[PyMOL] slab mode fine-tuning
Dear pymol users, I am looking for a way to zoom in a molecule, like the slab mode when you are rolling the scroll wheel. The reason why rolling the scroll wheel does not work in my case is that the resulting change is too coarse grained, i.e. either I cannot see all the atoms I want to or there are some atoms in front of the part I am interested in. I tried as well clip slab, x, but then not just atoms in front of the interesting part are not shown but as well behind it. So, what I need is a cross-sectional view of my system, in which only everything in front of the cut is not shown (but everything behind). Thank's a lot for any help, Nadine Dr. Nadine Utz MMB - IRB Barcelona -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] slab mode fine-tuning
Nadine, Probably the command line is your best friend here. Look into the 'clip near,x' and 'clip far,x' command, which allows to move the front and back clipping planes in x increments. Positive values move towards you, negative values of x away from you. If that does not provide enough fine grained control you may want to think about making a composite picture to 'fake' clipping planes per object. Cheers, Carsten -Original Message- From: Nadine Utz [mailto:nad...@mmb.pcb.ub.es] Sent: Tuesday, March 29, 2011 6:12 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] slab mode fine-tuning Dear pymol users, I am looking for a way to zoom in a molecule, like the slab mode when you are rolling the scroll wheel. The reason why rolling the scroll wheel does not work in my case is that the resulting change is too coarse grained, i.e. either I cannot see all the atoms I want to or there are some atoms in front of the part I am interested in. I tried as well clip slab, x, but then not just atoms in front of the interesting part are not shown but as well behind it. So, what I need is a cross-sectional view of my system, in which only everything in front of the cut is not shown (but everything behind). Thank's a lot for any help, Nadine Dr. Nadine Utz MMB - IRB Barcelona --- --- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] slab mode fine-tuning
Hi, On Tue, 29 Mar 2011 6:12 AM Nadine Utz [mailto:nad...@mmb.pcb.ub.es] wrote: Dear pymol users, I am looking for a way to zoom in a molecule, like the slab mode when you are rolling the scroll wheel. The reason why rolling the scroll wheel does not work in my case is that the resulting change is too coarse grained, i.e. either I cannot see all the atoms I want to or there are some atoms in front of the part I am interested in. I tried as well clip slab, x, but then not just atoms in front of the interesting part are not shown but as well behind it. So, what I need is a cross-sectional view of my system, in which only everything in front of the cut is not shown (but everything behind). Thank's a lot for any help, On Tue, 29 Mar 2011 07:56:09 -0400 Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: Nadine, Probably the command line is your best friend here. Look into the 'clip near,x' and 'clip far,x' command, which allows to move the front and back clipping planes in x increments. Positive values move towards you, negative values of x away from you. If that does not provide enough fine grained control you may want to think about making a composite picture to 'fake' clipping planes per object. You can also control the front and rear clipping planes independently by holding down the Shift key along with the right mouse button (assuming you are in the standard 3-button viewing mode). Moving the mouse vertically changes the front clipping plane and moving it horizontally changes the rear clipping plane. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
