[Chimera-users] saving several pdb files in one

[Tom Goddard]

Hi Dieter,

Ok, I am surprised it is slow, 100 atomic models of 1000 atoms each is only 100,000 atoms and that is not a lot -- single structures like ribosomes are larger and move just fine.  Maybe Chimera is somehow inefficient moving so many models.  If you have something selected Chimera can be slow because drawing the selection outline is slow.

To fit them all as a rigid group in the map just select them all and use the Fit in Map tool with the Fit "selected atoms".

ChimeraX our newer program is better at handling large models.

	Tom

> On Feb 18, 2021, at 10:06 AM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> 
> Hi Tom,
> 
>    this is surely possible but very slow to move them all together. Furthermore, I am wondering how I might be able to finally fit the entire ensemble into the map!
> 
> bw Dieter
> 
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Mobile: 0043 699 1942 1659
> e-mail: dieter.blaas at meduniwien.ac.at
> ------------------------------------------------------------------------
> 
> On 18.02.2021 19:03, Tom Goddard wrote:
>> Hi Dieter,
>> 
>>   What is difficult with 100 coordinate files?  Don't you just inactivate the map and the 100 models as a group and then use the vop zone command?
>> 
>> 	Tom
>> 
>> 
>>> On Feb 18, 2021, at 7:05 AM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
>>> 
>>> Dear Elaine and all,
>>> 
>>>    I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so?
>>> 
>>> Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates!
>>> 
>>> I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess....
>>> 
>>> Is there an easy way of doing so?
>>> 
>>> Thanks, best, Dieter
>>> 
>>> ------------------------------------------------------------------------
>>> Dieter Blaas,
>>> Max Perutz Laboratories
>>> Medical University of Vienna,
>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>> Dr. Bohr Gasse 9/3,
>>> A-1030 Vienna, Austria,
>>> Tel: 0043 1 4277 61630,
>>> Mobile: 0043 699 1942 1659
>>> e-mail:dieter.blaas at meduniwien.ac.at
>>> ------------------------------------------------------------------------
>>> 
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>