From: Paul W. E. <pa...@un...> - 2006-09-20 07:00:24
|
Hi, please have a look at this image: http://pwe.no-ip.org/other/1.png I'm having trouble with the edge of a surface selection. It seems that there is always some more surface shown than the selected part. What I did is, that I selected the red part to show the surface in obj1 and to hide the surface in obj2 which is grey. obj1 and obj2 are copies of each other. I hoped that this would show a sharp border red/grey as I want to change the transparency in obj2 (grey) to fade out. How do I get pymol to show sharp borders and have no overlapping (dotted) parts as in the image? Paul |
From: Robert I. <imm...@gm...> - 2006-09-20 11:28:05
|
Paul, I think the reason the surface coloring "spills over" is because there are some surface triangles that are shared by the selection you want (red) and the neighboring residues (grey)... So it should work if you only use one selection, by saying something like: load my_protein.pdb, show surface, color grey, color red, (something at the center of the pocket) expand 8 Hope this helps, -bob On 9/20/06, Paul Wilhelm Elsinghorst <pa...@un...> wrote: > Hi, > > > please have a look at this image: http://pwe.no-ip.org/other/1.png > > > I'm having trouble with the edge of a surface selection. It seems that > there is always some more surface shown than the selected part. What I > did is, that I selected the red part to show the surface in obj1 and to > hide the surface in obj2 which is grey. obj1 and obj2 are copies of each > other. I hoped that this would show a sharp border red/grey as I want to > change the transparency in obj2 (grey) to fade out. > > > How do I get pymol to show sharp borders and have no overlapping > (dotted) parts as in the image? > > > Paul > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: <Mat...@im...> - 2006-09-20 15:39:07
|
pym...@li... wrote on 09/20/2006 07:28:00 AM: > Paul, > > I think the reason the surface coloring "spills over" is because > there are some surface triangles that are shared by the selection you > want (red) and the neighboring residues (grey)... So it should work > if you only use one selection, by saying something like: > load my_protein.pdb, > show surface, > color grey, > color red, (something at the center of the pocket) expand 8 > > Hope this helps, > > -bob > I think this is the right approach. If you invert the selection for the other surface, you should be able to avoid having triangles in both surfaces. Like this: load my_protein.pdb create pocket, chain a create rest_of_protein, chain a color red, pocket color gray, rest_of_protein show surface, pocket and resi 10-15 show surface, rest_of_protein and not(resi 10-15) set transparency=0.5, rest_of_protein This gave a sharp edge when I just tried it. If you don't like the jagged look of the edge, try changing the color statements above, to color gray, pocket color red, pocket and resi 10-15 color gray, rest_of_protein Now your red triangles will fade into the semi-transparent gray surface. Hope that helps, Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. |
From: Jason T M. <jm...@bi...> - 2006-09-20 13:36:45
|
I believe that you need to make these new objects to correct the problem, at least this is a quick fix that I have done in the past. There may be a more elegant solution: load my.pdb, obj1 load my.pdb, obj2 [whatever to each obj] When loaded separately you don't have this problem. Cheers, JTM "We can be sure that if a detailed understanding of the molecular basis of chemo-therapeutic activity were to be obtained, the advance of medicine would be greatly accelerated." Linus Pauling, Nobel Laureate 1954 "...everything that living things do can be understood in terms of the jigglings and wigglings of atoms." Richard Feynman, Nobel Laureate 1965 **************************************** Jason Thomas Maynes, MD/PhD Department of Biochemistry and Molecular Biophysics Resident in Anaesthesia and Paediatrics Faculty of Medicine Washington University in St. Louis jm...@bi... **************************************** > Paul, > > I think the reason the surface coloring "spills over" is because > there are some surface triangles that are shared by the selection you > want (red) and the neighboring residues (grey)... So it should work > if you only use one selection, by saying something like: > load my_protein.pdb, > show surface, > color grey, > color red, (something at the center of the pocket) expand 8 > > Hope this helps, > > -bob > > On 9/20/06, Paul Wilhelm Elsinghorst <pa...@un...> wrote: >> Hi, >> >> >> please have a look at this image: http://pwe.no-ip.org/other/1.png >> >> >> I'm having trouble with the edge of a surface selection. It seems that >> there is always some more surface shown than the selected part. What I >> did is, that I selected the red part to show the surface in obj1 and to >> hide the surface in obj2 which is grey. obj1 and obj2 are copies of each >> other. I hoped that this would show a sharp border red/grey as I want to >> change the transparency in obj2 (grey) to fade out. >> >> >> How do I get pymol to show sharp borders and have no overlapping >> (dotted) parts as in the image? >> >> >> Paul >> >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share >> your >> opinions on IT & business topics through brief surveys -- and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |