how to export the volume data which is stored in the memory?
Hi, I loaded some volume data (mrc files) into Chimera remotely from a network hard drive. Unfortunately, the network hard drive crashed so I can not access those mrc files anymore. But in Chimera which was started before the drive crash, I still have the volume data and am still able to manipulate them. Apparently, these are stored in the memory. Does anyone know how can I export these data onto a hard drive. I tried "save as" but there is an I/O error since the computer was simply trying to duplicate data from the crashed drive. Any suggestion is appreciated. Thanks, Zhiheng
Hi Zhiheng, Chimera keeps the map in memory if it is being displayed. You can see if your maps are in memory using the Chimera volume dialog menu entry Features / Data Display Options and pressing the data cache "Current use" button. If your map is displayed with step size > 1 then only a subsampled copy of the map is in memory (e.g. every other data plane). The fact that you get an IO error when trying to save the map from Chimera with volume dialog menu entry File / Save map as... suggests that the map is not all in memory and is trying to read the map in order to write the full resolution file. If you sent the Chimera traceback I could give a more definitive answer. There is no capability to write out just the subsampled part of the map which is in memory. Tom
Hello everyone, I am trying to calculate water occupancies from a pdb trajectory. The trajectory was generated with gromacs and loaded correctly in Chimera. I load the trajectory and it looks fine, I select the water molecules but I get this error log (below) when issuing the "calculate occupancy" command. Any clues as to what's wrong? I have osx 10.411 on a dual core mac book pro running Chimera 1.2470. BTW I also wasn't able to directly load the gromacs trajectory (tpr and trr), the bonds were all messed up from the third frame on. Any help would be appreciated Regards, Andrea AttributeError Exception in Tk callback Function: <function command at 0x14757ab0> (type: <type 'function'>) Args: () Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 238, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 452, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/Movie/VolumeDialog.py", line 105, in Apply volumeName=name+" ["+atomType+"]") File "/Applications/Chimera.app/Contents/Resources/share/Movie/gui.py", line 356, in computeVolume self.model.LoadFrame(fn, makeCurrent=False) File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/__init__.py", line 94, in LoadFrame crds = self._ensemble[frame] AttributeError: PdbTraj instance has no attribute '__getitem__' -- Andrea C. Vaiana Theoretical Biology and Biophysics Mail stop K710, T-10 Los Alamos, NM 87545 Los Alamos National Laboratory
Hi Andrea, I _believe_ this indicates that your frames aren't consecutively numbered. Is your PDB input a single file with multiple MODEL records. If so, are the numbers on these MODEL records consecutive? Chimera should probably handle non-consecutive numbering (at least when there's a regular "stride") but it doesn't yet. I'd also be interested in looking at your tpr/trr problem if you could get the files to me. How big are they? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 3, 2007, at 7:51 PM, Andrea C. Vaiana wrote:
Hello everyone,
I am trying to calculate water occupancies from a pdb trajectory. The trajectory was generated with gromacs and loaded correctly in Chimera. I load the trajectory and it looks fine, I select the water molecules but I get this error log (below) when issuing the "calculate occupancy" command. Any clues as to what's wrong? I have osx 10.411 on a dual core mac book pro running Chimera 1.2470. BTW I also wasn't able to directly load the gromacs trajectory (tpr and trr), the bonds were all messed up from the third frame on.
Any help would be appreciated
Regards, Andrea
AttributeError Exception in Tk callback Function: <function command at 0x14757ab0> (type: <type 'function'>) Args: () Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.4/site- packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/ baseDialog.py", line 238, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/ baseDialog.py", line 452, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/Movie/ VolumeDialog.py", line 105, in Apply volumeName=name+" ["+atomType+"]") File "/Applications/Chimera.app/Contents/Resources/share/Movie/gui.py", line 356, in computeVolume self.model.LoadFrame(fn, makeCurrent=False) File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/ __init__.py", line 94, in LoadFrame crds = self._ensemble[frame] AttributeError: PdbTraj instance has no attribute '__getitem__'
--
Andrea C. Vaiana Theoretical Biology and Biophysics Mail stop K710, T-10 Los Alamos, NM 87545 Los Alamos National Laboratory
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric, Thanks for the prompt reply. Yes, my pdb is a single file with multiple MODEL records. The numbers on the records are consecutive, so I guess that's not the problem. My original tpr + trr files are a total of ~25M (do you think your email can handle it?). The pdb file was >100M but I've tried on a smaller one (with only the first 4 frames of the run) and get the same error message. I guess email can handle the small pdb file (1M zipped), I will send this in a separate email. Let me know if/how I can send you the tpr/trr files. Andrea Eric Pettersen wrote:
Hi Andrea, I _believe_ this indicates that your frames aren't consecutively numbered. Is your PDB input a single file with multiple MODEL records. If so, are the numbers on these MODEL records consecutive? Chimera should probably handle non-consecutive numbering (at least when there's a regular "stride") but it doesn't yet. I'd also be interested in looking at your tpr/trr problem if you could get the files to me. How big are they?
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
-- Andrea C. Vaiana Theoretical Biology and Biophysics Mail stop K710, T-10 Los Alamos, NM 87545 Los Alamos National Laboratory
Hi Andrea, It turns out that not all functions of MD Movie (such as occupancy calculation) were able to handle trajectories where the first coordinate set was numbered as zero -- as was the case with your file where the first MODEL was zero. I have fixed the code now and it should be available tomorrow from the "Daily Builds" link on the Chimera home page (check the date on the build to make sure the build worked -- the date on tomorrow's build should be Dec 5 since it will build this evening). If you want to do something before then your options are: 1) delete MODEL zero from your file 2) renumber the MODELs in your file 3) Change zero to the highest model number + 1 4) I can send you the changes to the MD Movie module (let me know) --Eric P.S. My mailer should be able to handle the tpr/trr combo. Give it a whirl. If it fails, let me know -- there are other transfer options. On Dec 5, 2007, at 10:18 AM, Andrea C. Vaiana wrote:
Hi Eric,
Thanks for the prompt reply. Yes, my pdb is a single file with multiple MODEL records. The numbers on the records are consecutive, so I guess that's not the problem. My original tpr + trr files are a total of ~25M (do you think your email can handle it?). The pdb file was >100M but I've tried on a smaller one (with only the first 4 frames of the run) and get the same error message. I guess email can handle the small pdb file (1M zipped), I will send this in a separate email. Let me know if/how I can send you the tpr/trr files.
Andrea
Eric Pettersen wrote:
Hi Andrea, I _believe_ this indicates that your frames aren't consecutively numbered. Is your PDB input a single file with multiple MODEL records. If so, are the numbers on these MODEL records consecutive? Chimera should probably handle non-consecutive numbering (at least when there's a regular "stride") but it doesn't yet. I'd also be interested in looking at your tpr/trr problem if you could get the files to me. How big are they?
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
--
Andrea C. Vaiana Theoretical Biology and Biophysics Mail stop K710, T-10 Los Alamos, NM 87545 Los Alamos National Laboratory
Hi Tom, Thanks for your prompt reply. All my maps are displayed with stepsize 1,1,1. I can rotate them, change contour level and do all sorts of manipulations as normal. But I can not save them. I attached the traceback as a file. Thanks for your help. Zhiheng Tom Goddard wrote:
Hi Zhiheng,
Chimera keeps the map in memory if it is being displayed. You can see if your maps are in memory using the Chimera volume dialog menu entry Features / Data Display Options and pressing the data cache "Current use" button. If your map is displayed with step size > 1 then only a subsampled copy of the map is in memory (e.g. every other data plane).
The fact that you get an IO error when trying to save the map from Chimera with volume dialog menu entry File / Save map as... suggests that the map is not all in memory and is trying to read the map in order to write the full resolution file. If you sent the Chimera traceback I could give a more definitive answer. There is no capability to write out just the subsampled part of the map which is in memory.
Tom
Hi Zhiheng, You must be using an older version of Chimera. Old versions read the original file even if the map was in memory when writing out the data. Maybe I can give you a script that will write the maps out from memory if you tell me what version of Chimera you are running (menu entry Help / About UCSF Chimera). Tom
participants (4)
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Andrea C. Vaiana -
Eric Pettersen -
Tom Goddard -
Zhiheng Yu