Hi Jason, if I use the program Chimera it directly situates the volume correctly in relation to the protein, therefore the position information must be somewhere in the MRC file. I have to admit that my pymol knowledge is not good enough to move the volume manually, I mean from Voss Volume Voxelator you get the COM coordinates of the volume in relation to the proteins origine. This could help?
If this is too complicated I will just use Chimera for this application. Again thanks alot, Max On 2012/01/07, at 2:30, Jason Vertrees wrote: > Maximilian, > >> First of all thanks for the answer. I was able to load the MRC file and get >> the surface representation of the volume in pymol. However, the position >> relative to the pdb enzyme structure is not correct anymore. The center of >> the map seems to be located now at the coordinates 0,0,0 instead. Do you >> have any idea how to fix that? In addition, would there be a possibility to >> smoothen such a surface? I tried to follow this >> http://www.pymolwiki.org/index.php/Surface but had little success. > > I'm glad you got the data into PyMOL. You should be able to either > symmetry-expand (http://www.pymolwiki.org/index.php/Symexp) the > protein into the map, or you should be able to move the volume onto > the protein (if you know the 3D offset) I think using transform_object > or similar. I'll look into this. Actually, you could also translate > the protein to the origin using a PyMOL script > (http://www.pymolwiki.org/index.php/Com). > > I think you can smooth the surface, but it might be tedious. Start > here: > http://www.pymolwiki.org/index.php/Surface#Smooth_surface_accurate_.28blob.29. > I'll look into this as well. Also, please do not forget you can use > volume rendering in PyMOL too (http://pymol.org/volume; make sure you > look at the images and movies). > > Also, when seeking answers, it's always best to CC the pymol-users > list. Many times they'll come up with a quick and succinct answer. > > Cheers, > > -- Jason > > >> On 2012/01/06, at 16:21, Jason Vertrees wrote: >> >>> Hi Maximillian, >>> >>>> I am using the webtool http://3vee.molmovdb.org/index.php. The density map >>>> is in a file format called MRC (I guess it is re-formated by the webtool in >>>> a MRC file compatible to pymol at least this is what it says), which if I >>>> understand it correctly is a similar file format as CCP4. However, I can't >>>> isomesh the map. Does anybody knows how to compute MRC files from voss >>> >>> >>> I just tried this and the volumes look great. This looks like a really >>> useful web-based tool. Here's how to do it. >>> >>> Download their file and decompress it: gunzip yourFile.mrc.gz. Then >>> load it into PyMOL as: >>> >>> load yourFile.mrc, format=ccp4 >>> >>> The map data are most likely not a normal distribution, so I suggest >>> unsetting normalize_ccp4_maps, before loading: >>> >>> unset normalize_ccp4_maps >>> >>> At this point, the idea of a map "level" is no longer valid (since the >>> maps are not normalized). But, that's the only way to change the >>> representation, so use the 'isolevel' command >>> (http://www.pymolwiki.org/index.php/Isolevel). >>> >>> This should be documented on the PyMOLWiki somewhere under 3rd Party >>> Tools (or web servers). >>> >>> Cheers, >>> >>> -- Jason >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrodinger, LLC >>> >>> (e) jason.vertr...@schrodinger.com >>> (o) +1 (603) 374-7120 >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox _______________________________________________ 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
