Re: [ccp4bb] is it valid to compare the B factors of corresponding domains or regions of molecules from different crystal structures

[Jan Dohnalek]

I think that a simple and straight answer is NO.
Individual crystal structures compensate for various and differing factors
by their individual Bs.

Jan D.
IMC Prague


On Fri, Aug 24, 2012 at 8:29 PM, Michael Murphy  wrote:

> I am looking to compare the B-factors of a particular stretch of DNA bases
> when bound by several different proteins. I have crystal structures for
> each, but the structures are of different resolutions and also then
> different Wilson B-factors. Is it valid to compare those B-factors
> directly? (probably not) or to set the B-factors from the different
> structures to a common scale based on the Wilson B-factors from their
> respective data sets?




-- 
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

Re: [ccp4bb] wilson B and ARP/wARP

[Ben]

Problem has been resolved.  There was a space in one of the directory names 
where my files were stored.  This prevented ccp4 from displaying log graphs in 
the summary window of jobs, and prevented ARP/wARP from calculating the wilson 
B.  Removing the space in the directory name took care of both issues.

Thanks to everyone who replied.

Re: [ccp4bb] wilson B and ARP/wARP

[Eleanor Dodson]

I haven't seen that message, but I think you could provide Arp/Warp with the 
model, plus the original data, and it would probably work.

Eleanor 
On 25 Aug 2012, at 16:38, Ben wrote:

> I recently processed a dataset in HKL2000, imported the scaled data to mtz 
> format in CCP4, and obtained a molecular replacement solution with PHASER.  
> However, upon trying to use ARP/wARP to build a model with the phases from 
> PHASER I get the following error ...
> 
> "can't read Wilson B: no such variable exists"
> 
> ARP/wARP does not display a Wilson B or solvent content under crystal 
> parameters.  All other crystal parameters are displayed.
> Has anyone else encountered this issue, or have a resolution to the problem?
> 
> Thanks,
> Ben

[ccp4bb] TENURE-TRACK FACULTY POSITION IN BIOCHEMISTRY AT VANDERBILT UNIVERSITY

[Eichman, Brandt F]

TENURE-TRACK FACULTY POSITION IN BIOCHEMISTRY AT VANDERBILT UNIVERSITY



The Department of Biological Sciences at Vanderbilt University invites 
applications for a tenure-track faculty position in biochemistry at the rank of 
Assistant Professor. The ideal candidate will pursue innovative research that 
complements existing areas of strength in the department 
(http://sitemason.vanderbilt.edu/biosci). We particularly encourage 
applications in the area of mechanistic biochemistry, including but not limited 
to single-molecule, chemical biology, and structural methodologies. We welcome 
use of cross-disciplinary approaches that may include molecular, imaging and 
system analyses. The central criteria for the position are excellence in 
research and the ability to teach undergraduate and graduate students with a 
high level of effectiveness.  Women and under-represented minority candidates 
are especially encouraged to apply. Applicants should send a single PDF 
containing a letter of application, curriculum vitae, statement of current and 
future research interests, and evidence of teaching effectiveness to 
barbara.a.sidw...@vanderbilt.edu . 
Applicants should arrange for three letters of recommendation to be sent to the 
same address. Review of applicants will begin October 15, 2012, and will 
continue until the position has been filled.  Vanderbilt University is an 
Affirmative Action / Equal Opportunity Employer.

[ccp4bb] dear ccp4

[rana ibd]

Dear ccp4 
   I am working on hbx (Hepatitis B x protein for both that duck and the human) 
I worked first on the dhbx which  contained the vector pRSET-A and I didn’t get 
any results, then I changed the vector ( thanks to many of you who provided me 
with information, papers and books) using p-MAL c2x which worked perfectly 
throughout the whole procedure, I even now have about 60% soluble protein, then 
I started working on the hhbx,also changing the vector from pRSET-A to p-MAL 
c2xat first the PCR was successful with an obvious band on the gel, so I 
proceeded with double digestion using both restriction enzymes which are BamH1 
and Hind111, incubated 3h then applied the insert on the gel, surprisingly what 
I observed was a slight band on the gel, after purifying the insert I checked 
the concentration which decreased from 35ng/ul before purification to 5.2ng/ul 
after purification, I would be grateful if any one has any idea or suggestions 
regarding this situation
Best Regards
Rana    

[ccp4bb] Dear ccp4

[rana ibd]

Dear ccp4 
   I am working on hbx (Hepatitis B x protein for both that duck and the human) 
I worked first on the dhbx which  contained the vector pRSET-A and I didn’t get 
any results, then I changed the vector ( thanks to many of you who provided me 
with information, papers and books) using p-MAL c2x which worked perfectly 
throughout the whole procedure, I even now have about 60% soluble protein, then 
I started working on the hhbx,also changing the vector from pRSET-A to p-MAL 
c2xat first the PCR was successful with an obvious band on the gel, so I 
proceeded with double digestion using both restriction enzymes, incubated 3h 
then applied the insert on the gel, surprisingly what I observed was a slight 
band on the gel, after purifying the insert I checked the concentration which 
decreased from 35ng/ul before purification to 5.2ng/ul after purification, I 
would be grateful if any one has any idea or suggestions regarding this 
situation
Best Regards
Rana    

Re: [ccp4bb] compatibility issue between coot and refmac

[Robbie Joosten]

Dear Norman,

Refmac version 5.0 sounds unlikely, the version with CCP4 6.3 is 5.7.0029. 
Anyway, your DNA seems to have asterisks in the atom names, which is 'so last 
decade' (they were removed in 2008). Refmac and Coot may not be equally 
forgiving for legacy formats. IMO neither should be. The best you can do is 
upgrade your PDB to a new format. There is a tool in CCP4i for that and the 
MolProbity server can do it as well.

HTH,
Robbie

Date: Sun, 26 Aug 2012 00:40:02 -0700
From: zhunor...@gmail.com
Subject: [ccp4bb] compatibility issue between coot and refmac
To: CCP4BB@JISCMAIL.AC.UK

dear ccp4 forum 

Does anybody know which version of coot is compatible with which 
version of ccp4i, or more specifically, refmac?  I seem to be having DNA 
recognition problem between the two softwares.   I haven isolated the problem 
to the differences between naming conventions.  However, manipulating the 
naming convention would only cause the pdb file to work in one of the software 
but not both.  If it works for refmac the real space refinement in coot would 
not work.  The warning sign pops up for that would says 'failed to match these 
atoms names (O1P, C5*...etc)to the dictionary'  and if it works for the coot 
the refmac would not process the pdb file at all.

  
Naturally the first thing i thought of to do is to synchronize the 
dictionaries in both of these programs but doesn't seem to be that straight 
forward.  I suspect it has something to do with the import cif dictionary but i 
don't know where to import it from.  That's why i think it might be easier find 
a version of coot that's compatible or vice versa.  The versions of programs i 
currently running on are coot 0.6.2 and ccp4 6.3.0 interface 2.2.0.  The 
version of refmac in ccp4 is 5.0. 


 Please let me know if I am on the right track or if there is a 
easier way to do this.

Thanks 
Norm

  

[ccp4bb] compatibility issue between coot and refmac

[Norman zhu]

dear ccp4 forum

Does anybody know which version of coot is compatible with
which version of ccp4i, or more specifically, refmac?  I seem to be having
DNA recognition problem between the two softwares.   I haven isolated the
problem to the differences between naming conventions.  However,
manipulating the naming convention would only cause the pdb file to work in
one of the software but not both.  If it works for refmac the real space
refinement in coot would not work.  The warning sign pops up for that would
says 'failed to match these atoms names (O1P, C5*...etc)to the dictionary'
and if it works for the coot the refmac would not process the pdb file at
all.

Naturally the first thing i thought of to do is to synchronize
the dictionaries in both of these programs but doesn't seem to be that
straight forward.  I suspect it has something to do with the import cif
dictionary but i don't know where to import it from.  That's why i think it
might be easier find a version of coot that's compatible or vice versa.
The versions of programs i currently running on are coot 0.6.2 and ccp4
6.3.0 interface 2.2.0.  The version of refmac in ccp4 is 5.0.

 Please let me know if I am on the right track or if there is a
easier way to do this.

Thanks
Norm