Re: [PyMOL] Electron density maps
Hi Sree, After your map is loaded click: Wizard Density. The map will replicate according to the symmetry operators. Cheers, -- Jason On Thu, Dec 1, 2011 at 12:53 PM, SREEJESH SHANKER sreejes...@gmail.com wrote: Hi I am having trouble to generate an electron density map (2FoFc) around some selected residues and metal ion ligand. I have data as MTZfile which I use to generate my map using FFT in ccp4i then further add a .ccp4 extension for pymol to read. Then I give the map double command select the residues and Ion and use the isomesh command with 1.0sigma and 1.8 radius. The result I get is a very crappy broken map in the vicinity of the selected residues but not exactly surrounding it. I can see the map fitting nicely in coot. Any help is highly appreciated. Regards Sree -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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] electron density maps
On Sun, 08 Aug 2004 17:57:00 -0400, christopher faehnle funne...@hotmail.com wrote: I am a new pymol user and am trying to load an electron density map (ccp4 format). When I do this nothing happens. Any suggestions, tips, etc would be appreciated. The map probably loads just fine (there should be a new object showing up on the right side panel), but it's doesn't show anything you can see, it simply reads the map to memory. To actual create a representation of the map do something like isomesh meshname,mapname So if for example you had a ccp4 map called foo.ccp4, when you load it, it will create a foo object. To get the mesh simply do: isomesh mesh,foo If this is not the problem, then please describe pymol version/platform and give an example map where it doesn't work. Filipe -- Using M2, Opera's revolutionary e-mail client: http://www.opera.com/m2/
RE: [PyMOL] electron density maps
Scott, isomesh msh1, map1, 1.5, myobject, carve=2.1 The postfix carve=2.1 will trim density which is more than 2.1 A from myobject. You may want to play around with the exact cutoff... Cheers, Warren -Original Message- From: Scott Classen [mailto:clas...@uclink.berkeley.edu] Sent: Friday, September 20, 2002 3:11 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] electron density maps Hello fellow PyMOL users, I am trying to display a ccp4 map over just a ligand. I have successfully read in the map and displayed it around the ligand with: isomesh msh1, map1, 1.5, myobject but the map has bits and peices of the surrounding sidechains. Is there a way to only display the map around my ligand? Thanks, Scott == Scott Classen clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular Cell Biology 229 Stanley Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 == --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
