From: Richard <re...@co...> - 2006-08-06 02:33:16
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I just loaded a CCP4-format density map and am having a little trouble getting the map to cover the area of interest on the model. The displayed map covers the entire unit cell, but the model I am working with is located at the bottom corner with many of the atoms spilling over into neighboring unit cells. When I try to generate an isomesh around the residue of interest, nothing appears, because that residue is not in the main unit cell. I suppose I could generate lots of symmetry neighbors using symexp and delete the ones I don't want. Would be better if the isomesh automatically applied symmetry when extending outside the main unit cell. Perhaps I am overlooking some controls. Is there a better way to solve this problem? Richard Gillilan MacCHESS Cornell |
From: Jacob C. <jc...@be...> - 2006-08-06 03:31:10
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Hi Richard, Unfortunately, PyMOL will not do symmetry expansion. You could use ccp4s mapmask to extend an existing map around a molecule. An example script is below (BORDER is the number of angstroms around the input model to calculate the new map) mapmask \ XYZIN model.pdb \ MAPIN previous_map.map \ MAPOUT new_map.ccp4 \ << eof BORDER 5 end eof Jacob Richard wrote: > I just loaded a CCP4-format density map and am having a little > trouble getting the map to cover the area of interest on the model. > The displayed map covers the entire unit cell, but the model I am > working with is located at the bottom corner with many of the atoms > spilling over into neighboring unit cells. When I try to generate an > isomesh around the residue of interest, nothing appears, because that > residue is not in the main unit cell. I suppose I could generate lots > of symmetry neighbors using symexp and delete the ones I don't want. > Would be better if the isomesh automatically applied symmetry when > extending outside the main unit cell. Perhaps I am overlooking some > controls. Is there a better way to solve this problem? > > Richard Gillilan > MacCHESS > Cornell > > > > ------------------------------------------------------------------------- > 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: Richard G. <re...@co...> - 2006-08-09 19:36:33
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I have a couple of ribbons that come very close to exactly overlaying in places. This causes rendering artifacts (noise) that I suspect are due to the renderers (both hardware and software) having trouble telling which surface is on top. Things improve some when I make the clipping plane very narrow, but messy surface intersections persist. I could touch up the image with GIMP, but does anyone have a clever solution to this problem? Richard Gillilan MacCHESS Cornell |
From: <Mat...@im...> - 2006-08-09 20:45:58
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pym...@li... wrote on 08/09/2006 03:36:25 PM: > > I have a couple of ribbons that come very close to exactly overlaying > in places. This causes rendering artifacts (noise) that I suspect are > due to the renderers (both hardware and software) having trouble > telling which surface is on top. Things improve some when I make the > clipping plane very narrow, but messy surface intersections persist. > > I could touch up the image with GIMP, but does anyone have a clever > solution to this problem? > > > Richard Gillilan > MacCHESS > Cornell > > Hi Richard - How about making one ribbon thicker than the other, so there's no ambiguity about which is on top? You can set cartoon_rect_length and cartoon_rect_width for individual objects... In my experience, though, ambiguity about which surface is on top just produces mottled surfaces - one triangle of one color next to a triangle of the other color. Could you post a link to a picture of the artifacts? - 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. |