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Re: [ccp4bb] Refmac problems on Mac OS X Leopard
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: Lower completeness, decent R factors, but low B factor...
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-08-20		Next message:
Subject: Coot and OS X Leopard
From: "Winter, G (Graeme)" g {- dot -} winter {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-08-20


Subject: Re: Refmac problems on Mac OS X Leopard
From: Louise Gourlay louise {- dot -} gourlay {- at -} GUEST {- dot -} UNIMI {- dot -} IT
Date: 2008-08-20

Thanks to both, in the end I downloaded the new version of refmac and moved the characters,
Louise

----- Messaggio Originale -----
Da: Eleanor Dodson
Data: Martedi', Agosto 19, 2008 6:00 pm
Oggetto: Re: [ccp4bb] Refmac problems on Mac OS X Leopard
A: Louise Gourlay
Cc: CCP4BB@jiscmail.ac.uk

> You need to move the CA and CL names one character to the left
>
> ATOM   6190  O   HOH W 
> 64    26.387  33.040  -0.685  1.00
> 40.92           O
> ATOM   6191 CA   CA  B  
> 1    37.417  44.961  41.022  1.00
> 12.13          CA
>
> more like this..
>
> Eleanor
>
> Louise Gourlay wrote:
> > ATOM   6189  O   HOH W 
> 63    14.409  51.932   0.124 
> 1.00 46.53           O 
> > ATOM   6190  O   HOH W 
> 64    26.387  33.040  -0.685  1.00
> 40.92           O 
> > ATOM   6191  CA   CA B  
> 1      37.417  44.961 
> 41.022  1.00
> 12.13         CA 
> > ATOM   6192  CA   CA B  
> 2      23.027  43.324 
> 21.110  1.00 
> 5.01          CA 
> > ATOM   6193  CA   CA B  
> 3      52.444  49.349  
> 2.208  1.00
> 14.66          CA 
> > ATOM   6194  CA   CA B  
> 4      34.610  74.683  
> 4.564  1.00
> 10.52          CA 
> > ATOM   6195  CL    CL
> C   1      32.966 
> 46.780   3.090  1.00 
> 2.00           CL 
> > END
> >
> > I also tried Ca, Ca2+ but no luck.  I added them to the
> structure with coot. Also, I forgot to say that the refinement
> works when I use another computer so it's something to do with mine.
> > Thanks,
> > Louise
> >
> > ----- Messaggio Originale -----
> > Da: Louise Gourlay
> > Data: Martedi', Agosto 19, 2008 4:26 pm
> > Oggetto: [ccp4bb] Refmac problems on Mac OS X Leopard
> > A: CCP4BB@JISCMAIL.AC.UK
> >
> >  
> >> Dear All,
> >>
> >> I installed CCP4 on my Mac OS X Leopard system using fink. I
> >> have some problems with Refmac, it doesn't refine calcium or
> >> chlorine atoms, or any non-protein atom in general.  In
> the log
> >> file it doesn't recognize them and says:
> >> FORMATTED     
> OLD     file opened on unit  45
> >> Logical name: ATOMSF, Filename: /sw/share/xtal/ccp4-
> >> 6.0.2/lib/data/atomsf.lib No match for atom ID CL subtracting
> >> one character
> >>  No match for atom ID CA subtracting one character
> >>
> >> Thanks,
> >> Louise
> >>
> >>
> >>
> >>
> >> ----- Messaggio Originale -----
> >> Da: Garib Murshudov
> >> Data: Mercoledi', Luglio 30, 2008 2:28 pm
> >> Oggetto: Re: [ccp4bb] Preventing close contact between
> protein
> >> and ligand
> >> A: CCP4BB@JISCMAIL.AC.UK
> >>
> >>    
> >>> Dear Snageetha
> >>>
> >>> 1) Could you check please if specified atoms have zero
> >>> occupancy. 
> >>> Atoms with zero occupancy are considered as absent and there
> >>>      
> >> are
> >>    
> >>> not 
> >>> restraints on them
> >>> 2) symm y at the end of instructions means that the program
> >>> check all 
> >>> possible symmetry operators and finds minimal distance. Most
> >>> probably 
> >>> 5.024 is the distance between symmetry related atoms
> >>> 3) to remove antibumping between different chains there is
> >>> an 
> >>> undocumented keyword. It can be used. the keyword is (as an
> example)>>>
> >>> vdwrestraints exclude between chains A B
> >>>
> >>>
> >>> Please let me know if this instruction does not work.
> >>> NB: This option should not be used unless you know what you
> >>>      
> >> are
> >>    
> >>> doing 
> >>> (that is the reason why it has not been documented). If
> there
> >>> are 
> >>> clashes between chains then there are reasons for that. For
> example>>> if ligand has half occupancy then it is very likely
> that
> >>> surrounding 
> >>> atoms also have multiple conformation and you should model them.
> >>>
> >>>
> >>> regards
> >>> Garib
> >>>
> >>>
> >>> On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote:
> >>>
> >>>      
> >>>> Dear bb users,
> >>>>
> >>>> I am refining a protein-ligand complex (at 1.68 A
> >>>>        
> >> resolution)
> >>    
> >>> in 
> >>>      
> >>>> which the ligand lies on a 2-fold crystallographic symmetry
> >>>>        
> >>> axis. 
> >>>      
> >>>> The ligand occupancy is, therefore, 0.5 in each asymmetric unit.
> >>>>
> >>>> I am almost at the end of the refinement but one problem
> has
> >>>>        
> >>> me 
> >>>      
> >>>> stumped. Refmac keeps moving a carbon in the ligand too
> >>>>        
> >> close
> >>    
> >>> to a 
> >>>      
> >>>> serine OG and an oxygen too close to an arginine CD. Given
> >>>>        
> >>> that the 
> >>>      
> >>>> ligand is at the interface, the density is not perfect.
> >>>>        
> >>> However, I 
> >>>      
> >>>> rebuild the ligand to eliminate close contacts and still be
> >>>>        
> >>> within 
> >>>      
> >>>> density and refmac pulls it right back close to the
> protein.
> >>>>        
> >>> The 
> >>>      
> >>>> refined position does not even look better than the rebuilt
> >>>>        
> >>> one! It 
> >>>      
> >>>> almost always looks worse! Would refmac put less weight on
> >>>>        
> >>> close 
> >>>      
> >>>> contacts with the ligand because it is only partially occupied?
> >>>>
> >>>> I tried to use external restraints between the ligand and
> >>>>        
> >>> the 
> >>>      
> >>>> residues so that they are kept further away.
> >>>>
> >>>> Upon searching the net, I found this command line:
> >>>>
> >>>> external distance first chain [ch] residue [res] insertion
> >>>>        
> >>> [ins] -
> >>>      
> >>>> atom [n] [altcode [a]] second chain [ch] residue [res]
> >>>>        
> >>> insertion 
> >>>      
> >>>> [ins]-
> >>>> atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n]
> >>>>
> >>>> I thought (hoped) that the distance herein is the minimum
> >>>>        
> >>> distance 
> >>>      
> >>>> of approach between the specified atoms, I added these
> lines
> >>>>        
> >>> from 
> >>>      
> >>>> within "Developer options" in refmac interface:
> >>>>
> >>>> exte dist first chain A resi 59 atom CD seco chain X resi
> >>>>        
> >> 2001
> >>    
> >>> atom 
> >>>      
> >>>> O1 valu 3.2 sigm 0.02 symm Y
> >>>> exte dist first chain A resi 27 atom OG seco chain X resi
> >>>>        
> >> 2001
> >>    
> >>> atom 
> >>>      
> >>>> C10 valu 3.2 sigm 0.02 symm Y
> >>>>
> >>>> It didn't recognize these restraints at all.
> >>>>
> >>>> However, when I change these lines to:
> >>>>
> >>>> exte dist first chain A resi 59 atom CA seco chain X resi
> >>>>        
> >> 2001
> >>    
> >>> atom 
> >>>      
> >>>> O1 valu 3.2 sigm 0.02 symm Y
> >>>> exte dist first chain A resi 27 atom OG seco chain X resi
> >>>>        
> >> 2001
> >>    
> >>> atom 
> >>>      
> >>>> C10 valu 3.2 sigm 0.02 symm Y
> >>>>
> >>>> Refmac recognizes the first line but not the second - lines
> >>>>        
> >>> from 
> >>>      
> >>>> log file:
> >>>>
> >>>> Bond distance deviations from the ideal >10.000Sigma will
> be
> >>>>        
> >>> monitored>
> >>>      
> >>>> A     59 ARG CA  . - X  
> >>>>        
> >>> 2001 DIE O1  . mod.= 5.024 id.= 3.200 dev= 
> >>>      
> >>>> -1.824 sig.= 0.020
> >>>>
> >>>> This raises two concerns:
> >>>>
> >>>> Concern 1: From the first line of output: the restraints
> >>>>        
> >> here
> >>    
> >>> don't 
> >>>      
> >>>> seem to be minimizing close contact at all; it seems to
> >>>>        
> >> think
> >>    
> >>> they 
> >>>      
> >>>> are bonded somehow (the distance between these atoms is not
> >>>>        
> >>> 5.024; 
> >>>      
> >>>> it is 6.26 A; I don't know what 5.024 A is!).
> >>>>
> >>>> I am missing something here. It'd be great if someone can
> >>>>        
> >> tell
> >>    
> >>> me 
> >>>      
> >>>> what that is!
> >>>>
> >>>> Concern 2: This command only works when the first atom
> >>>>        
> >>> specified is 
> >>>      
> >>>> a C-alpha atom (or maybe a main chain atom; I didn't try
> >>>>        
> >>> using 
> >>>      
> >>>> other main chain atoms). Why is that?
> >>>>
> >>>> AND ULTIMATELY,
> >>>>
> >>>> is there some way I can tell refmac not to make the ligand
> >>>>        
> >>> and 
> >>>      
> >>>> protein clash?
> >>>>
> >>>> I'd really appreciate any help!
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Sangeetha.
> >>>>        
> >>>      
> >> Louise Gourlay Ph.D Dep. of Biomolecular Sciences and
> >> Biotechnology, Università degli Studi di Milano Via Celoria
> 26
> >> Milano 20133 http://users.unimi.it/biolstru/Home.html Italy
> >>
> >>
> >>
> >>    
> >
> > Louise Gourlay Ph.D Dep. of Biomolecular Sciences and
> Biotechnology, Università degli Studi di Milano Via Celoria 26
> Milano 20133 http://users.unimi.it/biolstru/Home.html Italy
> >
> >
> >
> >  
>
>

Louise Gourlay Ph.D Dep. of Biomolecular Sciences and Biotechnology, Università degli Studi di Milano Via Celoria 26 Milano 20133 http://users.unimi.it/biolstru/Home.html Italy
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