From: Geng T. <gen...@ho...> - 2006-04-18 20:30:00
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Hi, Noinaj: Thanks for your suggestion. I feel it is not the assignment problem. I tried using "cartoon tube" to show the 2nd structure and the strand part can showed up. Then I painted the molecule according to the secondary structure by using util.cbss("morphy_01","red","yellow","green") and the strand is color as "yellow" correctly in the cartoon tube mode. Then I tried another thing, I copy-pasted the second structure information from the ca trace pdb to my formal all stoms pdb, the strand showed up correctly. This means these information are correct. So I guess under the default "cartoon automatic" mode, pymol can't draw arrow for the strand residues which do not have the coordinates of N, C, O written in the PDB file. This might be a default setting of pymol I can't find to turn off or just an internal problem for "cartoon automatic" mode. Thank you again. Tiger >From: "Noinaj" <no...@uk...> >To: "Geng Tian" <gen...@ho...>,<pym...@li...> >Subject: Re: [PyMOL] another question about ca trace model. >Date: Tue, 18 Apr 2006 11:06:49 -0400 > >Tiger, > >Unfortunately I don't have much experience with this procedure. But one >thing came to mind, you can manually assign secondary structure within >DEEPVIEW/SWISS PDB Viewer [EDIT]. Not sure how many pdb files you have >generated for the morph, but if nothing else works, you could try manually >assigning secondary structures and see how that works out. Yep, a huge >pain in the buttocks I know, but it should work, in theory. > >Best of Luck. > > >Cheers, >Nick > > > >----- Original Message ----- From: "Geng Tian" <gen...@ho...> >To: <pym...@li...> >Sent: Tuesday, April 18, 2006 6:24 AM >Subject: [PyMOL] another question about ca trace model. > > >>Hi, there: >>I am trying to make a movie following the intruction at >>http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html >>From Lsqman, I got a serial of PDB files morphing between two >>conformations. These PDB files contain only alpha carbon and non-hydrogen >>side-chain atoms. Then I used DSSP to include the secondary structure >>information ito the PDB files. In the pymol, after set cartoon_trace, 1 >>the helix and loop showed up nicely. But all the strands are missing. I >>tried several setting about cartoon but just can't get them out. Do you >>have any idea how to solve this problem. >>Thank you. >>Tiger >> >>_________________________________________________________________ >>Express yourself instantly with MSN Messenger! Download today - it's FREE! >>http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ >> >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by xPML, a groundbreaking scripting >>language >>that extends applications into web and mobile media. Attend the live >>webcast >>and join the prime developer group breaking into this new coding >>territory! >>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 >>_______________________________________________ >>PyMOL-users mailing list >>PyM...@li... >>https://lists.sourceforge.net/lists/listinfo/pymol-users >> > > > >------------------------------------------------------- >This SF.Net email is sponsored by xPML, a groundbreaking scripting language >that extends applications into web and mobile media. Attend the live >webcast >and join the prime developer group breaking into this new coding territory! >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >https://lists.sourceforge.net/lists/listinfo/pymol-users _________________________________________________________________ On the road to retirement? Check out MSN Life Events for advice on how to get there! http://lifeevents.msn.com/category.aspx?cid=Retirement |