Re: [PyMOL] displaying protein with propeptide

[Eric Z. <zo...@ca...>]

Is there a similar command to force PyMOL to use only CONECT lines in=20
the pdb file instead of generating connectivity by distance?

Eric

Warren DeLano wrote:
> 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 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
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>>-----Original Message-----
>>From: pym...@li...=20
>>[mailto:pym...@li...] On Behalf Of=20
>>Joel Tyndall
>>Sent: Thursday, November 17, 2005 12:15 PM
>>To: Anne M=F8lgaard; pym...@li...
>>Subject: Re: [PyMOL] displaying protein with propeptide
>>
>>Hi Ann,
>>
>>I would change the chain id of the propeptide in a text=20
>>editor, to say P and remove the P from after the residue numbers.
>>
>>J
>>
>>Anne M=F8lgaard wrote:
>>
>>
>>>Hi,
>>>
>>>I am having problems displaying proteins with unusual residue=20
>>>numbering, such as proteins with propeptides. An example is=20
>>
>>1cs8, which=20
>>
>>>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 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 cartoon mode=20
>>>only part of the protein is shown. What do I have to do to=20
>>
>>show the whole sequence?
>>
>>>How do I select residues with a "P" appended to the residue=20
>>
>>number? If=20
>>
>>>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=20
>>
>>for Windows).
>>
>>>- Anne
>>>
>>>--------------------------------------------
>>>Anne M=F8lgaard, Ph.D.
>>>Center for Biological Sequence Analysis BioCentrum-DTU, Building 208=20
>>>DK-2800 Lyngby
>>>
>>>Email:  an...@cb...
>>>Phone:  (+45)4525 2472
>>>--------------------------------------------
>>>
>>>
>>>
>>>
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>>>
>>
>>--=20
>>Joel Tyndall, PhD
>>
>>Lecturer
>>National School of Pharmacy
>>University of Otago
>>PO Box 913 Dunedin
>>New Zealand                    =20
>>
>>Pukenga
>>Te Kura Taiwhanga Putaiao
>>Te Whare Wananga o Otago
>>Pouaka Poutapeta 913 Otepoti
>>Aotearoa
>>
>>Ph / Waea               +64 3 4797293=20
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>>
>>
>>
>>
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