[PyMOL] Align each state to another reference structure
Hi All, I have two structures that are homologous. One structure #1 contains 100 states and structure #2 contains only one state. I would like to align each state of structure #1 to structure #2 based upon some selection. From what I can understand, if I say: align struct1, struct2 This will align state #1 of structure #1 to state #1 of structure #2. align struct1, struct2, mobile_state=50 This will align state #50 of structure #1 to state #1 of structure #2. I believe that if I follow the first alignment command above with this one then I lose the first alignment. That is, state #1 of structure #1 will no longer be aligned to state #1 of structure #2. I understand that there is an "intra_fit" command but this only aligns all states of one structure with respect to one of the states in the same structure. This is not good enough for me. I want all states of one structure to be aligned with respect to another independent structure, structure #2. As well, I know that I could in theory split the states, align each structure, and group the structures back together but this seems extremely clumsy. Can this be done? Any suggestions would be greatly appreciated. Sean _ Windows Live: Keep your friends up to date with what you do online. http://go.microsoft.com/?linkid=9691815-- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ 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
[PyMOL] Autodock/Vina Pymol Plugin Windows problem
I can't seem to get the autodock Pymol plugin to work correctly in
Windows (XP). I think it's a bug somewhere.
I'm using the latest version of autodock grid and dock, and MGL Tools
1.5.4 on Windows XP with Python25, and PyMol 1.2r1
I've emailed the author, Daniel Seeliger, but haven't gotten a reply.
Has any had experience with this?
I'm getting at least 2 different errors:
first, in setting up a receptor. When I click on the PyMOL Selection and
"Generate Receptor" I get the following error:
"Batch: C:\Program Files\MGLTools
1.5.4\MGLToolsPckgs\AutoDockTools\Utilities24\prepare_receptor4.py -r
C:\Program Files\PyMOL\.ADplugin\receptor.dr1a.pdb -o
receptor.dr1a.pdbqt -A checkhydrogens
'{' is not recognized as an internal or external command,
operable program or batch file."
second, if I "Select as Flexible" in the Autodock plugin a PyMol
selection, I get the following Pymol error in background function,
Error: 1
Exception in Tk callback
Function: > (type: )
Args: ()
Traceback (innermost last):
File "C:\Program Files\PyMOL/modules\Pmw\Pmw_1_3\lib\PmwBase.py", line
1747, in __call__
return apply(self.func, args)
File "C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py", line
1800, in select_flexible_residues
receptor_object = self.receptor_dic[rec]
: ''
Jed
--
Jed Goldstone
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
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Re: [PyMOL] ConnectedCloud tool_syntax problems
Ilaria, ConnectedCloud was created to connect different objects, not atoms within a single object. Try changing(*) cmd.select( cName, "bo. " + subSel + " within 1 of " + cName ) to cmd.select( cName, subSel + " within " + radius + " of " + cName ) which should do the trick, actually. Your call to ConnectedCloud will now look like: connectedCloud yourObj and resi XYZ, yourObj, yourRadius Lastly, I haven't tested any of this, but it should work. :-) (*) -- This also corrects a bug I just found (an correspondingly updated on the wiki; I was ignoring the radius parameter). Hope this helps, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Thu, Jan 7, 2010 at 7:16 AM, ilaria carlone wrote: > Hi everyone! > > I am using PyMOL for creating molecular surfaces (SAS), starting form a pdb > file. I have some problems with "large" proteins like the head of a protein > kinase, because the program creates some internal surfaces, disconnected > from the larger one. > I have found the ConnecetdCloud tool and I would use it for selecting all > the connected surface atoms taking part to the calculus of the surface. I > don't know if it is a good way. Anyway, I tried to do this and the program > returned an invalid syntax error while specifing the origSel (I tried both > with atom name and aminoacid...). Can anyone help me? > > Thank you very much in advance, > > Ila > > > Foto delle vacanze? Crea il tuo album online e condividile con gli amici! > -- > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > ___ > 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 > -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ 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
[PyMOL] ConnectedCloud tool_syntax problems
Hi everyone! I am using PyMOL for creating molecular surfaces (SAS), starting form a pdb file. I have some problems with "large" proteins like the head of a protein kinase, because the program creates some internal surfaces, disconnected from the larger one. I have found the ConnecetdCloud tool and I would use it for selecting all the connected surface atoms taking part to the calculus of the surface. I don't know if it is a good way. Anyway, I tried to do this and the program returned an invalid syntax error while specifing the origSel (I tried both with atom name and aminoacid...). Can anyone help me? Thank you very much in advance, Ila _ Sei bravo con le parole? Gioca su Typectionary http://typectionary.it.msn.com/-- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ 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
