Re: [ccp4bb] Automated refinement convergence

[Robert Oeffner]

Thank you all for the replies. My goal was to learn about practical ways to 
achieve convergence during refinement even if the supplied model for the 
density will never be able to model the density adequately. I may experiment 
with refmac's ability to terminate refinement when a criteria has been met such 
as delta_Rfreehttps://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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[ccp4bb] Automated refinement convergence

[Robert Oeffner]

Hi,

I am wondering if authors of refinement programs would like to consider putting 
on their users wish list the ability of refinement programs to automatically 
terminate once the refinement has reached convergence. Various refinement 
metrics such as R factors, CC or RMS values typically will reach a plateau once 
the refinement of a macromolecular structure with X-ray or EM-data has 
converged and further macro-cycles of refinement will no longer improve the 
structure. The default number of macro-cycles in programs such as Phenix-refine 
and Refmac are probably sensible for most cases but in some cases it would be 
nice if the programs automatically extended the number of macro-cycles as 
needed (or decreased the number). 

The user can of course examine log files from refinement themselves and decide 
whether to continue refinement. But since starting a new session of refinement 
appears to always create an initial fluctuation in the refinement metrics 
before they align with the values of the last macro-cycles in the previous 
refinement session, the user is compelled to do at least, say 3 or more 
macrocycles in addition to whatever may be needed for reaching convergence. I 
guess it would therefore be more efficient if this was implemented directly in 
the refinement programs and presented as an option for the user to choose.

There could be cases where alternate conformations of a structure will 
repeatedly be oscillating in and out of density thus causing the refinement 
metrics also to oscillate. Hopefully such cases could be covered by gauging the 
level of fluctuations of the refinement metrics and terminate the refinement 
accordingly.

Many thanks,

Robert



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[ccp4bb] skewness in a good EM map?

[Robert Oeffner]

Hi,

In crystallography one of the features of a good map is that the histogram of 
map values has skewness. Does this also apply to EM maps? Whereas X-ray maps 
depicts the electron density EM maps depicts the electrostatic potential as I 
understand it. Any pointers about skewness or not in EM maps is greatly 
appreciated.

thanks,

Rob



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[ccp4bb] IUCR template for bibliography in Microsoft Word

[Robert Oeffner]

Hi

To those using Microsoft Word without a citation manager for writing 
papers to IUCR journals.


The (IUCr) IUCr Journals Microsoft Word template 
<https://journals.iucr.org/services/wordstyle.html> to be installed on a 
PC prior to writing a paper for an IUCR journal does not contain a 
bibliography style. Of the built in bibliography styles in Word the 
closest ones are probably "Havard Anglia" or "APA". Both of these 
truncate the list of authors in a publication after a maximum number has 
been reached or they have various fields (like date or year) rearranged 
compared to the style format of bibliographies in IUCR papers.


The workaround I have found is using tools from GitHub - 
codingo/BibWord: Microsoft Word and Bibliography Styles extender. 
<https://github.com/codingo/BibWord> Installing these on my PC the 
closest matching bibliography style to IUCR I found was "Harvard Exeter" 
Amendments to the maximum number of authors was needed as well as 
getting rid of title of cited article in the bibliography. This was far 
easier than trying to hack through any of the built in bibliography 
styles of Microsoft Word.


For those interested the attached bibliography style is named 
MyIUCR.XSL, It should go into the folder 
C:\Users\\AppData\Roaming\Microsoft\Bibliography\Style . Once 
there, Microsoft word will make it available from the "Style" drop-down 
list on the "References" tab.


Hope this helps someone,


Robert

--
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
The Keith Peters Building
Hills Road
Cambridge CB2 0XY

www.cimr.cam.ac.uk/investigators/read/index.html
tel: +44(0)1223 763234



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<>

Re: [ccp4bb] Generating symmetry mates using python

[Robert Oeffner]

b but it doesn't
>> quite solve the problem.
>>> I also tried opening PyMol through the command and generating
>> symmetry mates this way. It worked on a few files but failed quite
>> quickly (segmentation fault) and was also very slow.
>>> Can anyone suggest a useful solution, preferably clear to use
>> and/or well documented? Or even have a python script/code they can
>> share for this?
>>>
>>> Best regards,
>>> Orly
>>>
>>> --
>>>
>>> Orly Avraham, Ph.D.
>>> Postdoctoral fellow
>>> The lab of Prof. Oded Livnah
>>> and the lab of Prof. Ora Schueler-Furman
>>> The Hebrew University of Jerusalem
>>> Israel
>>>
>>>
>>> 
>>>
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>>>
>>>
>>> 
>>>
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>>
>>
>

>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> --
>>
>> Orly Avraham, Ph.D.
>> Postdoctoral fellow
>> The lab of Prof. Oded Livnah
>> and the lab of Prof. Ora Schueler-Furman
>> The Hebrew University of Jerusalem
>> Israel
>>
>> -
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>
> --
>
> Orly Avraham, Ph.D.
> Postdoctoral fellow
> The lab of Prof. Oded Livnah
> and the lab of Prof. Ora Schueler-Furman
> The Hebrew University of Jerusalem
> Israel



--

Orly Avraham, Ph.D.
Postdoctoral fellow
The lab of Prof. Oded Livnah
and the lab of Prof. Ora Schueler-Furman
The Hebrew University of Jerusalem
Israel




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--
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
The Keith Peters Building
Hills Road
Cambridge CB2 0XY

www.cimr.cam.ac.uk/investigators/read/index.html
tel: +44(0)1223 763234



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Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

[Robert Oeffner]

We build Phenix on all three platforms, i.e. Windows, Linux and MacOSX. 
Microsoft provides great C/C++compilers for free on Windows. One minor issue 
though is that since our software uses Python 2.7 binary compatibility with the 
python2.7 installer requires that the rest of Phenix is built with the older 
VS2008 compiler. That edition doesn't support the latest bells and whistles of 
esoteric C++ language features but this is not a showstopper.

Rob


Subject:  Re: Structural biology software that does not run on Windows or gives 
important Windows-specific problems
From:  Patrick Loll 
Date:  Fri, 14 Oct 2016 12:31:54 -0400
 
How about the ability to compile code? Are there decent compilers readily 
available for Windows? I like being able to write & compile the occasional 
fortran program {hic sunt dinosaurs}, and it’s easy to do this on a unix-based 
platform like OSX.

If your reasoned arguments fail, I have found that many institutions' 
information technology administrators are easily intimidated by a few random 
references to unix (Rsync! Grep! Bash!). Such words seem to function as charms 
that keep evil spirits (i.e. IT administrators) at bay.

> On 14 Oct 2016, at 11:14 AM, Mark J van Raaij  wrote:
> 
> Dear All,
> 
> our institution requires me to provide a reasoning not to buy a Windows 
> computer (I want to buy a new MacOSX system), so I am looking for software 
> that does not run or is limited on Windows.
> 
> Not available:
> (Auto)SHARP
> ARPWARP
> 
> Available on Windows but with significant limitations
> Phenix (no MR-Rosetta, no parallelization)
> CCP4 (limitations on file-names)
> 
> Please correct me if pertinent and provide additional examples if possible.
> 
> Gratefully yours,
> 
> Mark
> 
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] Installation of CCP4 under Windows 7

[Robert Oeffner]

Hi,
I have encountered this problem with CCP4 6.2.0 as well as for the past few 
years. Whenever I run the CCP4 installer for all users on my Windows Vista PC 
as administrator it only creates desktop icons and startup menu item for the 
administrator account, not for other users. 

It appears that the CCP4 desktop icon shortcut is put in 
C:\Users\Administrator\Desktop and the start menu CCP4 folder is put in 
C:\Users\Administrator\AppData\Roaming\Microsoft\Windows\Start 
Menu\Programs\CCP4-Packages-6.2.0. Both of these paths are incorrect as they 
are invisible when logging in as another user.

I'm not sure where the CCP4 desktop icon shortcut should go but placing the 
startup folder in C:\ProgramData\Microsoft\Windows\Start Menu\Programs makes it 
accessible to other users.

On a separate note, it also appears that there is a bug in the ActiveTCL 
installer which is recommended to be installed on Vista platforms. It only 
makes file associations with tcl files for the user who installed this program. 
Consequently when double clicking the CCP4 icon as a different user than 
administrator windows prompts the user asking what program the  file should be 
opened with. Again this can be overcome by making the wish.exe program from the 
ActiveTcl folder the default program to use.


Regards,

Robert Oeffner, Ph.D.
Research Associate, Read group
Department of Haematology, University of Cambridge
Cambridge Institute of Medical Research
Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY
www-structmed.cimr.cam.ac.uk, tel:01223763234

[ccp4bb] strange error in superpose

[Robert Oeffner]

Hi all,

When I use the superpose program for SSM aligning these two structures in 
the following command line:

superpose 3BT1.pdb -s B 1OC0.pdb -s B superposed.pdb

The screen output reads:

PDB file 3BT1.pdb has been read in.
... 312 atoms selected using CID 'B'
PDB file 1OC0.pdb has been read in.
... 289 atoms selected using CID 'B'

Transformed coordinates will be written to file superposed.pdb
*** empty graph for 1OC0.pdb.


If I try loading the same structures (or just use the PDB codes) in the SSM
server http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver it seems to work 
just fine.
Does anybody know how to avoid this error?


Many thanks,

Rob