In SHELXL this is handled by refining the ligand with "PART -1" and
occupancies
fixed at 0.25, and refining the rest of the structure normally. The
program ignores
interactions between symmetry generated atoms with negative PART numbers
when generating restraints, placing H-atoms etc. Positive PART numbers work
like the alternative locations A, B, C etc. in a PDB file but
unfortunately the PDB
file has no equivalent to negative PART numbers. Solvent and other
molecules
disordered on special positions are common in small molecule structures;
toluene just loves to sit on an inversion center.
George
On 02/08/2016 01:04 AM, Dale Tronrud wrote:
> My bad! As Boaz Shaanan pointed out to me, I missed the "NCS" in
> your subject line. This means that my answer was not relevant to your
> question.
>
> The source of the confusion surrounding your situation is that the
> PDB file format does not easily allow one to describe exactly what your
> model is. What you really have is a tetramer with a single ligand at
> its center, which breaks its symmetry and makes it a P1 particle. This
> entire particle sits in the crystal in a disordered fashion, since the
> outside has four-fold symmetry. Refinement programs are not going to
> like four entire tetramers at 1/4 occupancy where nearly all the atoms
> superimpose.
>
> Compounding the problem is the fact that the PDB file format does not
> really specify what the relationship is between the "A" alternative
> location of residue 1 and the "A" alternative location of residue 2. I
> would prefer to think that 1.A can bond to 2.A and have bad contacts
> with 2.A but not to 2.B, but the format doesn't say that. And if it
> did, we would run out of letters for alt locs pretty fast.
>
> If you define your ligand to have four different names, the
> refinement program will assume you mean that there are four residues in
> the same universe and assume there are bad contacts between them. If
> you give the ligands four different names but specify different alt locs
> (e.g. 1.A, 2.B, 3.C, and 4.D) the program still can't safely assume
> there should be no bad contacts (because of the vague format
> specification). You should be able to give all four molecules the same
> name but different alt locs (e.g. 1.A, 1.B, 1.C, and 1.D) and the bad
> contacts should be ignored. If there are alt locs for the surrounding
> protein atoms that match the alt locs of your ligand you are back to the
> format specification problem - it is not safe to assume that 123.A is in
> the same universe as 1.A.
>
> When you find that the program is pushing apart atoms that you don't
> think should be seeing each other, you can either change the names (and
> there may be no workable naming solution) or use the tool in the
> refinement program to tell it to ignore particular bad contacts. Every
> refinement program has such a tool. The fact that you have to add this
> ad hoc override is not a flaw in the program, it is a flaw in the file
> format.
>
> Dale Tronrud
>
>
> On 2/7/2016 7:03 AM, Boaz Shaanan wrote:
>> Hi Dale,
>>
>> Just wondering: is the scenario your're describing also valid for 4-fold NCS axis (as is the case here), where the occupancies may not be as strictly related ? It sounds to me more relevant to crystallographic 4-fold axis but I could well be wrong of course.
>>
>> Cheers,
>>
>> Boaz
>>
>>
>> Boaz Shaanan, Ph.D.
>> Dept. of Life Sciences
>> Ben-Gurion University of the Negev
>> Beer-Sheva 84105
>> Israel
>>
>> E-mail: [log in to unmask]
>> Phone: 972-8-647-2220 Skype: boaz.shaanan
>> Fax: 972-8-647-2992 or 972-8-646-1710
>>
>>
>>
>>
>>
>> ________________________________________
>> From: CCP4 bulletin board [[log in to unmask]] on behalf of Dale Tronrud [[log in to unmask]]
>> Sent: Saturday, February 06, 2016 10:46 PM
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] Ligand at four fold NCS axis
>>
>> If you have a ligand sitting on a four-fold axis, let's call the four
>> residues 1, 2, 3, 4. Residues 2, 3, and 4 are generated by the
>> refinement program using symmetry so the occupancy of 1 should be set to
>> 0.25 to generate a total occupancy of 1.0.
>>
>> Now you say that residue 1 has four conformations. Let's call them
>> 1.A, 1.B, 1.C and 1.D. The sum of the occupancies of these
>> conformations have to add up to the occupancy of 1. If their
>> occupancies are equal you have to set them to 0.0625 (or 1/16).
>>
>> The refinement program will generate 2.A, 3.C and all the rest.
>>
>> Dale Tronrud
>>
>> On 2/6/2016 11:41 AM, Appu kumar wrote:
>>> Dear CCp4 Users,
>>> I am refining a tetrameric protein which has ligand placed at the center
>>> axis. There is one tetramer in ASU. I added the ligand with 0.25
>>> occupancy and performed the refinement using both phenix and refmac.
>>> Refinement leaves lots of green density around the ligand inferring that
>>> there may be four different conformation of the ligand. When i made four
>>> different conformation of ligand (each with 0.25 occupancy) and started
>>> refinement, there is lot of clashes in ligand itself. Is there a ways to
>>> refine the four different conformation of ligand with different
>>> conformation with 0.25 occupancy avoiding clashes in ligands?
>>>
>>> I appreciate your input, suggestions on the refinement.
>>>
>>> Thank you
>>> Appu
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
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