[Chimera-users] Bug (?) with EnsembleCluster

[Francesco Pietra]

The lipid, all solvation water, and box information were removed by ptraj. I
used python to remove the single water molecule of crystallization. There is
nothing else than the protein and the ligand in the pdb. This is clear both
from vmd and a text editor.
francesco
--- Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> The only advice I have (which you may have already tried) is to also  
> strip the lipid bilayer using basically the same method as you did  
> with the water.
> 
> --Eric
> 
> On Jan 6, 2008, at 11:15 PM, Francesco Pietra wrote:
> 
> > Hi Elaine:
> > As I said privately, ptraj failed to remove one molecule of water.
> >
> > I loaded mdcr pmrtop to Chimera, saved the pdb, stripped that water  
> > (better:
> > wrote the lines that do not contain water) from the 549 models with
> >
> > f=open("prod1-3.pdb", "r")
> > for line in f:
> > 	line=line.rstrip()
> > 	if "WAT" not in line:
> > 		print line
> > f.close()
> >
> > outputting the edited file with tee.
> >
> >
> > The file is nice, it starts with 13 instances of helix (built by  
> > Chimera, as
> > there was no such information at any stage), and contains 549 models.
> >
> > With the desktop I use for Chimera (total 1GB ram) there is no way  
> > to open this
> > pdb. I removed from gnome all that was possible to remove except  
> > Chimera.
> > Opened top -i in parallel, which showed python to take rapidly  
> > about 99%
> > memory. I left the system on overnight: little mem and cpu were in  
> > use, though
> > Chimera had not opened the file.
> >
> > This is not to compare, simply to assure that the pdb is not bad:  
> > it can be
> > rapidly opened with vmd, which play all 549 models. Though, I have  
> > to go
> > through Chimera. So that, it seems to me that pure python finds  
> > problems with
> > long trajectories. As a naive user (who might well be wrong) I  
> > would add some
> > fast code to help python. An alternative is to add ram; don't know  
> > if my old
> > mainboard can add ram. I can't install Chimera on the amd64  
> > parallel machine,
> > where ram is plenty (4GB per processor). I can't even install X.
> >
> >
> >
> > --- Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> >> Hi Francesco,
> >> I agree it can be confusing - the error dialog always includes the
> >> "report bug" button, but it is not always a bug when that dialog
> >> appears.   We will have to look at your report to try to figure out
> >> what was happening in your case.
> >>
> >> We are still looking into the mdcrd.gz file issue.  In my tests, I
> >> could successfully specify multiple (uncompressed) mdcrd files as
> >> input to MD Movie.
> >> Best,
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> >> UCSF Computer Graphics Lab and Babbitt Lab
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>                       http://www.cgl.ucsf.edu/home/meng/index.html
> >>
> >>
> >>
> >>
> >> On Jan 5, 2008, at 1:26 PM, Francesco Pietra wrote:
> >>
> >>> Elaine:
> >>> Although I could argue that the "Report Bug" window was misleading,
> >>> I am better
> >>> saying that I was stupid enough.
> >>> francesco
> >>
> >>
> >
> >
> >
> >        
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> 
> 



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