Re: [ccp4bb] all of a sudden I cannot launch Coot nor ccp4i from the Terminal on my Mac laptop

[Mark Brooks]

Hi Pietro,
I guess this might be a GTK gsettings [1] problem; do you have a  
~/.config/dconf/user [2] file in your home directory? If so, maybe move this 
somewhere else for now and see of Coot opens OK (Is this a $home directory that 
has also been used via NFS or similar on a Linux computer? I don't think a Mac, 
not running Gnome desktop, would create such config files)
Good luck,
Mark
[1] 
https://discourse.gnome.org/t/there-is-a-way-to-set-gnome-apps-to-prefer-dark-theme-through-command-line/3160
[2] 
https://unix.stackexchange.com/questions/8922/where-does-gsettings-store-its-files


From: CCP4 bulletin board  On Behalf Of Roversi, Pietro 
(Dr.)
Sent: 09 March 2021 12:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] all of a sudden I cannot launch Coot nor ccp4i from the 
Terminal on my Mac laptop

[EXTERNAL]
Dear all,

sorry to bother you all with such mundane headaches - but all of a sudden I 
cannot launch Coot nor ccp4i from the Terminal on my Mac laptop (running MacOS 
Mojave):

[bioch3242-596:~] pietro% coot(coot-bin:15697): GLib-GObject-WARNING **: 
g_object_set_valist: object class 'GtkSettings' has no property named 
'gtk-application-prefer-dark-theme'

(Coot does not progress past the window with the coot)

[bioch3242-596:~] pietro% ccp4i
Top level CCP4 directory is /Applications/ccp4-7.1
Using CCP4 programs from /Applications/ccp4-7.1/bin
X Error of failed request:  BadName (named color or font does not exist)
  Major opcode of failed request:  45 (X_OpenFont)
  Serial number of failed request:  61
  Current serial number in output stream:  63

I suspect something is up with X-Quartz

Any suggestions?

THANKS

Pietro







Dr. Pietro Roversi, FHEA

Lecturer (Teaching and Research) 
https://le.ac.uk/natural-sciences/

LISCB Wellcome Trust ISSF Fellow

https://le.ac.uk/liscb/research-groups/pietro-roversi


Leicester Institute of Structural and Chemical Biology
Department of Molecular and Cell Biology, University of Leicester
Henry Wellcome Building
Lancaster Road, Leicester, LE1 7HB
England, United Kingdom

Skype: roversipietro
Mobile phone  +44 (0) 7927952047
Tel. +44 (0)116 2297237





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[ccp4bb] Positions available at Evotec

[Mark Brooks]

Dear All,
 There are 2 x positions currently open to join us at Evotec Princeton 
within our rapidly expanding Reagents Team.

If you're interested, please use the links below to apply for the positions 
through Workday:

* Senior Scientist - Protein Purification (Princeton)
https://evotecgroup.wd3.myworkdayjobs.com/en-US/Evotec_Career_Site/job/Princeton/Senior-Scientist---Protein-Purification_REQ-01105

Research Associate - Protein Purification (Princeton)
https://evotecgroup.wd3.myworkdayjobs.com/en-US/Evotec_Career_Site/job/Princeton/Research-Associate_REQ-01232

Many thanks,

Mark


[cid:image002.png@01D514C2.B80E8D30]

Dr. Mark Brooks
Project Leader,
mark.bro...@evotec.com<mailto:mark.bro...@evotec.com>
www.evotec.com<http://www.evotec.com/>

Evotec (U.S.) Inc
Building 303B,
College Road East,
Princeton,
NJ 08540,
USA.


STATEMENT OF CONFIDENTIALITY.

This email and any attachments may contain confidential, proprietary, 
privileged and/or private information.  
If received in error, please notify us immediately by reply email and then 
delete this email and any attachments from your system. Thank you!


https://www.evotec.com/en/about/site-information/data-protection-uk

Evotec (UK) Ltd is a limited company registered in England and Wales. 
Registration number:2674265. Registered office: 114 Innovation Drive, Milton 
Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom.



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Re: [ccp4bb] Dimer in SDS-PAGE

[Mark Brooks]

Dear Amit,
 Maybe try adding an equal volume of 8M urea to your sample before
adding the SDS-PAGE sample buffer. Then I'd test boiling and not boiling
that sample prior to loading on the gel.

Good luck,

Mark

On 21 February 2017 at 17:22, amit gaur  wrote:

> Hi all,
>   I am trying to purify a potassium ion channel from insect cell using
> baculovirus expression system. I am not seeing monomer of this protein in
> SDS instead a dimer appears.So,I increased DTT in SDS buffer but no change
> and dimer was intact. In size exclusion this protein appeared as a tetramer
> which is common oligomerizaton of potassium channel family with GYG motif.
> Can any body suggest what should I do in this case?
>
> Thanks and regards,
>
>
> --
> *Dr. Amit Gaur*
>
>
> *Post Doctoral ResearcherPI: Dr. Ji-Fang ZhangThomas Jefferson University*
> *1020, Locust Street, Suite 418*
> *Philadelphia, PA 19107*
>
>
>

Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop

[Mark Brooks]

Hi Marc,
  I have an Intel Iris Pro graphics chip on a Late 2013 MacBook 
Pro which works impressively well with all these programs, even on a 15 inch 
Retina display. I don’t know if the Nvidia one is better though...

Bonne chance,

Mark

> On 17 Mar 2015, at 16:12, Marc Graille  wrote:
> 
> Hello,
> 
> I would like to buy a MacBook Pro laptop that will allow me among others to 
> solve structures, build models and visualize electron density maps using 
> Pymol, Coot or Chimera.
> I have the choice between between Intel Iris Pro (5200 series) and Intel Iris 
> Pro + Nvidia GT 750M for the graphics cards but I don’t know which one is 
> fine for the programs I want to run.
> Can some of you share advices/feedback with me?
> 
> Thanks a lot for your answer.
> 
> Best wishes,
> 
> Marc
> 
> 
> 
> Dr Marc GRAILLE
> 
> Directeur de recherche CNRS
> 
> Team: Translation and degradation of eukaryotic mRNAs
> 
> Team supported by the ATIP-Avenir CNRS program
> 
> Laboratoire de Biochimie
> 
> ECOLE POLYTECHNIQUE - UMR7654 CNRS
> 
> 91128 PALAISEAU CEDEX
> 
> 
> Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09
> 
> 
> Office 033012B
> 
> Email: marc.grai...@polytechnique.edu 
> http://bioc.polytechnique.fr/spip.php?rubrique117 
> 
> 
>  
>  
> 

Re: [ccp4bb] A Moleman alternative?

[Mark Brooks]

baverage for atom numbers (protein/ligand/water), B factors 
http://www.ccp4.ac.uk/html/baverage.html

Mark

> On 17 Nov 2014, at 19:55, Yong Tang  wrote:
> 
> Dear all, I have no access to Moleman now but I need to compile a statistics 
> table for a structure, more specifically, for its atom numbers 
> (protein/ligand/water), B factors, RMS deviations etc. Is there an 
> alternative program for that in the CCP4 suite? Thank you in advance for your 
> help, -yong

Re: [ccp4bb] [phenixbb] [ot]: nedit on Mac 10.10 yosemite

[Mark Brooks]

Try reinstalling X-quartz.

IIRC, /usr/X11R6 is deleted during MacOS upgrades.

Mark

On 29 October 2014 14:45, Sebastiano Pasqualato <
sebastiano.pasqual...@gmail.com> wrote:

>
> Hi folks,
> sorry for the off-topic and slightly ‘demodée’ question, but, since I
> updated to Yosemite on my Mac, "nedit" does not work any more.
> Here’s the error message:
>
> Seba@host041:~> nedit
> dyld: Library not loaded: /usr/X11R6/lib/libXp.6.dylib
>   Referenced from: /Applications/nedit/nedit
>   Reason: image not found
> Trace/BPT trap: 5
> Seba@host041:~>
>
> Anybody knows if there is a fix for that?
> Thanks in advance,
> S
>
>
>
> --
> *Sebastiano Pasqualato, PhD*
> Crystallography Unit
> Department of Experimental Oncology
> European Institute of Oncology
> IFOM-IEO Campus
> via Adamello, 16
> 20139 - Milano
> Italy
>
> tel +39 02 9437 5167
> fax +39 02 9437 5990
> web http://is.gd/IEO_XtalUnit
>
>
>
>
>
>
>
> ___
> phenixbb mailing list
> pheni...@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>

Re: [ccp4bb] moleman2 install problem

[Mark Brooks]

Hmm. Maybe I'm doing something very wrong, because I get the following when
I try those binaries:

dyld: Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib

  Referenced from: /Users/brooks/Downloads/usf_osx_bin/./moleman2

  Reason: no suitable image found.  Did find:

/usr/local/gfortran/lib/libgfortran.3.dylib: mach-o, but wrong architecture

Trace/BPT trap: 5
What's that due to? (Stuff seems to break easily nowadays on Macs- perhaps
I'm just not as up to speed on libraries, architectures and compilers on
Apples as I need to be.)

Yamei, I compiled it from source and put a copy here:
https://dl.dropboxusercontent.com/u/30290835/bin/moleman2
Download it, then make it executable, & run it as follows:

chmod a+x ~/Downloads/moleman2

~/Downloads/moleman2

I hope this helps.

Mark
P.S. if I run this

lipo -info /usr/local/lib/libgfortran.3.dylib
it gives:

Non-fat file: /usr/local/gfortran/lib/libgfortran.3.dylib is architecture:
x86_64
x86_64 is the correct architecture, isn't it?


On 24 July 2014 13:45, Harry Powell  wrote:

> Hi Mark
>
> Unless you've done something very odd, Snow Leopard binaries should be
> compatible with Mavericks (and Yosemite, too, when you get to try that).
>
> 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)
>
> On 24 Jul 2014, at 13:39, Mark Brooks  wrote:
>
> Hi Yamei,
> If you're on OS X version 10.9.3, then I guess you're on
> Mavericks, not Snow Leopard ( https://www.apple.com/uk/osx/ ).
>
> Therefore, I guess you will need to download the source code and recompile
> it, since I don't know that Snow Leopard binaries are compatible with
> Mavericks. (Probably not, judging from all the re-compiling that I seem to
> have done recently). (Does anyone know better?)
>
> See below for instructions from http://xray.bmc.uu.se/usf/ for
> recompiling, although under OS X 10.6.
>
> Mark
> --->8-
>
> The distribution kit can be found here : Distribution_kit
> <http://xray.bmc.uu.se/markh/usf/usf_download.php?file=/markh/usf/usf_distribution_kit.tar.gz>
>  Organisation
> of the distribution kit35 programs are available, and each has its own
> directory with the same name as the program, under the parent directory
> 'usf'. In the top-level 'usf' directory there is a shell script called
> 'make_all.csh', and big surprise, if you execute that file it will will
> build all the programs, leaving executables in both the programs' own
> subdirectories and also in the collective directory 'usf/bin'.
> Building under OS XThe package has been built under Mac OS X v10.6 using
> the gfortran compiler. The kit is reported to work under 10.7 Lion, but
> Xcode 4.1 needs to be installed.
> Thanks to Jacques-Philippe Colletier for the Lion executables.
>
> In order to build yourself you will need to install XCODE which can be
> downloaded from http://developer.apple.com/technology/xcode.html, and
> gfortran which can be found here
> http://www.macresearch.org/gfortran-leopard. You will also find a
> gfortran dmg file in the distribution.
> Follow the instructions that come with these installation packages.
> To be able to download these packages, you will have to register as an
> Apple Developer.
> Then type "make_all.csh" in the downloaded USF directory.
>
>
>
>
> On 24 July 2014 06:19, Yamei Yu  wrote:
>
>> Hi all,
>>
>> I’m trying to install a copy of moleman2 for my new Mac. (the version is
>> 10.9.3).  while I copy the osx_moleman2 from xutil directory I got the
>> following message: The Finder can’t complete the operation because some
>> data in “osx_moleman2” can’t be read or written.
>> (Error code -36)
>> Could you tell me how to solve this problem?
>> Thank you so much!
>> Best wishes!
>>
>> yamei
>>
>> 
>>
>> Yamei Yu
>> State Key Laboratory of Biotherapy／Collaborative Innovation
>> Center of Biotherapy,
>> West China Hospital,
>> Sichuan University,Chengdu,610041, P.R.China
>> Tel: 15882013485
>> Email: ymyux...@gmail.com
>>ymyux...@163.com
>>yamei...@scu.edu.cn
>>
>>
>

Re: [ccp4bb] moleman2 install problem

[Mark Brooks]

Hi Yamei,
If you're on OS X version 10.9.3, then I guess you're on
Mavericks, not Snow Leopard ( https://www.apple.com/uk/osx/ ).

Therefore, I guess you will need to download the source code and recompile
it, since I don't know that Snow Leopard binaries are compatible with
Mavericks. (Probably not, judging from all the re-compiling that I seem to
have done recently). (Does anyone know better?)

See below for instructions from http://xray.bmc.uu.se/usf/ for recompiling,
although under OS X 10.6.

Mark
--->8-

The distribution kit can be found here : Distribution_kit

Organisation
of the distribution kit35 programs are available, and each has its own
directory with the same name as the program, under the parent directory
'usf'. In the top-level 'usf' directory there is a shell script called
'make_all.csh', and big surprise, if you execute that file it will will
build all the programs, leaving executables in both the programs' own
subdirectories and also in the collective directory 'usf/bin'.
Building under OS XThe package has been built under Mac OS X v10.6 using
the gfortran compiler. The kit is reported to work under 10.7 Lion, but
Xcode 4.1 needs to be installed.
Thanks to Jacques-Philippe Colletier for the Lion executables.

In order to build yourself you will need to install XCODE which can be
downloaded from http://developer.apple.com/technology/xcode.html, and
gfortran which can be found here http://www.macresearch.org/gfortran-leopard.
You will also find a gfortran dmg file in the distribution.
Follow the instructions that come with these installation packages.
To be able to download these packages, you will have to register as an
Apple Developer.
Then type "make_all.csh" in the downloaded USF directory.




On 24 July 2014 06:19, Yamei Yu  wrote:

> Hi all,
>
> I’m trying to install a copy of moleman2 for my new Mac. (the version is
> 10.9.3).  while I copy the osx_moleman2 from xutil directory I got the
> following message: The Finder can’t complete the operation because some
> data in “osx_moleman2” can’t be read or written.
> (Error code -36)
> Could you tell me how to solve this problem?
> Thank you so much!
> Best wishes!
>
> yamei
>
> 
>
> Yamei Yu
> State Key Laboratory of Biotherapy／Collaborative Innovation
> Center of Biotherapy,
> West China Hospital,
> Sichuan University,Chengdu,610041, P.R.China
> Tel: 15882013485
> Email: ymyux...@gmail.com
>ymyux...@163.com
>yamei...@scu.edu.cn
>
>

Re: [ccp4bb] Non-catalytic Rossmann fold domain

[Mark Brooks]

DprA, from the Streptococcus pneumoniae transformasome, is one, I believe:

http://www.ncbi.nlm.nih.gov/m/pubmed/22904190/

> On 22 Apr 2014, at 14:26, "Tanner, John J."  wrote:
> 
> Does anyone know of a protein that has a Rossmann dinucleotide binding domain 
> that does not participate in cofactor/substrate binding?   
> 
> Thanks.
> 
> Jack Tanner
> 
> 
> John J. Tanner
> Professor of Biochemistry and Chemistry
> University of Missouri-Columbia
> 125 Chemistry Building
> Columbia, MO  65211
> email: tanne...@missouri.edu
> phone: 573-884-1280
> fax: 573-882-2754
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
> 
> 
> 

Re: [ccp4bb] ipmosflm not connecting to XQuartz on Mac.

[Mark Brooks]

I had a similar problem with CCP4 generally after a recent computer upgrade. 

Re-installing xquartz worked for me, because some components had seemingly 
become deleted. 

HTH

Mark
> On 15 Apr 2014, at 21:54, Francis Reyes  wrote:
> 
> Hi all,
> 
> Anyone having issues getting ipmosflm to connect to XQuartz? I'm getting a 
> hang when running go just when I expect the old GUI to load. 
> 
> Thanks,
> 
> F
> 
> 
> 
> -
> Francis E. Reyes PhD
> 215 UCB
> University of Colorado at Boulder
> 
> --

Re: [ccp4bb] Convert DSSP to PDB format

[Mark Brooks]

Hi Wenhe,
   One answer to Q#2 is James Stroud's "dssp2pdb" to take the
output of DSSP & write HELIX and SHEET lines etc.
http://www.jamesstroud.com/software/dssp2pdb/

Mark
P.S. I believe the answer to question #1 is DSSP but I suspect the
answer is more complex.

On 1 March 2014 13:50, Wenhe  wrote:
> Dear CCP4 friends,
>
> I have two questions after I solving one structure:
>
> 1. What tool does PDB databank use to generate secondary structure 
> information which also shows in the pdb. file?
> 2. I had a secondary structure file which generated by DSSP, how I can 
> convert it to pdb format?
>
> Thank you.
>
> Kind regards,
> Wenhe

[ccp4bb] Off topic: Scientist Position in Protein Production and Expression at Evotec, near Oxford

[Mark Brooks]

Dear all,
  Please forward this job posting to any appropriate
candidates.

If interested, plese don't reply to me, but instead apply using the website
below.

Yours,

Mark


 *Scientist*

*Protein Production and Expression within our Structural Biology Department*



*Location: *Oxfordshire, UK

*Full time, Permanent*

*Salary: *from £19,825 - £33,500 dependent on experience



Evotec (UK) Ltd is currently seeking to add to the Protein Production group
within our Structural Biology Department based in Oxfordshire. The group
works closely with our Discovery Chemistry Department and with clients to
develop novel small molecule drugs.  The group is at the forefront of new
science and technology, and is seeking to expand as business need grows.



*Responsibilities may include:*



· Participating as part of a project team by designing, executing
and interpreting high quality laboratory research to meet agreed objectives

· Applying scientific knowledge to resolve research problems
encountered in achieving defined goals with some assistance from their line
manager or other team members to meet internal and project deadlines.

· Preparing reports of findings, present data, and collaborate with
other scientists at Evotec



*Desirable Knowledge, Skills and Abilities:*



· Protein expression in *E. coli*

· Protein purification using affinity tags e.g. 6His tags

· Understanding of GE Healthcare Akta systems (e.g. Xpress,
Purifier, Basic models) and Unicorn software.

· Purification of membrane proteins

· Protein production for crystallographic studies

· Cloning and design of synthetic gene constructs

· Crystallization of macromolecules


You will have excellent written and verbal communication skills and will be
a strong team player. Dynamic, accurate and innovative, you will be a
self-starter with a flexible approach who enjoys a challenge.


*Education and Experience:*



Educated to degree level or higher in a scientific discipline, or
equivalent.



We offer competitive salaries plus extensive benefits including annual
bonus, pension plan, private medical and dental cover.
If you feel that your skills and experience match what we are looking for,
please apply via the website: http://www.evotec.com by 22nd December 2013
though early application is recommended as interviews will be conducted as
suitable candidates apply.

Re: [ccp4bb] SA-omit map

[Mark Brooks]

Maybe try CNS or SFCheck:
http://groups.yahoo.com/neo/groups/cnsbb/conversations/messages/1720

To improve Phenix maps, maybe try increasing the number of boxes (the
parameter IIRC "n_box_target=" )
http://www.phenix-online.org/documentation/autobuild.htm

In CNS, you can decrease the starting temperature in the annealing section,
to reduce the 'violence' of the simulated annealing:
http://cns-online.org/cgi-bin/cns_solve_1.2/cns_view.cgi?&file=inputs/xtal_refine/composite_omit_map.inp
--->8---Snip--8<--
{* starting temperature *}
{===>} temperature=500;
--->8---Snip--8<--

As said elsewhere, if your map is still poor, maybe it's trying to tell you
something...

Mark







On 4 November 2013 06:36, dengzq1987  wrote:

>   Dear all,
>
>
>
>  Recently, I received the comments from referees, they asked for the
> SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated
> annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven
> thymidine nucleotide. Our data diffracted to 2.65A，but the data quality
> is not good and twin. We tried to produce SA-omit map using phenix. The map
> is really bad. Does anyone have suggestion to refine the map?  Thank you!
>
>
>
>
>
> Bests,
>
> zq Deng
> 2013-11-04
> --
> dengzq1987
>

Re: [ccp4bb] Off-topic: Crystallographic Symmetry Applications Available?

[Mark Brooks]

Tim has the more modern answer, but PDBSET
http://www.ccp4.ac.uk/html/pdbset.html is quite simple and scriptable.

If I recall correctly, the SYMGEN keyword may be of use.

>From the example in the documentation:

 Expand dimer to tetramer, rename chains, transform
#!/bin/csh -f
#
#  Make tetramer from dimer
#
pdbset xyzin ecrproducts268.pdb xyzout ecrprodpqrtet.pdb < wrote:

> Dear all,
>
> I have been trying to search for some softwares/applications that can
> display the crystal space group "lattice" based on the input of cell
> dimension and space group. Ideally, it can also apply the arbitrary
> symmetry operation to a molecule with given orientation and position in the
> unit cell. It would be perfect if it can output a PDB file. Does anybody
> heard of something like that?
>
> I know it might not be too hard to be realized with a script simply
> modifying the coordinates, but unluckily I am not a programmer. And
> actually, even some simple PDB files of different space group, in which
> molecules are represented as dots, would be very helpful.
>
> Thank you so much!
>
> Sincerely,
> Chen Zhao
>

Re: [ccp4bb] writing scripts-off topic

[Mark Brooks]

Hi Yuri,
  If you don't like Python, like myself (and I'm not alone, it
would seem), you could try Ruby (http://www.ruby-lang.org/en/). Some
examples of PDB file manipulation are below (taken from [1]).

The language is a great improvement in Perl and Python in my opinion, but
the downside is that there aren't as many crystallographic features as
CCTBX et al, I don't think.

Yours,

Mark

[1] http://bioruby.open-bio.org/wiki/SampleCodes
 Structure I/O and Manipulation How do I read a structure file?

The current implementation only reads PDB format files, there will
hopefully be code for parsing mmCIF and PDB XML files in the future. Adding
these new formats will probably change the API for reading and writing
structure files.

Given the above caveat, the current way to read a PDB file is to slurp the
file into a string which is fed to the constructor of the Bio::PDB class:

require 'bio/db/pdb'string = IO.read('pdb1tim.ent')
structure = Bio::PDB.new(string)

The new Bio::PDB object now contains all the annotations and coordinate data.

How do I write a structure file?

As with reading, the current implementation can only write in PDB format.

All the coordinate classes in the Bio::PDB heirarchy have .to_s methods
which return the object in PDB format. This makes output as simple as:

require 'bio/db/pdb'
file = File.new('pdb1tim.ent').gets(nil)
structure = Bio::PDB.new(file)puts structure.to_s # Writes whole
structureputs structure[nil]['A'].to_s # Writes chain A only

How do I access annotations?

The annotations from the PDB file are stored in Bio::PDB::Record objects.
You can retrieve a specific annotation by calling the '.record' method of a
Bio::PDB object with the name of the annotation as the argument:

structure.record("HEADER")

In fact '.record' returns an array of all Bio::PDB::Records of the given
type, so you'll need to call '.first' to get to the actual
Bio::PDB::Record. Bio::PDB::Record provides methods to get to the
individual data in each record. E.g. The 'HEADER' record provides
classification, depDate and idCode methods. You can look at the PDB format
to see what fields are available in each record, or just look in the pdb.rb
file which has a hash of all the definitions.

So, to get the title of a PDB file you would do it like this:

structure.record('TITLE').first.title

Some records have their own special methods:

structure.remark(num)  #Returns hash of the REMARK records based on 'num'
structure.jrnl #Returns a hash of the JRNL records
structure.jrnl('TITL') #Returns an array of all the TITL subfields from
   #the JRNL records
structure.helix(id)#Returns the HELIX records based on 'id'
   #Returns an array if no 'id' is given
structure.turn #Same interface as '.helix'
structure.sheet#Same interface as '.sheet'
structure.seqres(id)   #Returns the sequence given in the SEQRES record
   #as a Bio::Sequence::AA object
structure.keywords #returns a flattened lsit of keywords

And some methods are included for Bio::DB compatability:

structure.entry_id #Returns idCode
structure.accession#Same as entry_id
structure.definition   #Title
structure.version  #REVDAT

How do I access the coordinate data?

Coordinate data is stroed in a heirarchy of classes with Bio::PDB at the
top. A Bio::PDB object contains one or more Bio::PDB::Model objects which
contain one or more Bio::PDB::Chain objects which contain one or more
Bio::PDB::Residue objects which contain Bio::PDB::Atom objects.

There are two ways to access the coordinate data in a Bio::PDB object:
keyed access and iterators.

Keyed access provides the simplest way to get to data if you know which
residues or atoms you're interested in. For instance if you wanted to get
hold of chain 'A' you can do it like this:

chain = structure[nil]['A']

The nil refers to the model, which will be nil in crystal structures but
may have a number in NMR structures. Every level in the heirarchy can be
accessed this way. E.g. to get hold of the CA atom of residue 100 in chain
'A':

structure[nil]['A']['100']['CA']

or if you still have your chain object:

chain['100']['CA']

The residue identifier is not just the residue number. PDB residues can
have insertion codes and even negative numbers.

chain['100A']['CA']

could be valid.

Iterators are also provided so you can easily go through all objects in the
heirarchy. E.g:

structure.each{ |model|
  model.each{ |chain|
chain.each{ |residue|
  residue.each{ |atom|
puts atom
  }
}
  }}

Goes through every atom in the structure and outputs it. All the classes in
the heirarchy implement the standard Enumerable and Comparable mixins as
well.

Each class has a number of accessors to allow access to the data, most is
in the Bio::PDB::Atom class:

   - Bio::PDB::Model has a 'model_serial' accessor only.
   - Bio::PDB::Chain has an 'id' accessor for getting and setting the chain
   id.
 

Re: [ccp4bb] adxv

[Mark Brooks]

Dear Rajesh,
                  Are you using the Openmotif library? If so, do you
have an XKeysymDB file installed?
In as shell, issue:
$ locate XKeysymDB
You may need to symlink it to /usr/X11R6/lib/X11/XKeysymDB if it is
elsewhere [1].
I suspect you're not the only one to have seen this [2].

I hope this helps.

Mark
[1] 
ftp://ftp.parallelgeo.com/SPW_Products/Linux/Current_Release/ReadMe_for_recent_Linux_distributions.txt
[2] http://sbgrid.org/news/newsletters/2009/06 (search for the string "adxv")


On 20 November 2011 19:45, Rajesh kumar  wrote:
>
> Dear Tim,
> Thanks. Your suggestion of adding to PATH  works and its not completely 
> functional may be due to the Ximg/ssh or some thing to do with display.
> All three windows opened but couldn't open any image as it didn't display in 
> the list of autoload window. Pattern shows *.0.
>
> $adxv pin8_1_180.img
>
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> (standard_in) 1: parse error
> beam_center x = pixels , mm
> beam_center y = pixels , mm
> distance = mm
> overload = counts
> pixelsize = 0.172 mm
> wavelength = Angstroem
> Adxv Version 1.9.4-beta
> Copyright (C) 1994-2007 by Andrew Arvai, Area Detector Systems Corporation
> Using 24-bit TrueColor visual
> Warning: translation table syntax error: Unknown keysym name:  osfActivate
> Warning: ... found while parsing ':osfActivate:            
> ManagerParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfBeginLine
> Warning: ... found while parsing ':osfBeginLine:           
> ManagerGadgetTraverseHome()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfHelp
> Warning: ... found while parsing ':osfHelp:                        
> ManagerGadgetHelp()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfActivate
> Warning: ... found while parsing ':osfActivate:    
> ManagerParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfActivate
> Warning: ... found while parsing ':osfActivate:    
> PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfHelp
> Warning: ... found while parsing ':osfHelp:                Help()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfActivate
> Warning: ... found while parsing ':osfActivate:    
> PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfCancel
> Warning: ... found while parsing ':osfCancel:      MenuEscape()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfSelect
> Warning: ... found while parsing ':osfSelect:      ArmAndActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfActivate
> Warning: ... found while parsing ':osfActivate:            
> PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: Locale not supported for XmbTextListToTextProperty
> Warning: Cannot convert XmString to compound text
> Warning: translation table syntax error: Unknown keysym name:  osfPrimaryPaste
> Warning: ... found while parsing ':m osfPrimaryPaste:cut-primary()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfActivate
> Warning: ... found while parsing ':osfActivate:            
> PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfActivate
> Warning: ... found while parsing ':osfActivate:    
> PrimitiveParentActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfSelect
> Warning: ... found while parsing ':osfSelect:      ArmAndActivate()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfPrimaryPaste
> Warning: ... found while parsing ':m osfPrimaryPaste:cut-primary()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error: Unknown keysym name:  osfSelect
> Warning: ... found while parsing ':osfSelect:      ManagerGadgetSelect()'
> Warning: String to TranslationTable conversion encountered errors
> Warning: translation table syntax error:

Re: [ccp4bb] Akta Prime

[Mark Brooks]

Dear Mike,
               At Evotec (a UK site), we gave up using GE to service
our GE instruments (!) due to problems with their bureaucracy. Agilent
offer service contracts for Aktas that are competitively priced and
are a work-alike in our experience.

For call-outs, they sub-contract the usual GE engineers that you would
normally see to perform maintenance, and do this with their usual high
level of professionalism.

I think it’s a bit of a shame (for GE) that we have to use a third
party like this to organise the preventative maintenance visits etc.,
but it works very well for us.

Yours,

Mark

On 12 October 2011 19:28, Michael Colaneri  wrote:
>
> Dear all,
>
> We have an AktaPrime and GE Lifesciences stop servicing these instruments 
> because they are getting old.  Does anyone know of a third party company that 
> gives contracts to maintain these instruments?  Thank you.
>
> Mike Colaneri

Re: [ccp4bb] PYMOL installation in openSUSE 11.3 (64 bit)

[Mark Brooks]

Hi,
  If you're missing Python.h (since your compiler complains about it), I
guess you're missing the development package of python, whatever that's
called in SUSE. Probably "python-devel", according to this:
http://www.novell.com/products/linuxpackages/opensuse/python-devel.html

Good luck,

Mark
On 7 March 2011 17:21, Hena Dutta  wrote:

> Hello,
> I was trying to install PYMOL in my openSUSE 11.3 as follows:
>
> cd /usr/local
>
> hena@a:/usr/local>
> sudo svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymolpymol
>
> cd pymol
>
> hena@a:/usr/local/pymol>
>
> sudo python setup.py install
>
> And I got the following error at the end:
>
> package init file 'modules/web/javascript/__init__.py' not found (or not a
> regular file)
> package init file 'modules/web/javascript/__init__.py' not found (or not a
> regular file)
> running build_ext
> building 'pymol._cmd' extension
> creating build/temp.linux-x86_64-2.6
> creating build/temp.linux-x86_64-2.6/modules
> creating build/temp.linux-x86_64-2.6/modules/cealign
> creating build/temp.linux-x86_64-2.6/modules/cealign/src
> creating build/temp.linux-x86_64-2.6/ov
> creating build/temp.linux-x86_64-2.6/ov/src
> creating build/temp.linux-x86_64-2.6/layer0
> creating build/temp.linux-x86_64-2.6/layer1
> creating build/temp.linux-x86_64-2.6/layer2
> creating build/temp.linux-x86_64-2.6/layer3
> creating build/temp.linux-x86_64-2.6/layer4
> creating build/temp.linux-x86_64-2.6/layer5
> gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall
> -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
> -fasynchronous-unwind-tables -g -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE
> -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2
> -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Imodules/cealign/src
> -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c
> modules/cealign/src/ccealignmodule.cpp -o
> build/temp.linux-x86_64-2.6/modules/cealign/src/ccealignmodule.o -ffast-math
> -funroll-loops -O3
> In file included from modules/cealign/src/ccealignmodule.H:57:0,
>  from modules/cealign/src/ccealignmodule.cpp:32:
> layer0/os_python.h:30:19: fatal error: Python.h: No such file or directory
> compilation terminated.
> error: command 'gcc' failed with exit status 1
>
>
> Can someone advise me at this point or suggest the right pakage of PYMOL
> that I can install in open SUSE 11.3
>
> Thanks...
> Hena
>
>

Re: [ccp4bb] Protein sequencing service?

[Mark Brooks]

Jeff Keen is good, but just to add to the list "Cambridge Peptides"
http://www.cambridgepeptides.com/proteinsequencing.html based in Birmingham
(!), is fast and efficient from either membrane or directly from gel slices.

Yours,

Mark

On 24 September 2010 16:46, Rex Palmer  wrote:

>  Can anyone please recommend a UK protein sequencing service. Our protein
> is dimeric with reported molecuar weight of about 85kDa.Our funds are
> somewhat limited.
>
> Thanks in advance.
>
> Rex Palmer
> Birkbeck College, London
>
>
> RexPalmer2010.homestead.com 
>

Re: [ccp4bb] pdf to text

[Mark Brooks]

For OCR without installing software, "Free OCR" http://www.free-ocr.com/ works
quite well for me, but beware that you may need to do corrections
afterwards.

Just upload your file to this web site, as long as it isn't secret!

The OCR in Adobe Acrobat works better for me though, and is worth the money,
I think.

HTH,

Mark

On 13 September 2010 14:30, Oganesyan, Vaheh wrote:

>  Colleagues,
>
>
>
> I have coordinates of “small” molecule in pdf format, i.e. its an image of
> pdb file and it doesn’t let me select text. The molecule has >150 atoms, so
> doing it by hand is not an option. How would one go around it?
>
> The molecule is polymyxin B and doesn’t exist in databases like CSD, Hic-up
> or PDB. If some of you happen to have it please share. Thank you.
>
>
>
> PS The pdf is available from ACS website as a supplementary material and is
> also attached here.
>
>
>
> Thank you.
>
>
>
> *Vaheh Oganesyan, PhD*
>
> *Antibody Discovery and Protein Engineering*
>
> *MedImmune, LLC.*
>
> *1 MedImmune Way**, Gaithersburg, MD 20878*
>
> *o**ganesy...@medimmune.com* 
>
>
>
>
>
>
> To the extent this electronic communication or any of its attachments
> contain information that is not in the public domain, such information is
> considered by MedImmune to be confidential and proprietary. This
> communication is expected to be read and/or used only by the individual(s)
> for whom it is intended. If you have received this electronic communication
> in error, please reply to the sender advising of the error in transmission
> and delete the original message and any accompanying documents from your
> system immediately, without copying, reviewing or otherwise using them for
> any purpose. Thank you for your cooperation.
>
<>

Re: [ccp4bb] database-assisted data archive

[Mark Brooks]

Dear Andreas,
If you really want to do this, and want to define what is
the data is, it's not _so_ difficult to do it yourself, with Ruby on Rails (
http://rubyonrails.org/)

You have to know how to script a bit, and know a bit about
Model/View/Controller frameworks. http://www.youtube.com/watch?v=Gzj723LkRJY

That's not what you asked, but if you want to define what is the data to be
input, you end up being unhappy with someone else's implementation.

Mark

2010/8/18 Andreas Förster 

> Dear all,
>
> going through some previous lab member's data and trying to make sense of
> it, I was wondering what kind of solutions exist to simply the archiving and
> retrieval process.
>
> In particular, what I have in mind is a web interface that allows a user
> who has just returned from the synchrotron or the in-house detector to fill
> in a few boxes (user, name of protein, mutant, light source, quality of
> data, number of frames, status of project, etc) and then upload his data
> from the USB stick, portable hard drive or remote storage.
>
> The database application would put the data in a safe place (some file
> server that's periodically backed up) and let users browse through all the
> collected data of the lab with minimal effort later.
>
> I doesn't seem too hard to implement this, which is why I'm asking if
> anyone has done so already.
>
> Thanks.
>
>
> Andreas
>
> --
>Andreas Förster, Research Associate
>Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>http://www.msf.bio.ic.ac.uk
>



-- 
Skype: markabrooks

Re: [ccp4bb] software for predicting protein solubility, stabililty and disorders

[Mark Brooks]

Hi,
   My favourite is Phyre: http://www.sbg.bio.ic.ac.uk/~phyre/

A benefit of this is that it predicts your domains, makes sequence
alignments with the similar proteins, and makes homology models which are
sometimes good enough to start building with when you've phased the
structure!
Another benefit is that the server runs "disopred", the disorder prediction
server for you, and then aligns the output with the domain predictions.
These domain predictions are then a good place to start when designing
constructs...

Good luck,

Mark
On 29 July 2010 07:58, vikrant saa  wrote:

>   I want to do cloning of  a 40 Kd protein in pRSETA, and pGEX-KT vector.
> I don't have any idea about protein solubility, its multimeric
> form, stability  and disorder etc. There is nothing known in the literature
> also. Is there any software that can predict  these parameters, so that i
> can decide which domain i need to  clone for  soluble and stable protein
> purification.
> *Vikrant
> ***
>
> 
> ***Junior Research Fellow (CSIR) *
> *Lab No. 101, Dr. Varma Lab*
> *Cancer Research Institute
> Advance Centre for Treatment, Research and Eduction in Cancer (ACTREC)
> Tata Memorial Hospital, Kharghar, Navi Mumbai-410210 *
> #
>
>
>
>


-- 
Skype: markabrooks

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

[Mark Brooks]

Dear Nasos & Hailiang,
  Gerard Kleywegt's MAPMAN calculates the
RSR, discussed here:

http://xray.bmc.uu.se/usf/mapman_man.html#S41

Mark

On 21 May 2010 23:54, Athanasios Dousis  wrote:

>  Hello all,
>
> I'm forwarding a question from my labmate Hailiang Zhang regarding
> OVERLAPMAP and real-space R factors.
>
> Thanks in advance for your suggestions.
>
> Nasos Dousis
> Rice University
>
> P.S. Can someone please add haili...@bcm.tmc.edu to the CCP4BB listserv?
>
>  Original Message   Subject: calculate the real space R
> factor using OVERLAPMAP  Date: Fri, 21 May 2010 17:48:47 -0500  From: Zhang,
> HailiangTo:
> ndou...@rice.edu  
>
> Hi,
>
> I wanted to calculate the real space R factor using OVERLAPMAP. According to 
> the general definition of real space R value 
> (http://reference.iucr.org/dictionary/Real-space_residual), everything should 
> be absolute value in the formula. However, the results by OVERLAPMAP were 
> giving massive negative values. I also checked OVERLAPMAP documentation and 
> found that the absolute sign seems absent in the R factor formula 
> )http://smb.slac.stanford.edu/facilities/software/ccp4/html/overlapmap.html). 
> I was just wondering whether there is some other tools in eg CCP4, Phenix or 
> CNS to calculate real-space R in the general way in absolute values.
>
> Thanks!
>
>


-- 
Skype: markabrooks

Re: [ccp4bb] ncsfind

[Mark Brooks]

Hello,
        If you have Phenix, try phenix.find_ncs (sorry for the non-CCP4 answer).

The example run in the PHENIX documentation is:
phenix.find_ncs anb.pdb mlt.mtz
This will then write out the NCS operators in various flavours.

Basically if you have a list of Se sites it calls RESOLVE, but has a
simpler, command-line interface.
http://www.phenix-online.org/documentation/find_ncs.htm#anch20
Good luck,
Mark

On 20 May 2010 23:47, Karin van Straaten  wrote:
>
> Dear all,
>
> Does anyone know if NCSFIND is still available or how I can get it. If not is 
> there another program that I can use to determine noncrystallographic 
> symmetry between Se-sites.
>
> Thanks in advance,
>
> Karin


--
Skype: markabrooks

Re: [ccp4bb] control of nucleation

[Mark Brooks]

Dear Zq Deng,
I've had success with the dilution method as described
by Dunlop and Hazes: http://scripts.iucr.org/cgi-bin/paper?en5016

For me it worked for a couple of projects, and gives you a bit more to
permutate than just varying the protein:mother liquor ratios, as Thomas
Edwards helpfully suggested.

Good luck,

Mark

On 6 May 2010 09:03, zq deng  wrote:

> hello,everybody . due to excess nucleation,I often get many tiny crystals
> instead of  few,large crystals.i wana optimize the condition, does anyone
> have adivce about this?
>
> Best regards.
>



-- 
Skype: markabrooks

Re: [ccp4bb] align DNA structures

[Mark Brooks]

Anna Pyle's group came out with a powerful idea- a simplified set of
torsion angles for nucleic acids (NA).
http://nar.oxfordjournals.org/content/vol31/issue16/images/small/gkg682f1.gif
http://nar.oxfordjournals.org/cgi/content/abstract/31/16/4755

This is implemented in a Perl program, called PRIMOS (
http://www.pylelab.org/software/index.html ), which you use to
generate 'worms' corresponding to all the nucleic acid structures in
the database that you're working on. You then search with a worm
corresponding to the structure of interest.

It works very well for RNA, at least, but you have to download the
entire NDB yourself and make worms using the PERL scripts (store the
worms carefully, you don't want to do this more than once!).

A COOT or web (EBI?!) interface would be very welcome, since this
process is quite involved.

HTH,

Mark

2009/10/21 Mike England :
> Hi all,
>
> I will highly appreciate your help regarding following:
>
> How to align  two  DNA structures in Pymol or Coot or any other softwares?
> ( I tried regular "align" in Pymol, but it doesn't work for DNA; it
> works great for protein structures.)
>
>
> Thanks a lot in advance !
>
>
> Mike
>



-- 
Mark Brooks, IBBMC, UMR8619 - Bâtiment 430,
Université de Paris-Sud, 91405 Orsay, France.
Tel: (33) 169157968
Fax: (33) 169853715
Skype: markabrooks

Re: [ccp4bb] NADP - ADP binding

[Mark Brooks]

This is a good start for Rossmann folds, I find. (I'm not sure if this
is what you want though.)

"Chemical and biological evolution of a nucleotide-binding protein."
Michael G. Rossmann, Dino Moras & Kenneth W. Olsen. Nature Vol. 250
July 19 1974, p194.
(Structural alignments in 1974 - wow!)

If anyone has votes for other favourite papers of this ilk, I'm all ears!

Mark

2009/10/20 Vellieux Frederic :
> Michael Rossmann and colleagues did some work on the binding of fragments of
> cofactors to dogfish lactate dehydrogenase. In the 70's I think. Can be
> found on google scholar. Perhaps that's what you are after? Can't find the
> reference right now (it's in one of my drawers but I don't know which
> one...). I passed the reference on to Nicolas Coquelle @ualberta
> (coque...@ualberta.ca) a few days ago  but that was from my home e-mail
> address so I don't have it here in the office.
>
> Fred.
>
> sajid akthar wrote:
>>
>> Dear All
>>
>> Can any one mention some reference regarding the binding of NADPH  or ADP
>> in the surface of the protein. Is there any rules that dominate these two
>> cofactors to select the surface istead of typical Rossmann fold.
>>
>> Thank you
>>
>> Sajid
>>
>>
>>
>>      Yahoo! India has a new look. Take a sneak peek
>> http://in.yahoo.com/trynew
>>
>>
>>
>
>



-- 
Mark Brooks, IBBMC, UMR8619 - Bâtiment 430,
Université de Paris-Sud, 91405 Orsay, France.
Tel: (33) 169157968
Fax: (33) 169853715
Skype: markabrooks

Re: [ccp4bb] amino acid analysis for SeMet incorporation

[Mark Brooks]

Hi Maria,
  maybe SeMet incorporation is not something they do in
Grenoble per se, but they do similar experiments on their MALDI-TOF
very competently (I guess you contacted Eric Forest's group?
http://www.ibs.fr/Plates-formes/Caracterisation-de-proteines/Spectrometrie-de-Masse/
.They have an Applied Biosystems Voyager if I recall correctly.)

In Paris (Orsay, IBBMC the institute where I am) there is also
Christophe Marchand, who has an almost identical instrument and does
SeMet incorporation experiments regularly.
http://www.ibbmc.u-psud.fr/spip.php?rubrique41

Try 2 samples- one of your protein alone, and one of a mix of native
protein mixed with SeMet labelled protein- you should have a credible
mass difference between the 2 peaks, and that gives you a nice
internal standard.

Good luck.

Mark
P.S. Contact me off-list if you need more info.

2009/9/28 Marija Backovic :
> Dear all -
>
> Does anyone know of a facility that provides amino acid analysis for
> determination of SeMet incorporation in a recombinant protein?
>
> I contacted centers at Grenoble and Uppsala, but SeMet determination is not
> something they routinely do.
>
> Any suggestions would be highly appreciated!
>
> Best,
>
> Marija
>
>
> Marija Backovic, Ph.D.
>
> Pasteur Institute
> Department of Virology
> 25 rue du Dr Roux
> 75015 Paris
> France
>
> +33 (0)1 45 68 82 87
>



-- 
Mark Brooks, IBBMC, UMR8619 - Bâtiment 430,
Université de Paris-Sud, 91405 Orsay, France.
Tel: (33) 169157968
Fax: (33) 169853715
Skype: markabrooks

Re: [ccp4bb] Regarding CCP4 on mac

[Mark Brooks]

Hi Mohinder,

 Are you having problems because the CCP4I_TCLTK
environment variable is not set correctly? From the shell, you can
check
~$ echo  $CCP4I_TCLTK
/usr/local/bin

...so you should have a tclsh binary there:
/usr/local/bin/tclsh

Otherwise, check the troubleshooting page for more information
http://www.ccp4.ac.uk/ccp4i/trouble_shooting.html#send

I hope that helps.

For the easiest route, I find installing CCP4 from Fink is best (
http://www.finkproject.org/ ).

Issue "fink install ccp4" at the terminal, since it installs
everything and also updates to the latest version, although you may
need your compilers installed from the Xcode package.

Mark
P.S. You may have other tclsh binaries around on the Mac from Fink, or MacPorts.
( /sw/bin/tclsh8.4 & /usr/local/bin/tclsh8.5 respectively, so beware).

2009/9/16 Mohinder Pal 
>
> Dear ccp4bb,
>
> I have just installed ccp4 6.1.2 with ccp4i 1.4.2 on a MacBook Pro running 
> OSX 10.5.8.
> When I try to run Refmac5 (or phaser) I get the status "starting" in the GUI 
> but the program
> fails to run and no log file is generated. I source:
>
> /usr/local/ccp4-6.1.2/bin/ccp4.setup-sh
>
> before running the GUI, and the programs are definitely present and run in 
> the ccp4 bin
> directory.
>
> Does anyone know what could be going wrong?
>
> Thanks,
>
> Mohinder



--
Mark Brooks, IBBMC, UMR8619 - Bâtiment 430,
Université de Paris-Sud, 91405 Orsay, France.
Tel: (33) 169157968
Fax: (33) 169853715
Skype: markabrooks

Re: [ccp4bb] phaser troubles

[Mark Brooks]

Hi,

 is the problem related to one of the problems listed below?
(taken from the CCP4i troubleshooting page
http://www.ccp4.ac.uk/ccp4i/trouble_shooting.html ):

If I recall correctly, once I saw similar behaviour when my
$CCP4I_TCLTK/tclsh was pointing to an incorrect directory.

I hope that helps,

Mark

Jobs run but are reported as STARTING in the Job Window
=

When CCP4i runs a job it starts a separate process and this process
reports back to the main CCP4i on progress - returning the status
RUNNING, REMOTE,FINISHED or FAILED. However sometimes after jobs are
reported as STARTING, the status never gets updated (even though the
job runs or fails).

There are several known problems which cause this to happen:

On Windows systems, this may be a symptom of having spaces in
directory or file names. Having spaces causes a variety of problems,
and is best avoided.

In older versions of the gui (pre CCP4 4.1) the communication between
the two processes used the Tcl/Tk command send which didn't not work
in Tcl/Tk built with the default options. As of CCP4 4.1 send is no
longer used so this problem shouldn't arise.

Check your version of CCP4 and upgrade, if necessary.

When running jobs, CCP4i needs to be able to find the tclsh command in
the directory pointed to by the CCP4I_TCLTK environment variable. For
Unix/Linux systems this is set when you source the ccp4.setup file. If
tclsh is not present then jobs may start but never actually run.

Check that $CCP4I_TCLTK/tclsh exists, and edit your ccp4.setup file to
point to the correct directory if it doesn't.

This problem will also be observed if localhost is not defined in the
system /etc/hosts. In this case a number of other symptoms will also
be observed, for example 1) a warning message about running scripts
being unable to connect to the server port; 2) neither the Run and
view com file nor the Kill job options work.

The fix is to make sure that localhost is defined in the /etc/hosts file.

2009/8/24 Sylvia Fanucchi 
>
> Hi
>
> This is probably an obvious one but I’m having trouble getting Phaser to run. 
> It simply says the status is “starting” and will not give me more information 
> in the log file. I suspect the problem has to do with the F and Sigma F 
> values but I am not sure what to assign them as?
>
> Any help would be appreciated
>
> Sylvia
>
>
>
> This communication is intended for the addressee only. It is confidential. If 
> you have received this communication in error, please notify us immediately 
> and destroy the original message. You may not copy or disseminate this 
> communication without the permission of the University. Only authorized 
> signatories are competent to enter into agreements on behalf of the 
> University and recipients are thus advised that the content of this message 
> may not be legally binding on the University and may contain the personal 
> views and opinions of the author, which are not necessarily the views and 
> opinions of The University of the Witwatersrand, Johannesburg. All agreements 
> between the University and outsiders are subject to South African Law unless 
> the University agrees in writing to the contrary.


--
Mark Brooks, IBBMC, UMR8619 - Bâtiment 430,
Université de Paris-Sud, 91405 Orsay, France.
Tel: (33) 169157968
Fax: (33) 169853715
Skype: markabrooks

Re: [ccp4bb] song CRT Multiscan E540 monitor for stereo view

[Mark Brooks]

Hi Eric,
 I use a Sony Mutiscan E530. I'm not sure of the
difference in specifications, but I posted my xorg.conf file here,
which works under Ubuntu 8.10 in stereo for Coot & O.

http://82.239.206.16/xorg.conf

HTH,

Mark

2009/2/4 Eric Liu :
> Hi All,
>
> I would like to explore if anybody had experience using song CRT multiscan
> E540 monitor for stereo view? I connected the monitor to our linux machine
> (Red Hat Enterprise 5.0). When I launch coot, I don't see a stereo view of
> the structure. Do I need to do some kind of configuration in order to get
> the stereo view?
>
> Thanks,
>
> Eric
>
>
>



-- 
Mark Brooks,
IBBMC,
UMR8619 - Bâtiment 430,
Université de Paris-Sud,
91405 Orsay CEDEX.
Tel: 0169157968
Fax: 0169853715
Skype: markabrooks

Re: [ccp4bb] OT: VectorNTI alternatives

[Mark Brooks]

Hi Darren,
  My favourite program for editing sequences (apart from
Vector NTI, which I suppose I'm going to have to delete soon), is
BioEdit:
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
It has an old fashioned & cluttered interface, but does do sequence
editing, translation into proteins, ClustalW alignments and contig
assemblies (a bit like ContigExpress in Vector NTI). It opens ABI
files for sequencing data, to view the chromatograms. It uses the
external programs such as clustalw alignments or cap3 to do the contig
assemblies, and its licence doesn't expire! BioEdit is quite
impressive, and sometimes I use it instead of Vector NTI, even
(honestly!).

For storing everything, I put my primers, plasmid sequences, insert
sequences in a MySQL database, with an HTML front end I wrote:
http://plasmidb.sourceforge.net/
Plasmi::db also has a "homespun" feel to it, and only works with
Firefox, for example (not other browsers). There is a primer designer
page, for traditional cloning by restriction digestion etc.. I can't
pretend it's in the same league as Vector NTI, though. The data is
stored in a non-proprietary format; database tables which can be
viewed with either the HTML pages, or MS Excel, for example.

I never really believed that Vector NTI was going to stay free (even
to universities etc.) for a long time, and I do think that they
deserve some money for their (excellent) product. I hope that they can
decide on a reasonable pricing scheme though, instead of vacillating
between "huge sums" and "nothing". They seem to be heading towards a
moderate price nowadays, at least.

Mark

2009/1/28 Darren Hart :
> Hello,
> After several years of offering the molecular biology software VectorNTI
> free to the academic community (their "open access program") and building
> up a huge user base, Invitrogen have suddenly announced that they will no
> longer renew these free licences and the existing ones will be left to
> expire within the year. There are heavy renewal fees for anyone wishing to
> continue use of this software.
>
> Can anyone recommend decent alternative PC compatible alternatives? Main
> uses are construct and primer design, plus simple quick alignments,
> sequence data analysis etc. The database structure for storing sequences
> was pretty useful also.
>
> Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious
> have products, both free and paid. Any experience?
>
> Thanks,
> Darren
> EMBL Grenoble
>
> ps anyone using VNTI might consider a backup of their work by exporting
> files to .gb format. I don't know if a locked up (expired) version permits
> this and you will have no notice that it is about to expire.
>
>
>



-- 
Mark Brooks,
IBBMC,
UMR8619 - Bâtiment 430,
Université de Paris-Sud,
91405 Orsay CEDEX.
Tel: 0169157968
Fax: 0169853715
Skype: markabrooks

Re: [ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10

[Mark Brooks]

Hi,

In Ubuntu the use of Nvidia drivers is very slick, or should be.
https://help.ubuntu.com/community/BinaryDriverHowto/Nvidia

Go to the System menu, then:
System -> Administration -> Hardware Drivers

A window opens up which then searches for proprietary drivers, and propose
that you use "Nvidia accelerated driver 173", or some such version. Click
the activate button, and restart X.

Behind the scenes, this installs the "linux-restricted-modules" package,
which will update your Nvidia module every time you upgrade your linux
kernel, which is tiresome otherwise.

There is no need for this "Envy" thing in Ubuntu.

For stereo, you will need lines in /etc/X11/xorg.conf like:

Section "Device"
Identifier  "Configured Video Device"
Option  "AllowDFPStereo" "on"
Option  "Stereo""3"
Driver  "nvidia"
Screen 0
EndSection

Section "Extensions"
Option  "Composite" "off"
EndSection

Good luck,

Mark

2009/1/7 Chris Ulens 

> Hi,
> I'm trying to install a nVidia Quadro FX3000 card on a PC running Ubuntu
> 8.10 intrepid.
>
> I run into the following error when I install drivers I downloaded from the
> nVidia site:
> The installer fails to find a kernel interface from the nvidia ftp site and
> fails to compile the kernel.
>
> Any help would be greatly appreciated.
> Thanks and best wishes.
>
> -Chris
>
> Attached is the complete log file.
>
>
>
>
>
> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
>
>
>
>
>
> +++++++
> Chris Ulens, Ph.D.
> Lab of Structural Neurobiology
> Division of Pharmacology
> Campus Gasthuisberg, ON1
> Herestraat 49, PB 601
> B-3000 Leuven
> Belgium
> +++
>
>
>


-- 
Mark Brooks,
IBBMC,
UMR8619 - Bâtiment 430,
Université de Paris-Sud,
91405 Orsay CEDEX.
Tel: 0169157968
Fax: 0169853715
Skype: markabrooks

Re: [ccp4bb] to extract protein sequence from a rebuilt pdb file

[Mark Brooks]

You can do this quickly in Coot:
Calculate>Scripting>Scheme
And a scripting window opens.
See the Coot user manual (1) for detailed scheme instructions, but the
command now is in the form:
(print-sequence imol)
"imol" comes from the number shown in the display manager to the left
of the model name.
e.g.:
(print-sequence 0)
...for imol 0.
The sequences of each chain are output to the terminal.

If you have only python support in Coot:
Calculate>Scripting>Python
print_sequence(0) is the pythonized version of the command for imol 0.

(1) http://www.ysbl.york.ac.uk/~emsley/coot/doc/user-manual.html#SEC79

2008/10/1 Jane Bailey <[EMAIL PROTECTED]>
>
> Hi, all
>
> I am currently rebuilting my structure in coot, and the protein sequence is 
> around 98% rebuilt yet. I am looking for a way to extract protein sequence 
> from the rebuilt.pdb  so that I could see clearly which part need to be 
> rebuilt by sequence alignment. Any ideas about this? thanks
>
> Best
> Jane



--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [ccp4bb] regarding cloning

[Mark Brooks]

2008/9/1 Artem Evdokimov <[EMAIL PROTECTED]>

>  Hi,
>
>
>
> First of all – I am curious why did you decide to put in an extra step (the
> T/A cloning into an intermediate vector)?  You can happily digest your PCR
> product with NheI/BamHI, clean up and ligate into the appropriately digested
> pET-23a(+). If you have issues, you should definitely try this.
>
> Hello,

   Artem is right in making this point of course, but why?

I think the number of moles of DNA molecule that you get is important.  With
PCR you can get a huge number of moles, especially for a very intense 600bp
band.  As you go up in size of product, the yield often becomes lower, and
it becomes more difficult to clone, but still, you'll probably have more
moles of insert compared to using restriction enzymes to cleave a fragment
out of a vector.

So when is using a TA cloning vector step justifiable?  If you have a meagre
PCR product which you really can't clone any other way, TA cloning is the
most efficient with these low yields (for me).

Can high PCR yields inhibit restriction enzyme-based ligations? Yes, if you
don't cleave these products to completion. If you have PCR products where a
significant proportion are not cleaved properly, the non-cleaved molecules
will have an inhibitory effect on your reaction- one can imagine that
they'll mop up a large proportion of your vector and make it unusable.  So,
if you have a huge PCR product, try cleaving 10-30% of the entire reaction
either 4 hours or over night to make sure it's fully cleaved. (Again, as
Artem says, choose your buffer carefully here).

As a final piece of advice, make sure you have a copy of "Molecular Cloning,
a Laboratory Guide" (Cold Sring Harbor Press) nearby.
http://books.google.fr/books?id=YTxKwWUiBeUC&dq=molecular+cloning+a+lab+manual&pg=PP1&ots=FVO87K4uEt&sig=xTYcKpFP45dBqwsfRWZ0UXR0wb8&hl=en&sa=X&oi=book_result&resnum=1&ct=result
...You will probably have a recent or not-so-recent edition (A.K.A.
"Maniatis" for previous editions IIRC) in a University Library nearby.  I
recently frog-marched a technician here to read it when he was having
cloning problems. After persuading him that the PEG-additive protocol might
be helpful to help him with a particularly nasty cloning problem, he tried
it.  As he said, the results were "miraculous". (I have no affiliation to
CSHL press nor the authors BTW)

Good luck,

Mark


>
>
> Now, since you do have an intermediate step – did you verify that
> everything was OK after havig subcloned your insert into whatever vector
> you're using? Did you sequence the insert and most importantly did the
> sequencing confirm the nature of the linker regions?
>
>
>
> The enzyme pair that you chose has a slight issue with digestion buffer –
> most people would choose NEB buffer 2 (since buffer 3 is bad for Nhe) where
> Bam still has '100% activity' – however, in buffer 2 you can have star
> activity of the Bam due to the somewhat lower salt concentration (50 mM
> instead of the optimum 100 mM). It's not impossible to imagine that you have
> issues with digestion. This can be easily avoided by sequential digestion
> although of course it's slightly more work (but if you cut out the T/A
> cloning step that's actually still faster).
>
>
>
> So, in conclusion the most likely issue is digesiton (probably of the pET
> vector, to be more specific). Next likely issue could be ligation – make
> sure that you base your ligation ratio on the gel intensity of the bands as
> well as on the OD260 of your DNA. Faulty primers are not likely to be an
> issue since you seem to be able to restrict your insert out of the
> intermediate vector.
>
>
>
> Please note that you can often use SpeI or XbaI instead of Nhe since they
> have compatible sticky ends. Clearly this depends on the vector you're
> working with and I am too lazy to look up pET23 polylinker.
>
>
>
> Artem
>  --
>
> *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *vijay
> srivastava
> *Sent:* Monday, September 01, 2008 3:06 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] regarding cloning
>
>
>
> Hi,
>
> I am trying to clone a 1.2kb insert into a expression vector pET 23a
> through T/A cloning.  The restriction enzyme used is Nhe1(NEB) and BamH1
> (NEB) in the forward and reverse primer recpectively. I was succesful  in
> subcloning (T/A vector) and getting my insert at 1.2kb after  double
> digestion and also the vector at 3.7kb ,for the ligation i am using the
> ratio of vector to insert is 1:3,1:2,getting the colony after the
> transformation but some how  when i used to confirm my clone through double
> digestion i

Re: [ccp4bb] crystallisation

[Mark Brooks]

Indeed, if Phoebe Rice is right, and you have dimethyl arsenic bound to your
cysteines, you may have a homogeneity problem, not from the protein sample,
but from the chemical reaction which is occurring prior to crystallization.

If you have DTT, check that it is fresh. Make sure your cacodylate is fresh
also, since old stock may not react so well (yes, this happened to me).
Essentially the arsenic and DTT must react to form a reactive species which
then reacts with the cysteines.

Perhaps you will notice anomalous scattering with even with "native"
crystals around the arsenic edge, and perhaps also you can exploit this in
phasing.
http://skuld.bmsc.washington.edu/scatter/data/As.html

Good luck,

Mark

P.S.
Here's a reference for the reaction of cacodylate with cysteines.
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45M7T0C-1B&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C50221&_version=1&_urlVersion=0&_userid=10&md5=83f1ce7ecb1c07b7d0202220f556cf4e

2008/6/3 Phoebe Rice <[EMAIL PROTECTED]>:

> If you have high [DTT] in your buffer, you might be
> catalyzing the addition of dimethyl arsenic (from the
> cacodylate) to some of your cysteines?
> Also, 10% glyercol sounds quite low for reproducibly good
> freezing (at least in my experience).
> Phoebe
>
>  Original message 
> >Date: Mon, 2 Jun 2008 17:04:38 +0100
> >From: sajid akthar <[EMAIL PROTECTED]>
> >Subject: [ccp4bb] crystallisation
> >To: CCP4BB@JISCMAIL.AC.UK
> >
> >
> >Dear All
> >
> >My protein size is ~30kD and crystallizes with
> >19%Peg3350, 0.2M Nacl, and 0.1M Na Cacodylate buffer.
> >
> >Please refer the attached crystal image with this. The
> >crystal looks like good enough for home source. These
> >crystals appears in 4-5 days at room temp.
> >
> >Sometimes I'm getting crystals like this, but very few
> >in 24 well tray. Most of the time, I found the drop
> >contains needles. If I reduce the precipitant little
> >bit, I wont find any change in the drop even after
> >long time. Changing pH (or temp)of the buffer does not
> >help me any better. The crystal appears only around
> >5.5pH.
> >
> >The problem is mosaicity. This crystal diffracted in
> >home source upto 3.2A and the mosaicity is 2.5degree.
> >Almost all the good crystal like this having same
> >mosaicity.
> >
> >Good cryo condition so far that I found was
> >10%Glycerol with mother liquor. Other conditions
> >weekens the diffraction quality or increase mosaicity.
> >
> >In many crystal I could see some crack in the middle
> >of the crystal, it looks like twin crystal. Or the
> >crystal appears with some sattelite crystals.
> >
> >Can anyone suggest me some good way to overcome these
> >problems.
> >
> >Thankz
> >
> >Sajid
> >
> >
> >
> >  From Chandigarh to Chennai - find friends all over
> India. Go to http://in.promos.yahoo.com/groups/citygroups/
> >
> >DSCN0003.JPG (720k bytes)
> Phoebe A. Rice
> Assoc. Prof., Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
>
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>
> RNA is really nifty
> DNA is over fifty
> We have put them
>  both in one book
> Please do take a
>  really good look
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>



-- 
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [ccp4bb] CCP4 for bioinformatics?

[Mark Brooks]

A newer one for Ruby is (of course) BioRuby, which I use for simple
manipulation of sequences or chopping up structures.

It's quite nice for this, but I don't think it's as feature-rich as
Bio{Perl,Python,Java} though.

http://dev.bioruby.org/wiki/en/?cmd=view&p=How+do+I+get+the+sequence+of+a+chain%3F&key=PDB
http://dev.bioruby.org/wiki/en/?cmd=view&p=How+do+I+find+specific+atoms%2C+residues%2C+chains+or+models%3F&key=PDB
http://dev.bioruby.org/wiki/en/?cmd=view&p=How+do+I+write+a+structure+file%3F&key=PDB

Mark

On 22/01/2008, Claudine MAYER <[EMAIL PROTECTED]> wrote:
> Hi,
>
> You can use the on-line software EMBOSS.
> You can use it at the following site :
>
> http://bips.u-strasbg.fr/EMBOSS/
>
> enjoy it !
> Claudine
>
>
> Jacob Keller wrote:
>
> > Dear Crystallographers,
> >
> > Does anyone know of a bioinformatics counterpart of ccp4? It seems
> > like there should really be such an entity, so that folks would not
> > have to write scripts, reinventing the wheel all of the time. I am
> > trying right now to manipulate some sequences into various forms, and
> > I was imagining a "moleman" homolog for bioinformatics (perhaps
> > seqman?).
> >
> > Regards,
> >
> > Jacob Keller
> >
> > ***
> > Jacob Pearson Keller
> > Northwestern University
> > Medical Scientist Training Program
> > Dallos Laboratory
> > F. Searle 1-240
> > 2240 Campus Drive
> > Evanston IL 60208
> > lab: 847.491.2438
> > cel: 773.608.9185
> > email: [EMAIL PROTECTED]
> > ***
> >
> >
>
>
> --
> *
> Dr Claudine MAYER
> MCF  Université Paris 6
> LRMA  Equipe 12 UMR S 872
> Laboratoire de Bactériologie  (5ème étage gauche)
> Faculté de Médecine PITIE-SALPETRIERE
> 91 bd de l'Hopital
> 75634 PARIS Cedex 13
> tel :  01 40 77 95 56
> fax :  01 45 82 75 77
> mobil: 06 07 23 51 16
> [EMAIL PROTECTED]
> *
>
>
>
>


-- 
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
INSTITUT de BIOCHIMIE et de BIOPHYSIQUE MOLECULAIRE et CELLULAIRE
UMR8619 - Bât 430 - Université de Paris-Sud
91405 ORSAY CEDEX

Re: [ccp4bb] upgrading ccp4 broke my Coot stereo

[Mark Brooks]

Hi,
I wouldn't worry about the libbluecurve error.  GTK is very
talkative, and spews out warnings at every oportunity.  Libbluecurve
is being searched for because that's your GTK theme I guess (Redhat's
'Bluecurve' window manager theme).

The CATASTROPHIC ERROR part is probably more relevant.  Does O run in
stereo, for example? Can you post the relevant parts of your xorg.conf
file?

Mark

On 12/12/2007, Robert Grant <[EMAIL PROTECTED]> wrote:
> I recently upgraded from ccp4 version 5.99.5 to 6.02.
> In doing so I have lost the ability to run Coot with hardware stereo.
>
> When I fire up Coot it reports:
>
> Gtk-WARNING **: Unable to locate loadable module in module_path:
> "libbluecurve.s o"
>
> When I try to switch to hardware stereo it says:
>
> CATASTROPHIC ERROR:: in gl_extras no GtkGL widget!
> WARNING:: switch to hardware_stereo_mode failed
>
> The new version of ccp4 was downloaded along with the latest Coot,
> Phaser, TclTk, and Chooch. Nothing has changed in my
> /etc/X11/xorg.conf file, which I had to modify to get the stereo to
> work in the 1st place.
>
> It would appear that an environmental variable involving a library
> path is missing or wrong but I have not been able to figure out what
> it is.
>
> Any ideas?
>


-- 
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
INSTITUT de BIOCHIMIE et de BIOPHYSIQUE MOLECULAIRE et CELLULAIRE
UMR8619 - Bât 430 - Université de Paris-Sud
91405 ORSAY CEDEX

Re: [ccp4bb] Stereo setting in program O with stereo-ready graphic card in x86_64

[Mark Brooks]

Hi,
   there is an O-info mailing list, which you may find useful.

I had problems with the composite extension to the X.org X server in recent
Linux distributions.  Perhaps you are using Fedora Core 6 or Ubuntu Edgy?
If so, this thread has more information:

http://imsb.au.dk/pipermail/o-info/2007-February/008218.html

I hope this helps,

Mark

On 02/09/07, linwoo kang <[EMAIL PROTECTED]> wrote:
>
> Dear all:
>
> I try to install program O in x86_64 linux machine with stereo-ready
> graphic card.
> When I try to use stereo (setenv STEREO on), I get the following message.
>
>   No dials
>   Stereo enabled, hit F1
>   Gamepad disabled
> freeglut (lin_ono):  ERROR:  Internal error  capabilities not found> in function fgOpenWindow
> X Error of failed request:  BadWindow (invalid Window parameter)
>   Major opcode of failed request:  4 (X_DestroyWindow)
>   Resource id in failed request:  0x0
>   Serial number of failed request:  16
>   Current serial number in output stream:  19
>
> I guess it is due to the setting of X-window.
> Could you advise me?
>
> Thanks in advance.
>
> --
> Sincerely yours,
>
> Lin-Woo Kang, Ph.D.
>
> Assistant professor
> Konkuk university
> Dept. of advanced technology fusion
> Tel) 82-2-450-4090
> E-mail) [EMAIL PROTECTED]




-- 
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
INSTITUT de BIOCHIMIE et de BIOPHYSIQUE MOLECULAIRE et CELLULAIRE
UMR8619 - Bât 430 - Université de Paris-Sud
91405 ORSAY CEDEX

Re: [ccp4bb] oxidised cys

[Mark Brooks]

It worked well for me, on the selenium edge. Back-soaking out the remaining
cacodylate was necessary to find the sites.

Choe's group have used this fruitfully:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=pubmed&term=greenwald+butler+choe&tool=fuzzy&ot=Greenwald+Bultler+Choe

Meignan et al propose a reaction mechanism, involving an As(+3)-thiolate
intermediate ((CH3) 2AsSR), which then reacts with free cysteines by thiol
exchange:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&term=9735293&doptcmdl=Citation


Mark

On 13/04/07, Martyn Symmons <[EMAIL PROTECTED]> wrote:


Dear John
 I think this is a thiol-specific reaction - where it has happened
to Cys residues the Met residues appear normal. I wondered if anyone had
ever used this on purpose as a heavy atom derivative. Arsenic has quite a
good anomalous signal too I think.
  All the best
  Martyn

Martyn Symmons
Department of Pathology
University of Cambridge




Message Received: Apr 13 2007, 01:37 PM
From: "John Walker" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject: Re: [ccp4bb] oxidised cys

Can methionine be modified with these two reagents in a similar manner?

Cheers,

John

--
John R. Walker, Ph.D.
Structural Genomics Consortium
University of Toronto
Toronto, Ontario
Canada

On 4/13/07, Martyn Symmons <[EMAIL PROTECTED] > wrote:
> A possible modification for cysteine that adds extra density is
S-(dimethylarsenic) cysteine (CAS). Requires DTT and cacodylate buffer
conditions however. And does not crosslink so far as I know.
>
> Has been seen in a number of structures from cacodylate conditions - eg.
one of the Xrcc4 structures
>
> cheers
>   Martyn
>
> Martyn Symmons
> Department of Pathology
> University of Cambridge
>
>
>
>
> 
>  Message Received: Apr 12 2007, 06:06 PM
>  From: "Flip Hoedemaeker" < [EMAIL PROTECTED]>
>  To: [EMAIL PROTECTED]
>  Cc:
>  Subject: Re: [ccp4bb] oxidised cys
>
>  I've actually seen something like this on disulfides (or at least I
think
>  so, I havent seen your density obviously), turned out it was model bias
in
>  MR, if I used a different template for MR the feature went away. This
was
>  high resolution stuff (~1.0 Å).
>
>  Flip
>
>  -Original Message-
>  From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
>   [EMAIL PROTECTED]
>  Sent: Tuesday, April 10, 2007 20:44
>  To: [EMAIL PROTECTED]
>  Subject: Re: [ccp4bb] oxidised cys
>
>  Hi Stefano,
>
>  How certain are you that this link is truly what you think it is? If I
>  understand what you're saying - you want to create a (thioperoxythio)
link
>  - this chemistry should be hideously unstable. Can you explain this
using
>  disorder, or perhaps the residual density is a symmetry artifact?
>
>  Regards,
>
>  Artem
>
>  > Dear all
>  > in my structure I think I can see an oxidised Cys in cys-SO. Refining

>  > cys-SO
>  > I observe a residual density between the oxigen of one oxidised cys
and
>  > the
>  > one of the other molecule in AU.
>  > I'd like to try to refine it as cys-SO-OS-cys. I didn't find an
example of
>  > it in the pdb database. Could anyone tell me whether there are other
>  > cases?
>  > I guess I just didn't find them.
>  > Second question:
>  > How could I "explain" to refmac that there is the OO bond?
>  > I tried to write a line similar to the one for SSBOND in the pdb
header
>  > OOBOND   1 CEA A   42CEA D   42
>  > but refmac couldn't care less...
>  >
>  > thanks in advance
>  >
>  > Stefano
>  >
>  > _
>  > Express yourself instantly with MSN Messenger! Download today it's
FREE!
>  > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>  >
>
>





--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
INSTITUT de BIOCHIMIE et de BIOPHYSIQUE MOLECULAIRE et CELLULAIRE
UMR8619 - Bât 430 - Université de Paris-Sud
91405 ORSAY CEDEX