From: Demirci, H. <Has...@br...> - 2007-10-07 13:18:49
|
Hi everyone, There is no documentation about customizing the isomesh of the electron = density maps. The ones that I generated are really thick and I have to say ugly. Is there any way to change isomesh thickness and make it look more = sleek? By the way someone posted something like increasing the isomesh density = by playing with fft infrequently used options but i couldn't manage to = make it work. thanks =20 Hasan Demirci Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 69 Brown Street Providence, RI 02912 (401) 863-3652 lab (401) 226-7852 cell Hasan_Demirci@Brown.edu |
From: DeLano S. <de...@de...> - 2007-10-07 15:59:01
|
Hasan, The "mesh_width" setting controls the thickness of the mesh in pixel units, or you can override that with "mesh_radius" to control the absolute mesh cylinder radius in Angstroms. set mesh_width, 0.5 ray set mesh_radius, 0.02 ray Note that the size of the window determines the size of a pixel (even if you render at a much higher resolution) -- PyMOL attempts to deliver WYSIWYG at displayed resolution. That may explain why you were getting a thicker mesh than you wanted. map_double map-name can be used to double the sampling density of an existing map. Cheers, DeLano Scientific LLC PS. As for: > There is no documentation about customizing the isomesh of the > electron density maps. That is not entirely true -- but only current project sponsors have access to all available PyMOL documentation. I believe you are a member of a sponsoring lab, so please see http://delsci.info/dsc/dokuwiki/doku.php?id=command:isomesh and http://delsci.info/dsc/dokuwiki/doku.php?id=setting:mesh after logging into http://delsci.info/dsc > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Demirci, Hasan > Sent: Sunday, October 07, 2007 6:19 AM > To: pym...@li... > Subject: [PyMOL] customized "sleek looking" isomesh > > Hi everyone, > There is no documentation about customizing the isomesh of the > electron density maps. > The ones that I generated are really thick and I have to say ugly. > Is there any way to change isomesh thickness and make it look more > sleek? > By the way someone posted something like increasing the isomesh > density by playing with fft infrequently used options but i couldn't > manage to make it work. > thanks > > Hasan Demirci > Department of Molecular Biology, Cellular Biology & Biochemistry Brown > University > 69 Brown Street > Providence, RI 02912 > > (401) 863-3652 lab > (401) 226-7852 cell > > Hasan_Demirci@Brown.edu > |
From: Roger R. <RRo...@ma...> - 2007-10-07 16:04:16
|
You can find documentation for displaying CCP4 maps in Pymol at = http://www.pymolwiki.org/index.php/Display_CCP4_Maps. Cheers, -- ------------------------------------------------------------------------ Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rro...@ma... -----Original Message----- From: pym...@li... on behalf of Demirci, = Hasan Sent: Sun 10/7/2007 9:18 AM To: pym...@li... Subject: [PyMOL] customized "sleek looking" isomesh =20 Hi everyone, There is no documentation about customizing the isomesh of the electron = density maps. The ones that I generated are really thick and I have to say ugly. Is there any way to change isomesh thickness and make it look more = sleek? By the way someone posted something like increasing the isomesh density = by playing with fft infrequently used options but i couldn't manage to = make it work. thanks =20 Hasan Demirci Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 69 Brown Street Providence, RI 02912 (401) 863-3652 lab (401) 226-7852 cell Hasan_Demirci@Brown.edu -------------------------------------------------------------------------= This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |