[Chimera-users] Bug (?) with EnsembleCluster

[Eric Pettersen]

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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