Hi Xiaopeng, and those who are using the new interruptible "fit_protein..."
or "stepped_refine..." in wincoot 0.6.1:
I just took a look at wincoot 0.6.1's fitting.py file
(WinCoot\share\coot\python\fitting.py). It seems that in the old
"fit_protein()" and "stepped_refine_protein()" functions, the backup was
programmed to be turned off during the cycles when it steps through the
protein.
However when using the "Stepped refine..." from the "Extensions" menu, the
program starts to spit out tons of backup files. I then checked the
"extension.py". It turns out that these menu items are calling the new
"interruptible_fit_protein()" function instead of the old uninterruptible
ones. Some further experiment showed that this behavior was dependent on the
"backup state" variable of the model being refined. When the "backup state"
is 1 (the default value?), these new interruptible fitting functions will
save a compressed backup file on each step.
So, in order to save time when using the new interruptible protein fitting
functions, one can type the following command in the python script window to
tweak the "backup state" to 0:
make_backup(imol) #to save a backup
turn_off_backup(imol)
where imol is the number associated with the pdb file being fitted.
Do not forget to turn it back on after the fitting:
turn_on_backup(imol)
To check the current model's "backup state":
backup_state(imol)
Zhijie
--------------------------------------------------
From: "Xiaopeng Hu" <[email protected]>
Sent: Tuesday, March 29, 2011 9:02 AM
To: "Zhijie Li" <[email protected]>
Subject: Re: [ccp4bb] step refine speed of wincoot
Dear Zhijie,
Thanks for there suggestions.
I tried to turn off backup (with script command) and it did help although
not much. Is there any way to add this perference to setting of
coot/wincoot?
best
xiaopeng
----- 原始邮件 -----
发件人: "Zhijie Li" <[email protected]>
收件人: "Xiaopeng Hu" <[email protected]>
发送时间: 星期二, 2011年 3 月 29日 下午 7:46:05
主题: Re: [ccp4bb] step refine speed of wincoot
Hi,
If you feel the refinement to be too slow, you may turn off the smooth
centering (in preferences) or change the centering steps to a smaller
number
to save unnecessary graphical calculations. To go extreme, you may even
remove the real time display commands in the scripts - also a way to test
if
the difference observed is due to different graphical efficiency. Reducing
the size of the displayed map also helps.
The other thing you may need to consider is that coot/wincoot will save a
backup file each time it updates the model, which means on each step of
the
refinement you have a new file generated (take a look at the coot-backup
directory when doing stepped refinement). If your windows disk is terribly
fragmented then sure you will spend a lot of time on writing these files.
The other thing is, windows has a different file caching mechanism than
linux, this can also cause a huge difference when a few hundred small
temporary files are queued for writing. My impression is that both the
ext2/3 file system and the way linux handles caching are more efficient
for
this kind of situations. You may try deleting the files in
wincoot\coot-backup periodically and defragmenting that partition. Making
a
virtual disk in the RAM to put your backup directory there could be
something to experiment on too.
Zhijie
--------------------------------------------------
From: "Xiaopeng Hu" <[email protected]>
Sent: Sunday, March 20, 2011 9:22 AM
To: <[email protected]>
Subject: [ccp4bb] step refine speed of wincoot
Dear all,
I found the step refine speed of wincoot is much slower than that of
linux
coot (with the same pc). Is it normal or I need to configure something
with the wincoot?
best,
Xiaopeng Hu
