[Chimera-users] Bug (?) with EnsembleCluster
Francesco Pietra
chiendarret at yahoo.com
Wed Jan 9 15:32:30 PST 2008
Eric:
I installed the 8 JAN DailyBuild of Chimera.
Still found difficulties in loading more than one mdcrd, though this should be
my fault. I was not sure if the list of mdcrd is to be given at beginning or if
the other mdcrd files after the first one are to be given subsequently from the
menu. I tried with the "list" option but only the first mdcrd was opened.
Forget about that as not the focus here. I took the combined mdcrd from ptraj,
where the lipid had been wholly stripped, while one water molecule of the many
was not stripped (for unclear reasons).
Gave this combined mdcrd to Chimera using the prmtop used before embedding the
protein complex into lipid and solvate. This should be correct as that prmtop
was from DOCK amber_score_everything, i.e. concerned the best scored
protein-ligand complex that was used for MD after embedding into the membrane.
All docking had been carried out with a crystallization molecule of water in
the protein, so that WAT was in prmtop, as well as in mdcrd.
With the opened trajectory in Chimera, without playing, i.e. with the first
frame (where the water molecule was at the border of the protein, showing up as
a triangle because of SHAKE; if movie is started, that triangle moves around
within the protein from snapshot to snapshot).
In the "Define script.." I defined "select ligand z<10", then OK and a BUG
window was presented. Attached is the reply log (bug). I tried with z<4 with
the same result (actually, I don't remember if attached bug file refers to z<10
or z<4).
Thanks
francesco
--- Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Hi Francesco,
> I guess I do have a further suggestion which is to reduce the
> structure to just those residues that are interacting with the ligand
> at any time during the trajectory. The basic idea would be to run
> the trajectory to select those residues and then write a PDB file
> with just selected residues in it. Here's a recipe:
>
> open your trajectory
> delete solvent
> delete the lipid bilayer
> bring up the "Define script..." dialog from MD Movie's Per-Frame menu
> define a "Chimera commands" script that is just:
> select ligand z<N [where N is the distance you want to consider as
> "interacting"]
> click OK
>
> this will select the appropriate residues in the first frame. We
> want the selection to aggregate as the trajectory plays so we need to
> change the selection mode...
>
> choose Select->Selection Mode->append
> run the trajectory
>
> once the trajectory has played through, all residues that were ever
> within the cutoff distance will be selected. You may be interested
> in the list itself. You can write it out with:
>
> Actions->Write List...
>
> You can write a PDB limited to just the selected residues the same
> way you wrote the PDB before, just with the "Save selected atoms
> only" check button on.
>
> --Eric
>
> On Jan 7, 2008, at 12:50 PM, Francesco Pietra wrote:
>
> > 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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>
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