de Estructura de Macromoleculas
>>> Centro Nacional de Biotecnologia - CSIC
>>> c/Darwin 3
>>> E-28049 Madrid, Spain
>>> tel. (+34) 91 585 4616
>>> http://www.cnb.csic.es/~mjvanraaij
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
>>> 
 Dear Bing,
 
 can you post the exact command you were using, please? Also please check
 with a different PDB file. In case you are using baverage from the
 command line, can you make sure you are actually using the program from
 ccp4 by typing 'which baverage' at the command prompt?
 
 Regards.
 Tim
 
 On 06/02/2014 10:16 PM, Wang, Bing wrote:
> 
> Hi CCP4,
> 
> Recently when I input my pdb file and run the baverage in the ccp4 suit 
> to check the temperature factor, it always tell me "No tables were fund 
> in this file." Could you tell me how to fix this problem? Or is there 
> another software instead of baverage I could use to check the temperature 
> factor?
> 
> Thanks!
> 
> Bing
> 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
>> 
>> 
>> -- 
>> Scanned by iCritical.
>> 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

Re: [ccp4bb] baverage: no tables were found in this file

[Eugene Krissinel]

Dear Felix,

I, too, do not use spaces and file names in Russian :) However, these things 
are coming nearly for free and automatic with today's development tools, so 
little effort, if any, is required to adopt them, while the benefits in terms 
of user friendliness and convenience are not exactly negligible. Many thanks 
for understanding our situation

-- Eugene

On 3 Jun 2014, at 12:58, Felix Frolow wrote:

Possibility to have file names with the spaces is a curse put on the community 
by Microsoft, and it will be a big mistake to introduce this to CCP4 (my 
opinion).
I guess there are much more important things new CCP4 GUI should deal with. If 
CCP4 GUI will start to go this way,
file names with spaces will become file names with spaces and multilingual, in 
some these languages writing is going in the different direction.
In my introduction to UNIX, I teach in the beginning of practical protein 
crystallography my first demand from student is to forget about spaces in the 
fie names and the life will be much easier.
No fix is needed for that, concentrate on more important problems :-)
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Jun 3, 2014, at 14:47 , Eugene Krissinel 
mailto:eugene.krissi...@stfc.ac.uk>> wrote:

I take this chance to to confirm once more, as publicly as possible, that file 
paths with spaces are discouraged in today's CCP4. This inconvenience 
originates from ancient times in computing when good half of CCP4 was written 
and when spaces were disallowed on file system nodes.

Please take a notice of this fact as CCP4 core still receives (albeit 
infrequent) bug reports, where surprising behaviour is due to using file paths 
with white spaces.

Fixing this has proved to be a hard problem, purely because of technical 
choices made quite a number of years ago. But good news are that this 
limitation will be removed in new CCP4 Gui under development.

Eugene

On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:

This also occurred to me once where the file path had a space,(/Google Drive/), 
when I moved the file somewhere else it worked. I was using baverage from the 
CCP4i GUI.

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 3 Jun 2014, at 09:20, Tim Gruene wrote:

Dear Bing,

can you post the exact command you were using, please? Also please check
with a different PDB file. In case you are using baverage from the
command line, can you make sure you are actually using the program from
ccp4 by typing 'which baverage' at the command prompt?

Regards.
Tim

On 06/02/2014 10:16 PM, Wang, Bing wrote:

Hi CCP4,

Recently when I input my pdb file and run the baverage in the ccp4 suit to 
check the temperature factor, it always tell me "No tables were fund in this 
file." Could you tell me how to fix this problem? Or is there another software 
instead of baverage I could use to check the temperature factor?

Thanks!

Bing


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

GPG Key ID = A46BEE1A



--
Scanned by iCritical.




-- 
Scanned by iCritical.

Re: [ccp4bb] baverage: no tables were found in this file

[Eugene Krissinel]

I am afraid that it is us who will need to conform eventually :), same to say 
about "Program Files (x86)" and the overall culture in Windows, the system 
where some 40% () of CCP4 users have chosen to work.

Eugene


On 3 Jun 2014, at 13:03, Mark J van Raaij wrote:

> completely agree with avoiding spaces in paths and file names, but Google 
> Drive is very handy for sharing files, so every once in a while I forget to 
> move a file someone shares with me before running Unix programs on it and get 
> strange errors. Depending on how awake one is at the time finding out the 
> source can be time-consuming...Google should really remove the space!
> 
> Mark J van Raaij
> Lab 20B
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.cnb.csic.es/~mjvanraaij
> 
> 
> 
> 
> 
> On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:
> 
>> I take this chance to to confirm once more, as publicly as possible, that 
>> file paths with spaces are discouraged in today's CCP4. This inconvenience 
>> originates from ancient times in computing when good half of CCP4 was 
>> written and when spaces were disallowed on file system nodes.
>> 
>> Please take a notice of this fact as CCP4 core still receives (albeit 
>> infrequent) bug reports, where surprising behaviour is due to using file 
>> paths with white spaces.
>> 
>> Fixing this has proved to be a hard problem, purely because of technical 
>> choices made quite a number of years ago. But good news are that this 
>> limitation will be removed in new CCP4 Gui under development.
>> 
>> Eugene
>> 
>> On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
>> 
>>> This also occurred to me once where the file path had a space,(/Google 
>>> Drive/), when I moved the file somewhere else it worked. I was using 
>>> baverage from the CCP4i GUI.
>>> 
>>> Mark J van Raaij
>>> Lab 20B
>>> Dpto de Estructura de Macromoleculas
>>> Centro Nacional de Biotecnologia - CSIC
>>> c/Darwin 3
>>> E-28049 Madrid, Spain
>>> tel. (+34) 91 585 4616
>>> http://www.cnb.csic.es/~mjvanraaij
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
>>> 
 Dear Bing,
 
 can you post the exact command you were using, please? Also please check
 with a different PDB file. In case you are using baverage from the
 command line, can you make sure you are actually using the program from
 ccp4 by typing 'which baverage' at the command prompt?
 
 Regards.
 Tim
 
 On 06/02/2014 10:16 PM, Wang, Bing wrote:
> 
> Hi CCP4,
> 
> Recently when I input my pdb file and run the baverage in the ccp4 suit 
> to check the temperature factor, it always tell me "No tables were fund 
> in this file." Could you tell me how to fix this problem? Or is there 
> another software instead of baverage I could use to check the temperature 
> factor?
> 
> Thanks!
> 
> Bing
> 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
>> 
>> 
>> -- 
>> Scanned by iCritical.
>> 
> 


-- 
Scanned by iCritical.

Re: [ccp4bb] experimental phasing at low resolution

[Soisson, Stephen M]

Dear Vijay,

I managed success on a large, 4.5 Ang SeMet phasing years ago.  I strongly 
recommend trying to get a heavy atom derivative - even a crappy one -  that 
allows you to use difference Fouriers to find your Seleniums.  For me this was 
the only approach that worked, and it required bootstrapping from 5 initial 
peaks in the difference Fourier maps to eventually the full 70 in a.u.  It was 
a tedious process, always deleting sites to check if they come back, etc., but 
it is doable.

Good luck-

Steve

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of vijay 
srivastava
Sent: Tuesday, June 03, 2014 4:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] experimental phasing at low resolution

Dear All,
Does anyone know of a facility that provides amino acid analysis for 
determination of SeMet incorporation in a recombinant protein?
We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 350 amino acids (10 methionine are present) and 
naturally binds magnesium.  We have a SeMet data set at peak that goes down to 
5.4 angstroms.  We tried to find the heavy atom position with Shelxcde program. 
The log file is given as below.

Resl. Inf - 8.0 - 6.0 - 5.6 - 5.4 - 5.2 - 5.0 - 4.8 - 4.6 - 4.4 - 4.2 - 3.98
N(data) 529 643 241 29 0 0 0 0 0 0 0
 63.5 19.5 10.6 10.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
%Complete 94.1 98.9 99.2 18.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
 3.06 1.24 1.07 1.21

I am also attaching the .lst and .res file and from that we were considering 
that only one selenomethionine position.We have one monomer per AU 
(-unfortunately, MR is not working for this project). The space group is P3 .  
We also have a native set down to 3.4 angstroms.  While we understand that we 
may need more phasing information we're wondering if anyone might have some 
other suggestions or insights about how we can move forward given the data that 
we currently have. Can we extend the phases with our native data set. Thanks in 
advance for any advice.

regards

Vijay
Notice:  This e-mail message, together with any attachments, contains
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Re: [ccp4bb] baverage: no tables were found in this file

[Eleanor Dodson]

I thought the addition of " ..." around file names got round this problem

eg
"This_is_Mine.pdb" and "That is Yours.pdb"

Eleanor




On 3 June 2014 13:15, Eugene Krissinel  wrote:

> I am afraid that it is us who will need to conform eventually :), same to
> say about "Program Files (x86)" and the overall culture in Windows, the
> system where some 40% () of CCP4 users have chosen to work.
>
> Eugene
>
>
> On 3 Jun 2014, at 13:03, Mark J van Raaij wrote:
>
> > completely agree with avoiding spaces in paths and file names, but
> Google Drive is very handy for sharing files, so every once in a while I
> forget to move a file someone shares with me before running Unix programs
> on it and get strange errors. Depending on how awake one is at the time
> finding out the source can be time-consuming...Google should really remove
> the space!
> >
> > Mark J van Raaij
> > Lab 20B
> > Dpto de Estructura de Macromoleculas
> > Centro Nacional de Biotecnologia - CSIC
> > c/Darwin 3
> > E-28049 Madrid, Spain
> > tel. (+34) 91 585 4616
> > http://www.cnb.csic.es/~mjvanraaij
> >
> >
> >
> >
> >
> > On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:
> >
> >> I take this chance to to confirm once more, as publicly as possible,
> that file paths with spaces are discouraged in today's CCP4. This
> inconvenience originates from ancient times in computing when good half of
> CCP4 was written and when spaces were disallowed on file system nodes.
> >>
> >> Please take a notice of this fact as CCP4 core still receives (albeit
> infrequent) bug reports, where surprising behaviour is due to using file
> paths with white spaces.
> >>
> >> Fixing this has proved to be a hard problem, purely because of
> technical choices made quite a number of years ago. But good news are that
> this limitation will be removed in new CCP4 Gui under development.
> >>
> >> Eugene
> >>
> >> On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
> >>
> >>> This also occurred to me once where the file path had a space,(/Google
> Drive/), when I moved the file somewhere else it worked. I was using
> baverage from the CCP4i GUI.
> >>>
> >>> Mark J van Raaij
> >>> Lab 20B
> >>> Dpto de Estructura de Macromoleculas
> >>> Centro Nacional de Biotecnologia - CSIC
> >>> c/Darwin 3
> >>> E-28049 Madrid, Spain
> >>> tel. (+34) 91 585 4616
> >>> http://www.cnb.csic.es/~mjvanraaij
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
> >>>
>  Dear Bing,
> 
>  can you post the exact command you were using, please? Also please
> check
>  with a different PDB file. In case you are using baverage from the
>  command line, can you make sure you are actually using the program
> from
>  ccp4 by typing 'which baverage' at the command prompt?
> 
>  Regards.
>  Tim
> 
>  On 06/02/2014 10:16 PM, Wang, Bing wrote:
> >
> > Hi CCP4,
> >
> > Recently when I input my pdb file and run the baverage in the ccp4
> suit to check the temperature factor, it always tell me "No tables were
> fund in this file." Could you tell me how to fix this problem? Or is there
> another software instead of baverage I could use to check the temperature
> factor?
> >
> > Thanks!
> >
> > Bing
> >
> 
>  --
>  Dr Tim Gruene
>  Institut fuer anorganische Chemie
>  Tammannstr. 4
>  D-37077 Goettingen
> 
>  GPG Key ID = A46BEE1A
> 
> >>
> >>
> >> --
> >> Scanned by iCritical.
> >>
> >
>
>
> --
> Scanned by iCritical.
>
>

Re: [ccp4bb] baverage: no tables were found in this file

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Eleanor,

yes, it does. At least on Linux and OpenBSD (i.e. 'real' UNIX) typing
#> mkdir "dir with spaces"
#> cd dir\ with\ spaces/
#> touch "file with spaces"
#> echo "Some text" > file\ with\ spaces
causes no problems at all. Changing code reliably to include accents,
though, might be much more work than enclosing words with double quotes.

Best,
Tim

On 06/03/2014 02:23 PM, Eleanor Dodson wrote:
> I thought the addition of " ..." around file names got round this
> problem
> 
> eg "This_is_Mine.pdb" and "That is Yours.pdb"
> 
> Eleanor
> 
> 
> 
> 
> On 3 June 2014 13:15, Eugene Krissinel
>  wrote:
> 
>> I am afraid that it is us who will need to conform eventually :),
>> same to say about "Program Files (x86)" and the overall culture
>> in Windows, the system where some 40% () of CCP4 users have
>> chosen to work.
>> 
>> Eugene
>> 
>> 
>> On 3 Jun 2014, at 13:03, Mark J van Raaij wrote:
>> 
>>> completely agree with avoiding spaces in paths and file names,
>>> but
>> Google Drive is very handy for sharing files, so every once in a
>> while I forget to move a file someone shares with me before
>> running Unix programs on it and get strange errors. Depending on
>> how awake one is at the time finding out the source can be
>> time-consuming...Google should really remove the space!
>>> 
>>> Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas 
>>> Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049
>>> Madrid, Spain tel. (+34) 91 585 4616 
>>> http://www.cnb.csic.es/~mjvanraaij
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:
>>> 
 I take this chance to to confirm once more, as publicly as
 possible,
>> that file paths with spaces are discouraged in today's CCP4.
>> This inconvenience originates from ancient times in computing
>> when good half of CCP4 was written and when spaces were
>> disallowed on file system nodes.
 
 Please take a notice of this fact as CCP4 core still receives
 (albeit
>> infrequent) bug reports, where surprising behaviour is due to
>> using file paths with white spaces.
 
 Fixing this has proved to be a hard problem, purely because
 of
>> technical choices made quite a number of years ago. But good news
>> are that this limitation will be removed in new CCP4 Gui under
>> development.
 
 Eugene
 
 On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
 
> This also occurred to me once where the file path had a
> space,(/Google
>> Drive/), when I moved the file somewhere else it worked. I was
>> using baverage from the CCP4i GUI.
> 
> Mark J van Raaij Lab 20B Dpto de Estructura de
> Macromoleculas Centro Nacional de Biotecnologia - CSIC 
> c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 
> http://www.cnb.csic.es/~mjvanraaij
> 
> 
> 
> 
> 
> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
> 
>> Dear Bing,
>> 
>> can you post the exact command you were using, please?
>> Also please
>> check
>> with a different PDB file. In case you are using baverage
>> from the command line, can you make sure you are actually
>> using the program
>> from
>> ccp4 by typing 'which baverage' at the command prompt?
>> 
>> Regards. Tim
>> 
>> On 06/02/2014 10:16 PM, Wang, Bing wrote:
>>> 
>>> Hi CCP4,
>>> 
>>> Recently when I input my pdb file and run the baverage
>>> in the ccp4
>> suit to check the temperature factor, it always tell me "No
>> tables were fund in this file." Could you tell me how to fix this
>> problem? Or is there another software instead of baverage I could
>> use to check the temperature factor?
>>> 
>>> Thanks!
>>> 
>>> Bing
>>> 
>> 
>> -- Dr Tim Gruene Institut fuer anorganische Chemie 
>> Tammannstr. 4 D-37077 Goettingen
>> 
>> GPG Key ID = A46BEE1A
>> 
 
 
 -- Scanned by iCritical.
 
>>> 
>> 
>> 
>> -- Scanned by iCritical.
>> 
>> 
> 

- -- 
- --
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 Icedove - http://www.enigmail.net/

iD8DBQFTjb8eUxlJ7aRr7hoRApyPAKCGq/1XweO13d57W9vaho+DoXLHSgCeJXYW
7mc+g+F1Win65zZc8+nLN6I=
=U7dS
-END PGP SIGNATURE-

Re: [ccp4bb] baverage: no tables were found in this file

[Ed Pozharski]

This may not work if a program implements its own algorithm for parsing command 
line parameters


Sent on a Sprint Samsung Galaxy S® III

 Original message From: Tim Gruene 
 Date:06/03/2014  8:27 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] baverage: 
no tables were found in this file 
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Eleanor,

yes, it does. At least on Linux and OpenBSD (i.e. 'real' UNIX) typing
#> mkdir "dir with spaces"
#> cd dir\ with\ spaces/
#> touch "file with spaces"
#> echo "Some text" > file\ with\ spaces
causes no problems at all. Changing code reliably to include accents,
though, might be much more work than enclosing words with double quotes.

Best,
Tim

On 06/03/2014 02:23 PM, Eleanor Dodson wrote:
> I thought the addition of " ..." around file names got round this
> problem
> 
> eg "This_is_Mine.pdb" and "That is Yours.pdb"
> 
> Eleanor
> 
> 
> 
> 
> On 3 June 2014 13:15, Eugene Krissinel
>  wrote:
> 
>> I am afraid that it is us who will need to conform eventually :),
>> same to say about "Program Files (x86)" and the overall culture
>> in Windows, the system where some 40% () of CCP4 users have
>> chosen to work.
>> 
>> Eugene
>> 
>> 
>> On 3 Jun 2014, at 13:03, Mark J van Raaij wrote:
>> 
>>> completely agree with avoiding spaces in paths and file names,
>>> but
>> Google Drive is very handy for sharing files, so every once in a
>> while I forget to move a file someone shares with me before
>> running Unix programs on it and get strange errors. Depending on
>> how awake one is at the time finding out the source can be
>> time-consuming...Google should really remove the space!
>>> 
>>> Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas 
>>> Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049
>>> Madrid, Spain tel. (+34) 91 585 4616 
>>> http://www.cnb.csic.es/~mjvanraaij
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:
>>> 
 I take this chance to to confirm once more, as publicly as
 possible,
>> that file paths with spaces are discouraged in today's CCP4.
>> This inconvenience originates from ancient times in computing
>> when good half of CCP4 was written and when spaces were
>> disallowed on file system nodes.
 
 Please take a notice of this fact as CCP4 core still receives
 (albeit
>> infrequent) bug reports, where surprising behaviour is due to
>> using file paths with white spaces.
 
 Fixing this has proved to be a hard problem, purely because
 of
>> technical choices made quite a number of years ago. But good news
>> are that this limitation will be removed in new CCP4 Gui under
>> development.
 
 Eugene
 
 On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
 
> This also occurred to me once where the file path had a
> space,(/Google
>> Drive/), when I moved the file somewhere else it worked. I was
>> using baverage from the CCP4i GUI.
> 
> Mark J van Raaij Lab 20B Dpto de Estructura de
> Macromoleculas Centro Nacional de Biotecnologia - CSIC 
> c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 
> http://www.cnb.csic.es/~mjvanraaij
> 
> 
> 
> 
> 
> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
> 
>> Dear Bing,
>> 
>> can you post the exact command you were using, please?
>> Also please
>> check
>> with a different PDB file. In case you are using baverage
>> from the command line, can you make sure you are actually
>> using the program
>> from
>> ccp4 by typing 'which baverage' at the command prompt?
>> 
>> Regards. Tim
>> 
>> On 06/02/2014 10:16 PM, Wang, Bing wrote:
>>> 
>>> Hi CCP4,
>>> 
>>> Recently when I input my pdb file and run the baverage
>>> in the ccp4
>> suit to check the temperature factor, it always tell me "No
>> tables were fund in this file." Could you tell me how to fix this
>> problem? Or is there another software instead of baverage I could
>> use to check the temperature factor?
>>> 
>>> Thanks!
>>> 
>>> Bing
>>> 
>> 
>> -- Dr Tim Gruene Institut fuer anorganische Chemie 
>> Tammannstr. 4 D-37077 Goettingen
>> 
>> GPG Key ID = A46BEE1A
>> 
 
 
 -- Scanned by iCritical.
 
>>> 
>> 
>> 
>> -- Scanned by iCritical.
>> 
>> 
> 

- -- 
- --
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 Icedove - http://www.enigmail.net/

iD8DBQFTjb8eUxlJ7aRr7hoRApyPAKCGq/1XweO13d57W9vaho+DoXLHSgCeJXYW
7mc+g+F1Win65zZc8+nLN6I=
=U7dS
-END PGP SIGNATURE-

[ccp4bb] How to grow crystals for serial crystallography, neutron diffraction and other exciting techniques

[mesters]

Students, postdocs and scientists interested in the latest 
crystal-growth methodologies and advances regarding serial 
crystallography, neutron diffraction and other exciting techniques may 
wish to *join ICCBM15* (Sep. 17 - 20, Hamburg, www.iccbm15.org).

Early bird registrations deadline is July 15th.

As far as the *pre-conference workshop* is concerned (consisting of 
short presentations, practical demonstrations and hands-on exercises 
taught by an international team of experts), the number of free places 
for students and postdocs is steadily decreasing, so better sign up 
sooner than later.



Chairpersons: Christian Betzel and Jeroen Mesters

Re: [ccp4bb] baverage: no tables were found in this file

[Ed Pozharski]

Would a no-space symlink resolve this?


Sent on a Sprint Samsung Galaxy S® III

 Original message From: Mark J van Raaij 
 Date:06/03/2014  8:03 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] baverage: 
no tables were found in this file 
completely agree with avoiding spaces in paths and file names, but Google 
Drive is very handy for sharing files, so every once in a while I forget to 
move a file someone shares with me before running Unix programs on it and get 
strange errors. Depending on how awake one is at the time finding out the 
source can be time-consuming...Google should really remove the space!

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:

> I take this chance to to confirm once more, as publicly as possible, that 
> file paths with spaces are discouraged in today's CCP4. This inconvenience 
> originates from ancient times in computing when good half of CCP4 was written 
> and when spaces were disallowed on file system nodes.
> 
> Please take a notice of this fact as CCP4 core still receives (albeit 
> infrequent) bug reports, where surprising behaviour is due to using file 
> paths with white spaces.
> 
> Fixing this has proved to be a hard problem, purely because of technical 
> choices made quite a number of years ago. But good news are that this 
> limitation will be removed in new CCP4 Gui under development.
> 
> Eugene
> 
> On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
> 
>> This also occurred to me once where the file path had a space,(/Google 
>> Drive/), when I moved the file somewhere else it worked. I was using 
>> baverage from the CCP4i GUI.
>> 
>> Mark J van Raaij
>> Lab 20B
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> c/Darwin 3
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616
>> http://www.cnb.csic.es/~mjvanraaij
>> 
>> 
>> 
>> 
>> 
>> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
>> 
>>> Dear Bing,
>>> 
>>> can you post the exact command you were using, please? Also please check
>>> with a different PDB file. In case you are using baverage from the
>>> command line, can you make sure you are actually using the program from
>>> ccp4 by typing 'which baverage' at the command prompt?
>>> 
>>> Regards.
>>> Tim
>>> 
>>> On 06/02/2014 10:16 PM, Wang, Bing wrote:
 
 Hi CCP4,
 
 Recently when I input my pdb file and run the baverage in the ccp4 suit to 
 check the temperature factor, it always tell me "No tables were fund in 
 this file." Could you tell me how to fix this problem? Or is there another 
 software instead of baverage I could use to check the temperature factor?
 
 Thanks!
 
 Bing
 
>>> 
>>> -- 
>>> Dr Tim Gruene
>>> Institut fuer anorganische Chemie
>>> Tammannstr. 4
>>> D-37077 Goettingen
>>> 
>>> GPG Key ID = A46BEE1A
>>> 
> 
> 
> -- 
> Scanned by iCritical.
> 

[ccp4bb] HERCULES HSC16: Non-atomic resolution scattering for biology "New deadline: 15th June"

[David Flot]

Dear all,

A HERCULES special course on non-crystallographic X-ray and neutron 
scattering techniques for structural biology is organised by the ESRF, 
ILL and EMBL-Grenoble from the 14th to the 19th of September.


New dead line for registration: 15th of June.

Objective of the course: This HERCULES Specialized Course will address 
non-crystallographic X-ray and neutron scattering techniques for 
structural biology and soft matter with a focus on small angle 
scattering, reflectometry and fibre diffraction. An introduction to the 
theory as well as recent state-of-the-art examples from a multitude of 
systems (proteins, polymers, membranes, fibres, colloids etc.) will be 
presented as well as recent developments in sample environment and data 
analysis. Furthermore, two practical days on two ILL instruments (D17 
and D33) and two ESRF beamlines (BM02 and BM29) will be proposed. The 
course is aimed at PhD students, postdocs and scientists in the field of 
physics, chemistry and biology who want to learn more on the theoretical 
background, practical aspects and applications of these techniques.


More details are available on: 
http://www.esrf.fr/home/events/conferences/HSC/hsc16.html


Sincerely,

David Flot.

--

 
Dr David FLOT

Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63
Structural Biology GroupFax : (+33) 4 76 88 26 24
ESRF
B.P. 220, 6 rue Jules Horowitz  e-mail :david.f...@esrf.fr
F-38043 GRENOBLE CEDEX  http://www.esrf.eu

[ccp4bb] Searching for DNA structures in the PDB

[Sophie Bliss]

Hello,

I was wondering if anyone knows of a method that can be used to search
the PDB for DNA/RNA structures (essentially a Dali search for
DNA/RNA)?

I have recently obtained a 2.3 A protein structure bound in complex
with DNA.  X3DNA has shown the DNA to be B-form generally but the 3DNA
output and the structure both show a significant bend in the DNA
chain.  Other than apparently non-specific nuclease activity, we do
not know the function of the protein in vivo.  It would be very useful
to be able to look at other proteins that bind DNA/RNA that
target/produce similar bends in DNA/RNA structure, independent of base
sequence.  However, with thousands of structures in the PDB containing
DNA it would be impossible to do this by eye!  Thanks for reading, I
look forward to hearing your suggestions.

Sophie,
Sheffield University

Re: [ccp4bb] baverage: no tables were found in this file

[Eugene Krissinel]

Positive I'd imagine -- Eugene

On 3 Jun 2014, at 13:48, Ed Pozharski wrote:

Would a no-space symlink resolve this?


Sent on a Sprint Samsung Galaxy S® III


 Original message 
From: Mark J van Raaij
Date:06/03/2014 8:03 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] baverage: no tables were found in this file

completely agree with avoiding spaces in paths and file names, but Google Drive 
is very handy for sharing files, so every once in a while I forget to move a 
file someone shares with me before running Unix programs on it and get strange 
errors. Depending on how awake one is at the time finding out the source can be 
time-consuming...Google should really remove the space!

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:

> I take this chance to to confirm once more, as publicly as possible, that 
> file paths with spaces are discouraged in today's CCP4. This inconvenience 
> originates from ancient times in computing when good half of CCP4 was written 
> and when spaces were disallowed on file system nodes.
>
> Please take a notice of this fact as CCP4 core still receives (albeit 
> infrequent) bug reports, where surprising behaviour is due to using file 
> paths with white spaces.
>
> Fixing this has proved to be a hard problem, purely because of technical 
> choices made quite a number of years ago. But good news are that this 
> limitation will be removed in new CCP4 Gui under development.
>
> Eugene
>
> On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
>
>> This also occurred to me once where the file path had a space,(/Google 
>> Drive/), when I moved the file somewhere else it worked. I was using 
>> baverage from the CCP4i GUI.
>>
>> Mark J van Raaij
>> Lab 20B
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> c/Darwin 3
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616
>> http://www.cnb.csic.es/~mjvanraaij
>>
>>
>>
>>
>>
>> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
>>
>>> Dear Bing,
>>>
>>> can you post the exact command you were using, please? Also please check
>>> with a different PDB file. In case you are using baverage from the
>>> command line, can you make sure you are actually using the program from
>>> ccp4 by typing 'which baverage' at the command prompt?
>>>
>>> Regards.
>>> Tim
>>>
>>> On 06/02/2014 10:16 PM, Wang, Bing wrote:

 Hi CCP4,

 Recently when I input my pdb file and run the baverage in the ccp4 suit to 
 check the temperature factor, it always tell me "No tables were fund in 
 this file." Could you tell me how to fix this problem? Or is there another 
 software instead of baverage I could use to check the temperature factor?

 Thanks!

 Bing

>>>
>>> --
>>> Dr Tim Gruene
>>> Institut fuer anorganische Chemie
>>> Tammannstr. 4
>>> D-37077 Goettingen
>>>
>>> GPG Key ID = A46BEE1A
>>>
>
>
> --
> Scanned by iCritical.
>


-- 
Scanned by iCritical.

[ccp4bb] atom names for beta-D-xylopyranose

[Andrew Sharff]

Does anyone out there have some insight into, or a credible explanation 
for, why PDB ligand id XYP (beta-D-xylopyranose) has what seems like  
non-standard atom notation, at least compared to other sugars!


The standard atom naming convention for nearly all monosaccharides, 
including XYS (alpha-D-xylopyranose), is to name the ring carbons C1, C2 
etc and their attached oxygens O1, O2 etc - perfectly logical and 
understandable.


However, XYP has a totally different naming scheme. This makes 
automatically defining sugar linkages (based on atom naming) very difficult.


Quite apart from not understanding the logic of the naming convention 
for XYP, even more confusingly, XYP replaced the now deprecated 3-letter 
code for beta-D-xylopyranose (HSZ), and this older version has the more 
standard notation.


Thanks

Andrew

--
--
*Dr. Andrew J. Sharff D.Phil**
*Research Scientist / Software Developer
Global Phasing Ltd
Sheraton House
Castle Park
Cambridge CB3 0AX
UK
Tel: +(0)1223 353033
Fax: +(0)1223 366889

Re: [ccp4bb] baverage: no tables were found in this file

[Wang, Bing]

Thank you guys! Fix it already! It is the problem that a space was put into my 
file paths. When I move the files to other place as you guys said, it works!

Bing

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eugene Krissinel 
[eugene.krissi...@stfc.ac.uk]
Sent: Tuesday, June 03, 2014 8:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] baverage: no tables were found in this file

Positive I'd imagine -- Eugene

On 3 Jun 2014, at 13:48, Ed Pozharski wrote:

Would a no-space symlink resolve this?


Sent on a Sprint Samsung Galaxy S® III


 Original message 
From: Mark J van Raaij
Date:06/03/2014 8:03 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] baverage: no tables were found in this file

completely agree with avoiding spaces in paths and file names, but Google Drive 
is very handy for sharing files, so every once in a while I forget to move a 
file someone shares with me before running Unix programs on it and get strange 
errors. Depending on how awake one is at the time finding out the source can be 
time-consuming...Google should really remove the space!

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:

> I take this chance to to confirm once more, as publicly as possible, that 
> file paths with spaces are discouraged in today's CCP4. This inconvenience 
> originates from ancient times in computing when good half of CCP4 was written 
> and when spaces were disallowed on file system nodes.
>
> Please take a notice of this fact as CCP4 core still receives (albeit 
> infrequent) bug reports, where surprising behaviour is due to using file 
> paths with white spaces.
>
> Fixing this has proved to be a hard problem, purely because of technical 
> choices made quite a number of years ago. But good news are that this 
> limitation will be removed in new CCP4 Gui under development.
>
> Eugene
>
> On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
>
>> This also occurred to me once where the file path had a space,(/Google 
>> Drive/), when I moved the file somewhere else it worked. I was using 
>> baverage from the CCP4i GUI.
>>
>> Mark J van Raaij
>> Lab 20B
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> c/Darwin 3
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616
>> http://www.cnb.csic.es/~mjvanraaij
>>
>>
>>
>>
>>
>> On 3 Jun 2014, at 09:20, Tim Gruene wrote:
>>
>>> Dear Bing,
>>>
>>> can you post the exact command you were using, please? Also please check
>>> with a different PDB file. In case you are using baverage from the
>>> command line, can you make sure you are actually using the program from
>>> ccp4 by typing 'which baverage' at the command prompt?
>>>
>>> Regards.
>>> Tim
>>>
>>> On 06/02/2014 10:16 PM, Wang, Bing wrote:

 Hi CCP4,

 Recently when I input my pdb file and run the baverage in the ccp4 suit to 
 check the temperature factor, it always tell me "No tables were fund in 
 this file." Could you tell me how to fix this problem? Or is there another 
 software instead of baverage I could use to check the temperature factor?

 Thanks!

 Bing

>>>
>>> --
>>> Dr Tim Gruene
>>> Institut fuer anorganische Chemie
>>> Tammannstr. 4
>>> D-37077 Goettingen
>>>
>>> GPG Key ID = A46BEE1A
>>>
>
>
> --
> Scanned by iCritical.
>


--
Scanned by iCritical.

Re: [ccp4bb] Searching for DNA structures in the PDB

[Raji Edayathumangalam]

Hi Sophie,

The crystal structure of winged helix protein/transcription factor
HNF-3gamma bound to DNA comes to mind. Also, other transcription factors of
that ilk would be worth looking at.

Also, if you are looking for proteins that bend DNA in a
sequence-independent manner, one of the best examples to my knowledge is
the crystal structure of the nucleosome core particle (PDB id, 1aoi). With
histones having the job of compressing all of our genomic DNA into
discs-like nucleosome core particles (NCP), you may find it very
informative to see the many specifics of how histones bind the 146-bp DNA
in a sequence-independent fashion and bend the 146-bp DNA every or so base
pairs throughout the length of 146 base pairs. Look up Luger et al., 1997
(Nature) and related publications where the sequence-independent bending of
DNA is discussed in great detail.

Hope this helps.
Raji



On Tue, Jun 3, 2014 at 9:25 AM, Sophie Bliss 
wrote:

> Hello,
>
> I was wondering if anyone knows of a method that can be used to search
> the PDB for DNA/RNA structures (essentially a Dali search for
> DNA/RNA)?
>
> I have recently obtained a 2.3 A protein structure bound in complex
> with DNA.  X3DNA has shown the DNA to be B-form generally but the 3DNA
> output and the structure both show a significant bend in the DNA
> chain.  Other than apparently non-specific nuclease activity, we do
> not know the function of the protein in vivo.  It would be very useful
> to be able to look at other proteins that bind DNA/RNA that
> target/produce similar bends in DNA/RNA structure, independent of base
> sequence.  However, with thousands of structures in the PDB containing
> DNA it would be impossible to do this by eye!  Thanks for reading, I
> look forward to hearing your suggestions.
>
> Sophie,
> Sheffield University
>



-- 
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

Re: [ccp4bb] negative density around disulfide bond

[Sampson, Jared]

Hi Eze -

I’m glad to see you solved your problem.

On Jun 2, 2014, at 9:07 PM, Eze Chivi 
mailto:ezech...@outlook.com.ar>> wrote:

Thanks to everyone for the useful information.
I refined my structure in the reduced form (using the method suggested by 
Pavel). Negative density disappeared, and also R/Rfree improved a little bit. I 
attach two example pictures.
In parallel, I mutated Cys residues to Ala and re-refined again adding the 
simulated annealing option in phenix (Is this the way to make an omit map?).

In the future, instead of mutating to Ala, you could try using the 
delete-residue-sidechain function, which prunes the side chain of the active 
residue back to CB.  The function is bound to capital letter K (as “Kill 
Sidechain”) in Paul’s key bindings: 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Pauls-key-bindings-for-coot.
  That way, the sequence will remain correct, and until you add the atoms back 
into your model, you will be able to remind yourself about them via Extensions 
> Modeling > Residues with Missing Atoms.

Cheers,
Jared

Positive density appeared in the place of S atoms (another picture attached, 
the oxidized model is shown).
It appears that radiation damage caused full reduction...
Thank you again!
Regards
Ezequiel
PS: This protein was crystalized before by my group (and other group) in 
oxidized form (several times), it is a single point mutant. Data were collected 
at SLS using a Pilatus Detector.






--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/

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[ccp4bb] Observations-to-parameter ratio in Refmac

[Klaus Fütterer]

Hi CCP4BB readers, 

Does someone know whether Refmac outputs the observations-to-parameters ratio 
or, failing that, the number of refined parameters in the log file? 

Klaus

===
 
Dr. Klaus Fütterer
Deputy Head of School
Undergraduate Admissions
Room 717, Biosciences Tower

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  E: k.futte...@bham.ac.uk 
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===

Re: [ccp4bb] Searching for DNA structures in the PDB

[Eleanor Dodson]

The rscb has/had a nucleic acid database which included protein dan 
information. Have you checked that?
Eleanor

On 3 Jun 2014, at 16:51, Raji Edayathumangalam wrote:

> Hi Sophie,
> 
> The crystal structure of winged helix protein/transcription factor HNF-3gamma 
> bound to DNA comes to mind. Also, other transcription factors of that ilk 
> would be worth looking at.
> 
> Also, if you are looking for proteins that bend DNA in a sequence-independent 
> manner, one of the best examples to my knowledge is the crystal structure of 
> the nucleosome core particle (PDB id, 1aoi). With histones having the job of 
> compressing all of our genomic DNA into discs-like nucleosome core particles 
> (NCP), you may find it very informative to see the many specifics of how 
> histones bind the 146-bp DNA in a sequence-independent fashion and bend the 
> 146-bp DNA every or so base pairs throughout the length of 146 base pairs. 
> Look up Luger et al., 1997 (Nature) and related publications where the 
> sequence-independent bending of DNA is discussed in great detail.
> 
> Hope this helps.
> Raji
> 
> 
> 
> On Tue, Jun 3, 2014 at 9:25 AM, Sophie Bliss  wrote:
> Hello,
> 
> I was wondering if anyone knows of a method that can be used to search
> the PDB for DNA/RNA structures (essentially a Dali search for
> DNA/RNA)?
> 
> I have recently obtained a 2.3 A protein structure bound in complex
> with DNA.  X3DNA has shown the DNA to be B-form generally but the 3DNA
> output and the structure both show a significant bend in the DNA
> chain.  Other than apparently non-specific nuclease activity, we do
> not know the function of the protein in vivo.  It would be very useful
> to be able to look at other proteins that bind DNA/RNA that
> target/produce similar bends in DNA/RNA structure, independent of base
> sequence.  However, with thousands of structures in the PDB containing
> DNA it would be impossible to do this by eye!  Thanks for reading, I
> look forward to hearing your suggestions.
> 
> Sophie,
> Sheffield University
> 
> 
> 
> -- 
> Raji Edayathumangalam
> Instructor in Neurology, Harvard Medical School
> Research Associate, Brigham and Women's Hospital
> Visiting Research Scholar, Brandeis University
> 

Re: [ccp4bb] Observations-to-parameter ratio in Refmac

[Ethan A Merritt]

On Tuesday, 03 June, 2014 17:02:56 Klaus Fütterer wrote:

> Does someone know whether Refmac outputs the observations-to-parameters ratio 
> or, failing that, the number of refined parameters in the log file? 
> 
> Klaus

This turns out to be much more complex than you might think.
See:

  "To B or not to B: a question of resolution?" Acta Cryst. D68, 468-477.
http://scripts.iucr.org/cgi-bin/paper?S0907444911028320

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Observations-to-parameter ratio in Refmac

[Bernhard Rupp (Hofkristallrat a.D.)]

Ethan is right.
I also have compiled a few estimates how to get to this number 
pp638 ff 'Estimating the restraint count' in BMC

Best, BR

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan A 
Merritt
Sent: Tuesday, June 03, 2014 11:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Observations-to-parameter ratio in Refmac

On Tuesday, 03 June, 2014 17:02:56 Klaus F tterer wrote:

> Does someone know whether Refmac outputs the 
> observations-to-parameters ratio or, failing that, the number of refined 
> parameters in the log file?
> 
> Klaus

This turns out to be much more complex than you might think.
See:

  "To B or not to B: a question of resolution?" Acta Cryst. D68, 468-477.
http://scripts.iucr.org/cgi-bin/paper?S0907444911028320

--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

[ccp4bb] possible twinning issue in P4212 / I422

[Bjørn Panyella Pedersen]

Dear All,
I have a strange potential twinning issue that I cannot understand. I've 
searched high and low on all the internets to find an answer but have 
come up empty-handed, so I look to the wisdom of The Board to enlighten me.


I have a 4'ish Å dataset that processes nicely in P 4 21 2 (#90). 
However intensity distributions indicate possible almost perfect 
twinning (eg. /^2 : 1.592 ). So I speculate that the real space 
group might be P 4 (#75).


Recently we collected a new fairly low resolution (7.5Å) dataset, from 
the same type of crystals (same purification, same conditions).
But the space group in XDS and aimless now comes out very clearly as 
either I422 (#97) or I4212 (#98) (screw-axis is unclear given the data). 
The unit-cell parameters are exactly the same as in sg #90, which btw. 
means that in the body-centered lattice there is no way the protein can 
fit in the asym. unit.


So I guess what I don't understand is: Is it possible to go from a 
primitive lattice to a body-centered lattice by twinning. Is this just a 
low-resolution artifact? Or is this a P4 unitcell that can appear like 
P4212 or I422 depending on small variations (weak dehydration or similar).


Has anyone experienced something similar? Am I missing a basic facet of 
how twinning works, or is something else at play here?


Thanks for any insights or suggestions!

All the best,
/Bjørn

--
Bjørn Panyella Pedersen
Macromolecular Structure Group
University of California, San Francisco

[ccp4bb] Workshop on Advanced Topics in EM Structure Determination November 9-14, 2014

[Clint Potter]

Please note that the ap plication deadline is approaching for the Workshop on 
Advanced Topics in EM Structure Determination, hosted by the The National 
Resource for Automated Molecular Microscopy, to be held November 9-14, 2014.
If you would like to attend the workshop, please make sure to get your 
application submitted on time as the event has always been oversubscribed and 
it is very difficult to accommodate late applications.
The National Resource for Automated Molecular Microscopy
Workshop on Advanced Topics in EM Structure Determination
November 9-14, 2014
We invite applications to participate in a Workshop on Advanced Topics in EM 
Structure Determination.  The workshop is aimed at students, postdocs and 
faculty that already have some experience practicing cryoEM.  We can 
accommodate a total of 100 participants.
A major goal of the workshop will be to discuss the major new advances in EM 
methodology and how to best take advantage of these going forward.  Topics to 
be discussed will include improvements in specimen preparation, imaging, 
detectors, processing and reconstruction, and methods for validation. The basic 
format of the course will be theoretical lectures in the mornings followed by 
practical demonstrations and panel discussions in the afternoon. Evenings will 
be reserved for poster presentations by participants and research talks by 
instructors.
The instructors for the course will include: David Agard (UCSF), John Briggs 
(EMBL), Anchi Cheng (TSRI), Yifan Cheng (UCSF), Wah Chiu (Baylor), Rado Danev 
(MPI), David DeRosier (Brandeis), Joachim Frank (Columbia), Bob Glaeser (LBL), 
Niko Grigorieff (JFRC/HHMI), Richard Henderson (MRC), Gabe Lander (TSRI), Steve 
Ludtke (Baylor), Eva Nogales (Berkeley), Pawel Penczek (U. Texas), John 
Rubinstein (Toronto), Sjors Scheres (MRC), Henning Stahlberg (U. Basel), Holger 
Stark (MPI), Nigel Unwin (MRC), Elizabeth Villa (UCSD), Tom Walz (Harvard).
Application forms may be found online at the workshop web page: 
http://nramm.scripps.edu/2014-workshop/
A registration fee of $750 will be charged to participants from non-profit 
institutions. Some partial scholarship support may be available depending on 
the success of efforts to raise support. All meals will be provided as part of 
the workshop registration fee but participants will be expected to cover their 
own travel and lodging expenses. Cost of housing is estimated to be less than 
$100/night for a shared room and transportation will be provided between the 
hotel and the workshop venue.  Further details on these and other matters will 
be provided once the registration process begins.
The application deadline is 1 July and a final selection of participants will 
be made by 15 August.
Please see all other information pertaining to the course at the web site: 
http://nramm.scripps.edu/2014-workshop/
For other inquiries send email to:  
cryo2...@scripps.edu
Organizers: Bridget Carragher, Clinton S. Potter and Ronald A. Milligan
National Resource for Automated Molecular Microscopy, The Scripps Research 
Institute
The National Resource for Automated Molecular Microscopy is supported by the 
National Institute of General Medical Sciences.
Please feel free to post this announcement or pass it along to other interested 
parties.
--
Clint Potter, Professor,  Automated Molecular Imaging Group, Dept. of 
Integrative Structural and Computational Biology
US Postal  Mailing Address:  The Scripps Research Institute, 10550 N. Torrey 
Pines Rd.,  MC TRY-31,  La Jolla, CA  92037
Shipping Address: The Scripps Research Institute,  MC TRY-31 , 3215 Merryfield 
Row, San Diego, CA 92121
Ph: (858) 784-9050, Fax: (858) 784-9090, e-mail: 
cpot...@scripps.edu,
Office Location: Room 306,  Hazen Theory Building,   10640 John J Hopkins 
Drive, La Jolla Ca 92121
GPS: +32° 53' 41.78", -117° 14' 25.90"

NRAMM: National Resource for Automated Molecular Microscopy 
http://nramm.scripps.edu

Re: [ccp4bb] atom names for beta-D-xylopyranose

[Thomas Lütteke]

Hi Andrew,

I can only make a guess: As the atom that actually should be "O1" is called 
"O4A", and all the other atom names look fine apart from a "B" added to the 
them, it looks as if this residue was derived from a disaccharide, where the 
XYP part was linked to O4 of another residue. But I agree with you that the 
names used in this entry are non-standard.

By the way, HSZ is even worse because there the atoms are numbered the wrong 
way round, i.e. what should be the C1 is called C5 and vice versa. It would be 
even more difficult to create a correct sugar linkage based on those atom names.

Cheers,
Thomas


> Does anyone out there have some insight into, or a credible explanation for, 
> why PDB ligand id XYP (beta-D-xylopyranose) has what seems like  non-standard 
> atom notation, at least compared to other sugars!
> 
> The standard atom naming convention for nearly all monosaccharides, including 
> XYS (alpha-D-xylopyranose), is to name the ring carbons C1, C2 etc and their 
> attached oxygens O1, O2 etc - perfectly logical and understandable.
> 
> However, XYP has a totally different naming scheme. This makes automatically 
> defining sugar linkages (based on atom naming) very difficult.
> 
> Quite apart from not understanding the logic of the naming convention for 
> XYP, even more confusingly, XYP replaced the now deprecated 3-letter code for 
> beta-D-xylopyranose (HSZ), and this older version has the more standard 
> notation.
> 
> Thanks
> 
> Andrew