Dan,
First, get down to 26 or fewer objects, then issue the following commands:
objs = cmd.get_names('objects')
pairs = map(None, objs, range(65, 65+len(objs))
for pair in pairs: \
cmd.alter(pair[0], "chain='%s'"%chr(pair[1]))
NOTE: That last comment will take a little while...
Cheers,
Warren
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Dr. Daniel James White PhD
> Sent: Wednesday, April 14, 2004 7:47 AM
> To: Warren DeLano
> Cc: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Re: give unique chain identifiers
>
> Hi Warren,
>
> OK, that works just as you say it does.
>
> however, what I really need is each chain to have a unique
> chain identifier in the pdb file written out.
>
> I see there might be a problem here as there are 60
> molecules, and only
> 24 letters in the alphabet....
> I actually only want to have 15 of them in my model, so we
> could get 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, assign
> > a unique segment identifier to each subunit:
> >
> > load 1c8e.pdb1, 1c8e
> > split_states 1c8e
> > delete 1c8e
> > alter all, segi = 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
> > didn't return the viewer ro frame/state 1 after moving all
> of the data
> > to state 1.
> >
> > After the above, you'll now be able to address each subunit
> indepently
> > as:
> >
> > hide
> > show ribbon
> > color red, segi 0001
> > zoom segi 0001
> >
> > http://delsci.com/img/1c8e-subunit.jpg
> >
> > Cheers,
> > Warren
> >
> >
> >> -----Original Message-----
> >> From: pymol-users-ad...@lists.sourceforge.net
> >> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dr.
> >> Daniel James White PhD
> >> Sent: Tuesday, April 06, 2004 6:22 AM
> >> To: pymol-users@lists.sourceforge.net
> >> 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
> >> Jyväskylä Jyväskylä FIN 40014 Finland
> >> +358 14 260 4183 (work)
> >> +358 468102840 (new mobile)
> >> NEW PHONE NUMBER!!!
> >>
> >> http://www.chalkie.org.uk
> >> d...@chalkie.org.uk
> >> wh...@cc.jyu.fi
> >>
> >>
> >> -------------------------------------------------------
> >> This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux
> >> tutorial presented by Daniel Robbins, President and CEO of GenToo
> >> technologies. Learn everything from fundamentals to system
> >> administration.http://ads.osdn.com/?ad_id70&alloc_id638&op=ick
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyMOL-users@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>
> >
> >
> >
> Dr. Daniel James White BSc. (Hons.) PhD
> Cell Biology
> Department of biological and environmental science PO Box 35
> University of Jyväskylä Jyväskylä FIN 40014 Finland
> +358 14 260 4183 (work)
> +358 468102840 (new mobile)
> NEW PHONE NUMBER!!!
>
> http://www.chalkie.org.uk
> d...@chalkie.org.uk
> wh...@cc.jyu.fi
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials Free
> Linux tutorial presented by Daniel Robbins, President and CEO
> of GenToo technologies. Learn everything from fundamentals to
> system administration.http://ads.osdn.com/?ad_id70&alloc_id638&op=ick
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
