Can you send a bit of your PDB including the CA and CL?  Eleanor

Louise Gourlay wrote:
> 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 <[log in to unmask]>
> Data: Mercoledi', Luglio 30, 2008 2:28 pm
> Oggetto: Re: [ccp4bb] Preventing close contact between protein and ligand
> A: [log in to unmask]
>
>   
>> 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
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