[Chimera-users] saving several pdb files in one

[Dieter Blaas]

Hi Elaine and Eric,

  thanks a lot! Will Eric's suggestion handle thus many atoms? BTW: I 
could load all pdbs but moving them together is somewhat slow and 
tedious. Is there a way of handling them as one? I might then even use 
fit-in-map!

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
------------------------------------------------------------------------

On 18.02.2021 18:15, Eric Pettersen wrote:
> If you include at least one valid HELIX or SHEET record in your combined PDB file, then Chimera will think that secondary structure has been assigned and will not try to compute it itself.
>
> --Eric
>
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>
>
>> On Feb 18, 2021, at 9:08 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>
>> Hi Dieter,
>> I don't have any great ideas other than using zone like you said.  The program wasn't designed for this situation!   My only other ideas:
>>
>> (A) make a molmap (see "molmap" command) from all of those atoms, then adjust the molmap display threshold to where you want it, and then use the molmap surface to mask the original density map of interest.  However, that would no longer be a precise distance from all of the atom centers, because making a molmap "smears" them out and there will be additive effects from clumps of atoms. Also I don't know if creating the molmap from all those atoms would be slow or not.  Molmap command:
>> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
>>
>> (B) change the combined PDB file of atoms into a giant Chimera marker file instead to avoid chemical perception when it is read.  However, that would be a lot of work and I can't think of a way to make Chimera do the format conversion for you.  Marker files:
>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>> 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
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users