Hi Max, > 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?
PyMOL can reproduce isomesh and isosurface outside the unit cell, however it cannot yet do that for volumes. We are currently making symmetry operations better and a bit wiser in PyMOL. The new v1.5 of PyMOL will have some updates regarding this, and I suspect we'll have much better functionality for this in one the v1.5 updates. > If this is too complicated I will just use Chimera for this application. Just like I do, use whatever tool is best suited for the task at hand. Cheers, -- Jason > 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) [email protected] >>>> (o) +1 (603) 374-7120 >>> >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) [email protected] >> (o) +1 (603) 374-7120 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) [email protected] (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 ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
