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Re: [PyMOL] Missing parts in cartoon mode
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From: <ran...@ic...> - 2005-10-19 15:08:37
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Well ill be d......! The .pse file you send me shows the loops just fine. I=B4m still puzzled as to why PyMol 0.98 on win2000 fails to show those loops but now I can just use your .pse file as a template and work my way around it. Ill also try upgrading as Warren suggest. Anyways, thanks a lot for the help, it is greatly appreciated! =20 Cheers=20 kasper <-----Original Message-----> From: Joel Tyndall Sent: 10/18/2005 10:17:30 PM To: ran...@ic... Subject: Re: [PyMOL] Missing parts in cartoon mode=20 Hi again,=20 Hmmm had a look and it looks fine to me. I'm assuming you're looking at=20 chain H. See if you can open this pse file which is displaying the=20 cartoon. The only strange thing is that there is no residue 218. sorry I can't be of any more help. might be worth sending Warren/me a pse of the problem?=20 See ya=20 J=20 PS thats a windows pse file and should work=20 ran...@ic... wrote:=20 > Hi Joel=20 > The two missing loops of the 1DAN structure when in cartoon mode are=20 > located to res. 183-189 and 220-220. I=B4m using a standard PC with=20 > Windows 2000.=20 > Any suggestions? A fellow collegue in my lab is having identical=20 > troubles but he=B4s also using a PC with win2000. Its quite = frustrating=20 > because the rest of the structure looks great in PyMol!=20 >=20 > Cheers Kasper=20 > The two missing loops of the 1DAN structure when in cartoon mode are=20 > located to res. 183-189 and 220-220. I=B4m using a standard PC with=20 > Windows 2000.=20 > Any suggestions? A fellow collegue in my lab is having identical=20 > troubles but he=B4s also using a PC with win2000. Its quite = frustrating=20 > because the rest of the structure looks great in PyMol!=20 >=20 > Cheers Kasper=20 >=20 >=20 > <-----Original Message----->=20 > *From: Joel Tyndall*=20 > Sent: 10/17/2005 12:07:00 AM=20 > To: ran...@ic...=20 > Subject: Re: [PyMOL] Missing parts in cartoon mode=20 >=20 > Hey Kasper,=20 >=20 > which loops can't you see (amino acid nos./chain/)? what OS are you on > (OSX, PC, Linux?) I have had a look and it looks ok on windows=20 >=20 > Cheers=20 >=20 > J=20 >=20 > ran...@ic... wrote:=20 >=20 > > Hi everybody=20 > > I am getting quite desperate! For some strange reason PyMol do not=20 > > display certain areas (several loops) of my .pdb file (1DAN) when in > > cartoon display mode. When I display the structure in "lines" or=20 > > "sticks" everything is ok. Other pdb-viewers dont have this problem=20 > > with the same .pdb file. I have tried several things:=20 > > 1. Upgraded to the newest version og PyMol.=20 > > 2. Redefined secondary structure using the "alter" command.=20 > > 3. Imported the .pdb file into SwissViewer, saved as the imported=20 > > structure as a .pdb file, and then imported into PyMOl.=20 > >=20 > > None of these things have solved the problem. Help please! (I would=20 > > hate to have to start using another pdb-viewer!!) Cheers Kasper=20 > >=20 > > _______________________________________________________________=20 > > ICQ - You get the message, anywhere!=20 > > Get it @ http://www.icq.com=20 > >=20 > >=20 > >=20 >=20 > --=20 > Joel Tyndall, PhD=20 >=20 > Lecturer=20 > National School of Pharmacy=20 > University of Otago=20 > PO Box 913 Dunedin=20 > NNew Zealand=20 >=20 > Pukenga=20 > Te Kura Taiwhanga Putaiao=20 > Te Whare Wananga o Otago=20 > Pouaka Poutapeta 913 Otepoti=20 > Aotearoa=20 >=20 > Ph / Waea +64 3 4797293=20 > Fax / Waeawhakaahua +64 3 4797034=20 >=20 >=20 > .=20 >=20 > _______________________________________________________________=20 > ICQ - You get the message, anywhere!=20 > Get it @ http://www.icq.com=20 >=20 >=20 >=20 --=20 Joel Tyndall, PhD=20 Lecturer=20 National School of Pharmacy=20 University of Otago=20 PO Box 913 Dunedin=20 New Zealand=20 Pukenga=20 Te Kura Taiwhanga Putaiao=20 Te Whare Wananga o Otago=20 Pouaka Poutapeta 913 Otepoti=20 Aotearoa=20 Ph / Waea +64 3 4797293=20 Fax / Waeawhakaahua +64 3 4797034=20 =09 <P><font face="Arial, Helvetica, sans-serif" size="2" style="font-size:13.5px">_______________________________________________________________<BR><font face="Arial, Helvetica, sans-serif" size="2" style="font-size:13.5px">ICQ - You get the message, anywhere!<br>Get it @ <a href="http://www.icq.com" target=new>http://www.icq.com</a></font><br><br> </font></font> |
