[ccp4bb]
Thanks for the suggestion about using NCS constraint to apply change on one
subunit to other subunits. That should make life much easier.
About the problem of phenix realspace refinement, I figured it out. I used
GUI and when I checked the log file, the "ramachandran_restraints" was
turned off. It is odd since there does not seem to have any buttons to turn
"ramachandran_restraints" off in GUI. Then I tried command line, the
Ramachandron statistics look normal now ("ramachandran_restraints" is on in
log file).
Thanks.
On Fri, May 19, 2017 at 11:01 AM, Pavel Afonine wrote:
>
>
> Yes, that is what I have been doing. Build one subunit and assemble into
>> tetramer before realspace refinement (with "ncs" constraints). I used
>> tetramer for refinement because I want the distances between the inter
>> subunits interaction partners to be considered. The problem is, whenever I
>> want to make some manual adjustments of the model afterwards, I have to
>> break it into monomer and repeat the whole process again. I assume if the
>> map is in P4 spacegroup, I only need to modify one subunit of this protein
>> and changes will be automatically applied to the other subunits. Am I
>> right?
>>
>
> So you have 4 copies and NCS group consisting of one master (or reference)
> copy and three related by NCS symmetry. Then you make changes in master
> copy and when you run refinement with NCS constraints the changes will be
> propagated onto the related copies by applying NCS constraints. This is how
> this works in phenix.real_space_refine. So no need to make identical
> changes in all 4 copies or go to P4.
>
>
>
>> Another question is, when I tried to refine my model using phenix
>> realspace refinement (energy minimization and adp), the statistics
>> generally become better (map CC, rotamer outlier etc), however, the
>> ramachandron statistics become worse, with increase number of outliers
>> (from below 1% to around 5%) and allowed (from several percent to 10-20%).
>> Do you know what could be the cause? I know I am asking the right person...
>>
>
> This is not expected (about worsening Ramachandran plot outliers). I'm
> sure we can solve this problem if you send me model and map files (and
> resolution) off list (if files too large to send by email please use
> Dropbox or similar file sharing tools).
>
> Pavel
>
>
[ccp4bb]
Sorry for the confusion. I just want to avoid the hassle to go back and forth between one subunit and tetramer. My understanding is that I only need to modify one subunit of this protein and changes will be automatically applied to the other subunits if the map is changed to p4 spacegroup. I have seen people do that using MAPMAN in a couple of papers and just want to know what I am doing wrong. On Fri, May 19, 2017 at 12:15 AM, Dale Tronrud <de...@daletronrud.com> wrote: > >I'm sorry but I'm a little confused by your question. If your map > already has four-fold symmetry why can't you simply build your model > once in one quarter of the map? What do you hope to change by > specifying that the space group is P4? > > Dale Tronrud > > On 5/18/2017 10:06 PM, Qingfeng Chen wrote: > > Hi, > > > > I have an EM map of a tetrameric protein. It was painful to work with > > this map since it is in P1 spacegroup, although 4-fold symmetry was > > already applied during map reconstruction. > > > > I noticed that people used MAPMAN to transform spacegroup, however, it > > seems not working for me. The map remained in P1 spacegroup afterwards. > > > > I used mtz file converted from .mrc and the tetrameric protein model as > > input and choose "run fft to generate simple map". I also specified > > "output map in ccp4 format to cover all atoms in pdb". In "infrequently > > used options", I input P4 in "generate map in spacegroup". Everything > > else was left as default. > > > > Any suggestions will be appreciated. > > > > Thanks! >
[ccp4bb]
Yes, that is what I have been doing. Build one subunit and assemble into tetramer before realspace refinement (with "ncs" constraints). I used tetramer for refinement because I want the distances between the inter subunits interaction partners to be considered. The problem is, whenever I want to make some manual adjustments of the model afterwards, I have to break it into monomer and repeat the whole process again. I assume if the map is in P4 spacegroup, I only need to modify one subunit of this protein and changes will be automatically applied to the other subunits. Am I right? Another question is, when I tried to refine my model using phenix realspace refinement (energy minimization and adp), the statistics generally become better (map CC, rotamer outlier etc), however, the ramachandron statistics become worse, with increase number of outliers (from below 1% to around 5%) and allowed (from several percent to 10-20%). Do you know what could be the cause? I know I am asking the right person... On Fri, May 19, 2017 at 12:33 AM, Pavel Afonine <pafon...@gmail.com> wrote: > Just use P1 and "ncs" constraints. What's the problem? Or just keep entire > map and have only symmetry independent copy to work with until finishes, > then make the whole molecule. For real-space refinement it's totally > irrelevant whether you have whole molecule or 1/Nth of it. So.. it isn't > clear what the problem is.. > Pavel > > On Thu, May 18, 2017 at 10:06 PM, Qingfeng Chen <che...@gmail.com> wrote: > >> Hi, >> >> I have an EM map of a tetrameric protein. It was painful to work with >> this map since it is in P1 spacegroup, although 4-fold symmetry was already >> applied during map reconstruction. >> >> I noticed that people used MAPMAN to transform spacegroup, however, it >> seems not working for me. The map remained in P1 spacegroup afterwards. >> >> I used mtz file converted from .mrc and the tetrameric protein model as >> input and choose "run fft to generate simple map". I also specified "output >> map in ccp4 format to cover all atoms in pdb". In "infrequently used >> options", I input P4 in "generate map in spacegroup". Everything else was >> left as default. >> >> Any suggestions will be appreciated. >> >> Thanks! >> > >
[ccp4bb]
Hi, I have an EM map of a tetrameric protein. It was painful to work with this map since it is in P1 spacegroup, although 4-fold symmetry was already applied during map reconstruction. I noticed that people used MAPMAN to transform spacegroup, however, it seems not working for me. The map remained in P1 spacegroup afterwards. I used mtz file converted from .mrc and the tetrameric protein model as input and choose "run fft to generate simple map". I also specified "output map in ccp4 format to cover all atoms in pdb". In "infrequently used options", I input P4 in "generate map in spacegroup". Everything else was left as default. Any suggestions will be appreciated. Thanks!
[ccp4bb] Use MAPMAN to transform spacegroup of an EM map from P1 to P4
Hi, I have an EM map of a tetrameric protein. It was painful to work with this map since it is in P1 spacegroup, although 4-fold symmetry was already applied during map reconstruction. I noticed that people used MAPMAN to transform spacegroup, however, it seems not working for me. The map remained in P1 spacegroup afterwards. I used mtz file converted from .mrc and the tetrameric protein model as input and choose "run fft to generate simple map". I also specified "output map in ccp4 format to cover all atoms in pdb". In "infrequently used options", I input P4 in "generate map in spacegroup". Everything else was left as default. Any suggestions will be appreciated. Thanks! QC
