RE: [PyMOL] displaying protein with propeptide

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

Anne,

> "select resi  1P-5P" still gives me both 1-5 and 1P-5P.
> However, "select resi 1P+2P+3P+4P+5P" gives me what I want. =20

Say you have residues 36, 37A, 37B, and 38, and you tell PyMOL you wish =
to select residues in the range 36-38.  Naturally, you'd want 37A and =
37B included in that.  It is this behavior that gives rise to the =
selection behavior you've noted above, wherein residue insertion codes =
are effectively ignored inside numerical ranges. =20

In PyMOL, ranges are defined numerically for reasons of performance.  =
Defining them based on peptide connectivity would be orders of magnitude =
slower.  Defining them based on their input file order could give okay =
performance, but the concept of input order is not always valid given =
that molecules are graphs not lists.

I agree though, that it would be nice to equip PyMOL with these =
alternate ranging concepts -- ideas for the future.

Fortunately, there is another workaround:  segment identifiers.  With =
wildcard selection in PyMOL beta builds, you can do something like this:

alter resi *B, segi=3D'SEG1'
alter not resi *B, segi=3D'SEG2'

Now you could use ranges without trouble, leaving your chain IDs =
unperturbed.

select segi SEG1 and resi 1-5

or more concisely:

select SEG1//1-5/

as distinct from

select SEG2//1-5/

> but many PDB files have insertions which are numbered with "A"s and =
"B"s after the residue number,

As for insertion codes that appear at the proper location in sequence =
(NOT the case with pathological PDB 1cs8), recent PyMOL betas handle =
such situations automatically and will draw connected cartoons.=20

Cheers,
Warren

Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Anne M=F8lgaard
> Sent: Friday, November 18, 2005 12:47 AM
> To: pym...@li...
> Subject: RE: [PyMOL] displaying protein with propeptide
>=20
> Thanks for the comments. The "retain_order" setting solves=20
> the problem with cartoons and ribbons, but there is still a=20
> small problem with selection of these residues. "select resi=20
> 1P-5P" still gives me both 1-5 and 1P-5P.
> However, "select resi 1P+2P+3P+4P+5P" gives me what I want. =20
>=20
> I don't really want to change the chain ID in the PDB file.=20
> It makes sort of sense in the case of a propeptide (although=20
> it is covalently linked to the mature protein, so it is=20
> really only one chain), but many PDB files have insertions=20
> which are numbered with "A"s and "B"s after the residue=20
> number, and in those cases it really doesn't make sense to=20
> change the chain ID. For an example, see 1cgh below.=20
>=20
> Thanks for your help!
>=20
> - Anne
>=20
> ATOM    213  OE1 GLN A  36       8.532  36.321  21.186  0.00 25.64
> O =20
> ATOM    214  NE2 GLN A  36       7.727  36.504  19.104  0.00 25.95
> N =20
> ATOM    215  H   GLN A  36       8.523  31.138  18.943  0.00 20.00
> H =20
> ATOM    216 1HE2 GLN A  36       7.711  37.475  19.199  0.00 20.00
> H =20
> ATOM    217 2HE2 GLN A  36       7.446  36.036  18.288  0.00 20.00
> H =20
> ATOM    218  N   SER A  36A      4.622  31.686  20.477  0.00 27.20
> N =20
> ATOM    219  CA  SER A  36A      3.235  31.238  20.479  0.00 28.70
> C =20
> ATOM    220  C   SER A  36A      2.315  32.417  20.162  0.00 29.65
> C =20
> ATOM    221  O   SER A  36A      2.664  33.569  20.429  0.00 30.07
> O =20
> ATOM    222  CB  SER A  36A      2.878  30.647  21.845  0.00 28.71
> C =20
> ATOM    223  OG  SER A  36A      3.565  29.428  22.077  0.00 29.15
> O =20
> ATOM    224  H   SER A  36A      5.000  32.029  21.306  0.00 20.00
> H =20
> ATOM    225  HG  SER A  36A      4.526  29.487  22.051  0.00 20.00
> H =20
> ATOM    226  N   PRO A  36B      1.124  32.146  19.598  0.00 30.41
> N =20
> ATOM    227  CA  PRO A  36B      0.593  30.825  19.240  0.00 31.02
> C =20
> ATOM    228  C   PRO A  36B      1.323  30.182  18.061  0.00 31.62
> C =20
> ATOM    229  O   PRO A  36B      2.169  30.814  17.426  0.00 31.58
> O =20
> ATOM    230  CB  PRO A  36B     -0.867  31.125  18.914  0.00 30.83
> C =20
> ATOM    231  CG  PRO A  36B     -0.789  32.492  18.316  0.00 30.95
> C =20
> ATOM    232  CD  PRO A  36B      0.147  33.200  19.269  0.00 30.41
> C =20
> ATOM    233  N   ALA A  37       0.991  28.925  17.777  0.00 32.51
> N =20
> ATOM    234  CA  ALA A  37       1.608  28.191  16.677  0.00 33.56
> C =20
>=20
> --------------------------------------------
> Anne M=F8lgaard, Ph.D.
> Center for Biological Sequence Analysis
> BioCentrum-DTU, Building 208
> DK-2800 Lyngby
>=20
> Email:  an...@cb...
> Phone:  (+45)4525 2472
> --------------------------------------------=20
>=20
> -----Original Message-----
> From: Warren DeLano [mailto:wa...@de...]
> Sent: 18. november 2005 02:28
> To: Joel Tyndall; Anne M=F8lgaard; pym...@li...
> Subject: RE: [PyMOL] displaying protein with propeptide
>=20
> A quick fix is to use the "retain_order" setting.
>=20
> set retain_order
>=20
> which will force PyMOL to honor the order of ATOMs in the PDB=20
> file over the numeric ordering of residue identifiers.
>=20
> Cheers,
> Warren
>=20
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist
>=20
> . DeLano Scientific LLC =20
> . 400 Oyster Point Blvd., Suite 213          =20
> . South San Francisco, CA 94080 USA  =20
> . Biz:(650)-872-0942  Tech:(650)-872-0834    =20
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...     =20
> =20
>=20
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of Joel=20
> > Tyndall
> > Sent: Thursday, November 17, 2005 12:15 PM
> > To: Anne M=F8lgaard; pym...@li...
> > Subject: Re: [PyMOL] displaying protein with propeptide
> >=20
> > Hi Ann,
> >=20
> > I would change the chain id of the propeptide in a text=20
> editor, to say=20
> > P and remove the P from after the residue numbers.
> >=20
> > J
> >=20
> > Anne M=F8lgaard wrote:
> >=20
> > >Hi,
> > >
> > >I am having problems displaying proteins with unusual residue=20
> > >numbering, such as proteins with propeptides. An example is
> > 1cs8, which
> > >starts off like
> > >this:
> > >
> > >ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
> > >N =20
> > >ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
> > >C =20
> > >ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
> > >C =20
> > >ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
> > >O =20
> > >ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
> > >C =20
> > >ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
> > >O
> > >.
> > >.
> > >.
> > >And later on comes the sequence corresponding to the=20
> mature protein:
> > >
> > >ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
> > >N =20
> > >ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
> > >C =20
> > >ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
> > >C =20
> > >ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
> > >O =20
> > >ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
> > >C
> > >Etc.=20
> > >
> > >If I open 1cs8 with PyMol, I can see everything in the "lines",=20
> > >"sticks" and "surface" representation, but in ribbon or=20
> cartoon mode=20
> > >only part of the protein is shown. What do I have to do to
> > show the whole sequence?
> > >
> > >How do I select residues with a "P" appended to the residue
> > number? If
> > >I say "select resi 1P-5P" I get both 1P-5P and 1-5.
> > >
> > >Any help will be appreciated! (I am using PyMol version 0.98
> > for Windows).
> > >
> > >- Anne
> > >
> > >--------------------------------------------
> > >Anne M=F8lgaard, Ph.D.
> > >Center for Biological Sequence Analysis BioCentrum-DTU,=20
> Building 208=20
> > >DK-2800 Lyngby
> > >
> > >Email:  an...@cb...
> > >Phone:  (+45)4525 2472
> > >--------------------------------------------
> > >
> > >
> > >
> > >
> > >-------------------------------------------------------
> > >This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today=20
> > >Register for a JBoss Training Course.  Free Certification Exam for=20
> > >All Training Attendees Through End of 2005. For more info visit:
> > >http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick
> > >_______________________________________________
> > >PyMOL-users mailing list
> > >PyM...@li...
> > >https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >
> > > =20
> > >
> >=20
> > --
> > Joel Tyndall, PhD
> >=20
> > Lecturer
> > National School of Pharmacy
> > University of Otago
> > PO Box 913 Dunedin
> > New Zealand                    =20
> >=20
> > Pukenga
> > Te Kura Taiwhanga Putaiao
> > Te Whare Wananga o Otago
> > Pouaka Poutapeta 913 Otepoti
> > Aotearoa
> >=20
> > Ph / Waea               +64 3 4797293=20
> > Fax / Waeawhakaahua     +64 3 4797034
> >=20
> >=20
> >=20
> >=20
> >=20
> > -------------------------------------------------------
> > This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today=20
> > Register for a JBoss Training Course.  Free Certification=20
> Exam for All=20
> > Training Attendees Through End of 2005. For more info visit:
> > http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >=20
> >=20
> >=20
> >=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today Register for a JBoss Training Course.  Free=20
> Certification Exam for All Training Attendees Through End of=20
> 2005. For more info visit:
> http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] displaying protein with propeptide

PyMOL is an OpenGL based molecular visualization system

RE: [PyMOL] displaying protein with propeptide