February 2013 - Chimera-users - RBVI Mailing Lists

questions about modeller and task panel
by Smith, Susan Margaret Ellen 19 Feb '13

19 Feb '13

Hello, I am trying to use Chimera as an interface to a local installation of Modeller on my Mac. I have two questions: 1) When I open the task panel, I can see the current tasks and the completed tasks (nice visual cuing), but I do not see any way to kill a job. How can I select a job and how can I stop it? 2) When I run the tutorial example for Modeller, I get the following message, which seems like it is telling me that something is wrong (although the job appears to still be running in the task panel). I have re-installed the Modeller package, but I don't know what 'environment variable' was not set ... It seems like the program doesn't know where to put the output, although I specified a path for the temporary output. Can you help with this? Thanks, Susan Target seq: oprd_human Template structures: 4DKL (#0)Run locally, the Modeller binary location: /Library/modeller-9.11/bin/mod9.11_mac10v4 Now, modeller is running locally... MODELLER process output ----------------------- FATAL ERROR: MODINSTALL9v11 environment variable not set: incomplete MODELLER installation ----------------------- MODELLER process errors ----------------------- ----------------------- Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "/Applications/Chimera.app/Contents/Resources/share/chimera/SubprocessMonitor.py", line 166, in statusCB self.finished() File "/Applications/Chimera.app/Contents/Resources/share/chimera/SubprocessMonitor.py", line 201, in finished self._after(self._aborted) File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 635, in _collectResultsCB OKModels = self._showingOKmodels(self.pathTemp) File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 646, in _showingOKmodels modelsInfoFile = osOpen(os.path.join(outputPath, "ok_models.dat")) File "/Applications/Chimera.app/Contents/Resources/share/OpenSave/__init__.py", line 324, in osOpen raise UserError(val) UserError: [Errno 2] No such file or directory: '/Users/dlambe/Desktop/ok_models.dat' ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Mirror
by Sebastian Mock 19 Feb '13

19 Feb '13

Hi everyone, is it possible, when I docked two enzymes and want to dock a second one (e.g. multienzymes complex with one sort of the first and two of the second enzyme) on the opposite site in the same orientation, to just mirror the coordinates and angles? Greets Sebastian

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Sequence
by Sebastian Mock 18 Feb '13

18 Feb '13

Hi all, how can I save a docking result as one sequence/chain only? I have a dimer docked to a tetramer and I want this to be the new Receptor in the Docking Process. Therefore, I need the two enzymes in only one sequence, as it were just one molecule. Any ideas? Removing the "ter" commands in the pdb file, did not change anything. Greets Sebastian

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Re: [Chimera-users] two questions: link card in pdb and bond commans
by Elaine Meng 17 Feb '13

17 Feb '13

Hi Boaz, (1) Chimera does connect atoms for which there are LINK records, but it may be considered a metal-coordination bond and just get a dashed line pseudobond. However, there are examples where it is a regular covalent bond. I was just using build 38277 from Feb 13, but I don't think anything related to this has changed recently. Example of where it becomes a metal coordination bond: 4HHB.pdb:LINK NE2 HIS A 87 FE HEM A 142 1555 1555 2.14 Example of where it is a regular covalent bond: 1HZH.pdb:LINK O2 MAN H 482 C1 NAG H 483 1555 1555 1.38 Maybe there is something incorrect about the LINK record. I don't remember the details of when you would use LINK records as opposed to CONECT or SSBOND, but they are all described at the wwPDB site: <http://www.wwpdb.org/documentation/format33/v3.3.html> (2) Maybe I'm misunderstanding the question, but you could use command alias ^dobond bond sel ... which would make "dobond" appear in an Aliases menu, and this menu entry would work when you have two atoms selected. Also, there is a corresponding GUI, Tools... Structure Editing... Build Structure, the "Adjust Bonds" section. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 16, 2013, at 12:05 PM, Boaz Shaanan wrote: > Hi, > 1) I thought Chimera connects two atoms that are marked as linked by the LINK card in the pdb header, is that not the case? It certainly does not work in build 38218 from 5 February (linux x86-64). I'm not sure whether it's my ignorance or a bug hence I'm sending it to the list. > > 2) The 'bond' command (for making a bond between two atoms in the same model) only works in command line? If so, will it be difficult to add it to the pull-downs similar to the distance panel (for 2-clicks lazy people like myself)? > Cheers, > Boaz

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Re: [Chimera-users] Modification of COX Demo
by Noel Pace 14 Feb '13

14 Feb '13

Dear Elaine, Thank you very much for the quick reply I am really happy about the news. How should I refer ucsf chimera in my dissertation? Thanks, Noel

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Re: [Chimera-users] moving to coordinates
by Sebastian Mock 13 Feb '13

13 Feb '13

Hi Conrad, first you have to convert the mentioned angles to degree. They are represented as rad here. (first 3 values in the translation file) The formula for this would be rad*180/pi. We don't know why, but for the y angle you have to switch the algebraic sign. Simply multiplied by -1. We just did the conversions in Excel. The rotation in PatchDock is in XYZ notation, first rotation, than translation (this would be the order you also have to use by appling the coordinates) Then we just loaded the receptor as well as the ligand, apply the changes you want (e.g. color active sites etc.) save it into a session file and wrote a little chimera command file containing the following: close session open Z:\Sebastian\2013\Liganden\ohne Liganden\PatchDock\2+3\reference.py cofr 0.0,0.0,0.0 cofr fixed turn x -28.32 models 1 turn y -42.12 models 1 turn z 128.78 models 1 move x 33.96 models 1 move y 68.95 models 1 move z 212.57 models 1 now you can just edit the turn and move values, open the command file and Chimera will perform the orientation. Greets Sebastian 2013/2/12 Conrad Huang <conrad(a)cgl.ucsf.edu> > Hi, Sebastian. > > Just out of curiosity, what is your solution? Thanks. > > Conrad > > > On 2/12/2013 6:00 AM, Sebastian Mock wrote: > >> Hi again, >> >> we figured it out by ourselves. No need to investigate this further! >> >> Thanks anyway! :-) >> >> Sebastian >> >> 2013/2/11 Conrad Huang <conrad(a)cgl.ucsf.edu <mailto:conrad@cgl.ucsf.edu>> >> >> >> Can you please send me the receptor and ligand PDB files as well? >> Perhaps we can cobble together something. >> >> Conrad >> >> >> On 2/7/13 1:13 AM, Sebastian Mock wrote: >> >> Hi, >> >> I am using Patchdock Algorithm to dock two Enzymes. >> >> I get the pdb's and can load them into Chimera without having >> problems. >> >> Because Patchdock only performs a jigsaw puzzle with the two >> molecules, >> I have to look at all the solutions it gave me and judge them by >> some >> criteria. >> This is very time consuming, as I have to match every single >> solution >> with the appropriate molecules in chimera and I get tons of >> solutions. >> I found the following two lists with imo coordinates of the >> dockings. Is >> it possible to load these into Chimera or at least to enter the >> coordinates, so that chimera moves the >> docking partner and I can just look at it and discard or accept? >> >> These are the example lists >> http://bioinfo3d.cs.tau.ac.il/**__PatchDock/runs/1_Hexokinase_** >> __combined.pdb_2_G6PIsomerase_**__combined.pdb_37_58_16_6_1_** >> 113/__trans.txt<http://bioinfo3d.cs.tau.ac.il/__PatchDock/runs/1_Hexokinase___combined.pdb_…> >> <http://bioinfo3d.cs.tau.ac.**il/PatchDock/runs/1_** >> Hexokinase_combined.pdb_2_**G6PIsomerase_combined.pdb_37_** >> 58_16_6_1_113/trans.txt<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6…> >> > >> http://bioinfo3d.cs.tau.ac.il/**__PatchDock/runs/1_Hexokinase_** >> __combined.pdb_2_G6PIsomerase_**__combined.pdb_37_58_16_6_1_** >> 113/__docking.res<http://bioinfo3d.cs.tau.ac.il/__PatchDock/runs/1_Hexokinase___combined.pdb_…> >> >> <http://bioinfo3d.cs.tau.ac.**il/PatchDock/runs/1_** >> Hexokinase_combined.pdb_2_**G6PIsomerase_combined.pdb_37_** >> 58_16_6_1_113/docking.res<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6…> >> > >> >> Thanks in advance >> Sebastian >> >> >> ______________________________**___________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.**ucsf.edu<Chimera-users(a)cgl.ucsf.edu> >> > >> http://plato.cgl.ucsf.edu/__**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/__mailman/listinfo/chimera-users> >> <http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> **> >> >> >>

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how to reduce EM map resolution (Chimera 1.6.2)
by Sergey Ryazantsev 12 Feb '13

12 Feb '13

Hello I have low-resolution (~15A) model of decorated F-actin. I want to localize the "decoration" element by subtracting normal F-actin model obtained from Cryo-EM (EMD-5168) from my decorated model. The problem is that EMD-5168 has a higher resolution and "vop" command did not work. Even if it would work, it would be difficult to interpret the result of such subtraction. I think, both maps should be at approximately the same resolution. I know how to create low-resolution map from PDB, but I could not find any solution how to lower the resolution of the EMD-5168.map Any help would be greatly appreciated. Many thanks in advance. Sergey -- ____________________________________________________________________ Sergey Ryazantsev Ph. D. Electron Microscopy Laboratory (EMi) Department of Biological Chemistry, David Geffen School of Medicine University of California, Los Angeles. Phone: (310) 825-1144 (office) mailto:sryazant@ucla.edu

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Re: [Chimera-users] moving to coordinates
by Sebastian Mock 12 Feb '13

12 Feb '13

Hi again, we figured it out by ourselves. No need to investigate this further! Thanks anyway! :-) Sebastian 2013/2/11 Conrad Huang <conrad(a)cgl.ucsf.edu> > Can you please send me the receptor and ligand PDB files as well? Perhaps > we can cobble together something. > > Conrad > > > On 2/7/13 1:13 AM, Sebastian Mock wrote: > >> Hi, >> >> I am using Patchdock Algorithm to dock two Enzymes. >> >> I get the pdb's and can load them into Chimera without having problems. >> >> Because Patchdock only performs a jigsaw puzzle with the two molecules, >> I have to look at all the solutions it gave me and judge them by some >> criteria. >> This is very time consuming, as I have to match every single solution >> with the appropriate molecules in chimera and I get tons of solutions. >> I found the following two lists with imo coordinates of the dockings. Is >> it possible to load these into Chimera or at least to enter the >> coordinates, so that chimera moves the >> docking partner and I can just look at it and discard or accept? >> >> These are the example lists >> http://bioinfo3d.cs.tau.ac.il/**PatchDock/runs/1_Hexokinase_** >> combined.pdb_2_G6PIsomerase_**combined.pdb_37_58_16_6_1_113/**trans.txt<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6…> >> http://bioinfo3d.cs.tau.ac.il/**PatchDock/runs/1_Hexokinase_** >> combined.pdb_2_G6PIsomerase_**combined.pdb_37_58_16_6_1_113/**docking.res<http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6…> >> >> Thanks in advance >> Sebastian >> >> >> ______________________________**_________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> >>

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Installing Chimera on Mac
by Corey Fugate 11 Feb '13

11 Feb '13

Hi, I'm trying to run Chimera on my Mac. I put it in the Applications folder, but when I open the program a dialogue appears that says, "Cannot find writable directory for saving preferences file". How can I fix this? Thanks, Corey

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moving to coordinates
by Sebastian Mock 07 Feb '13

07 Feb '13

Hi, I am using Patchdock Algorithm to dock two Enzymes. I get the pdb's and can load them into Chimera without having problems. Because Patchdock only performs a jigsaw puzzle with the two molecules, I have to look at all the solutions it gave me and judge them by some criteria. This is very time consuming, as I have to match every single solution with the appropriate molecules in chimera and I get tons of solutions. I found the following two lists with imo coordinates of the dockings. Is it possible to load these into Chimera or at least to enter the coordinates, so that chimera moves the docking partner and I can just look at it and discard or accept? These are the example lists http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6… http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6… Thanks in advance Sebastian

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