[Chimera-users] Bug (?) with EnsembleCluster

Eric Pettersen pett at cgl.ucsf.edu
Tue Jan 8 13:03:43 PST 2008

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  
	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.


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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