[PyMOL] Re: give unique chain identifiers

[Dr. D. J. W. P. <da...@ch...>]

Hi Warren,

OK, that works just as you say it does.

however, what I really need is each chain to have a unique chain=20
identifier in the pdb file written out.

I see there might be a problem here as there are 60 molecules, and only=20=

24 letters in the alphabet....
I actually only want to have 15 of them in my model, so we could get=20
round it that way, by deleting the ones I dont want....
but then how to give them unique pdb chain identifiers?

I want to load the 15 molecule model in Bodil to do my actual modelling.

cheers

Dan


On 6 Apr 2004, at 21:36, Warren DeLano wrote:

> Dan,
>
> 	That's the not expected result, but indeed you have a problem --
> each of those subunits will have identical atoms.  To resolve this,=20
> assign a
> unique segment identifier to each subunit:
>
> load 1c8e.pdb1, 1c8e
> split_states 1c8e
> delete 1c8e
> alter all, segi =3D model[-4:]
> rewind
> save test.pdb, all
>
> dele all
> load test.pdb
>
> The reason why you were getting a PDB file with just END is that you=20=

> didn't
> return the viewer ro frame/state 1 after moving all of the data to=20
> state 1.
>
> After the above, you'll now be able to address each subunit indepently=20=

> as:
>
> hide
> show ribbon
> color red, segi 0001
> zoom segi 0001
>
> http://delsci.com/img/1c8e-subunit.jpg
>
> Cheers,
> Warren
>
>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of
>> Dr. Daniel James White PhD
>> Sent: Tuesday, April 06, 2004 6:22 AM
>> To: pym...@li...
>> Subject: [PyMOL] save all not working for multiple objects
>> from split_states?
>>
>> Hi all,
>>
>> I opened a "biological unit" pdb file of a viral capsid
>> protein containing the 60 "states" or "models" making up the
>> whole viral capsid structure.
>>
>> I did
>> split_states
>> to get all 60 molecules as individual objects
>>
>> sweet!
>>
>> then I deleted the ones I didnt want, leaving 15 molecules
>> around one of the 5 fold symmetry axes.
>>
>> now I want to save these molecules to a pdb file.
>>
>> so I did
>>
>> save 5fold.pdb, all
>>
>> this gave no errors, but the pdb file written only contains
>>
>> END
>>
>> what am I doing wrong? I expect it is my simple mistake?
>>
>> cheers
>>
>> Dan
>>
>>
>> Dr. Daniel James White BSc. (Hons.) PhD
>> Cell Biology
>> Department of biological and environmental science PO Box  35
>> University of Jyv=E4skyl=E4 Jyv=E4skyl=E4 FIN 40014 Finland
>> +358 14 260 4183 (work)
>> +358 468102840 (new mobile)
>> NEW PHONE NUMBER!!!
>>
>> http://www.chalkie.org.uk
>> da...@ch...
>> wh...@cc...
>>
>>
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>
>
Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology
Department of biological and environmental science
PO Box  35
University of Jyv=E4skyl=E4
Jyv=E4skyl=E4 FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
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