- 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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suggestion: savepos
by Dougherty, Matthew T 06 Feb '13

06 Feb '13

It would be helpful to have the option in preferences to prevent the overwrite of keyframes. Something that would check to see if it exists, and then give an error if it does. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Amira map file reader
by Tom Goddard 06 Feb '13

06 Feb '13

I made Chimera able to read Amira map files, file suffix ".am", also known as AmiraMesh files, with format described here http://www.mpi-inf.mpg.de/~weinkauf/notes/amiramesh.html Chimera only reads scalar (not vector) files. This is in the current Chimera daily build. http://www.cgl.ucsf.edu/chimera/download.html#daily Tom

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Mirror
by Sebastian Mock 06 Feb '13

06 Feb '13

Hi, is there any possibility to mirror / copy a molecule. E.g. you have two docked molecules. If I want the docking partner to be mirrored to the other side of the receptor molecule in the same exact location, but mirrored. Thanks in advance Sebastian

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(no subject)
by rashmi gupta 06 Feb '13

06 Feb '13

Sir I want to know that if i had modeled a protein structure and want to categorize it into different chain or domain then how would i do this through chimera? Plz give the solution of question -- Rashmi Research scholar IMS, BHU

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Re: [Chimera-users] Chimera on a virtualbox
by Greg Couch 05 Feb '13

05 Feb '13

(Forgot to send reply to whole list) -------- Original Message -------- Subject: Re: [Chimera-users] Chimera on a virtualbox Date: Tue, 05 Feb 2013 13:51:47 -0800 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: chris.wood(a)stfc.ac.uk Hi Chris, So what are you trying to do with Chimera inside a virtual machine? Presumably, you're not trying to use it graphically because virtualized graphics performance is usually abysmal. Chimera benefits immensely from direct access to the graphics hardware. So that leaves using Chimera as a server, and for that the headless version of Chimera is usually better -- the headless version uses a software implementation of OpenGL and thus avoids any driver issues. That said, this bug is still likely to be related to OpenGL support in VirtualBox. Make sure the computer that VirtualBox is running on has an up-to-date OpenGL graphics driver. It doesn't matter what VirtualBox does if the underlying system has a bad graphics driver. To confirm that the bug is in the graphics driver, get a backtrace of where the error occurs by using gdb as follows in a Terminal window (and assuming there is a symbolic link to the chimera binary on your path): % export CHIMERA=`chimera --root` % export LD_LIBRARY_PATH=$CHIMERA/lib % gdb $CHIMERA/bin/python2.7 (gdb) break_exit (gdb) run $CHIMERA/share/__main__.py --debug (gdb) bt The '%' and '(gdb)' parts are the shell and gdb prompts, respectively. The output from the bt command will probably be in Chimera's molecular drawing code (as opposed to drawing the UI). If you need help interpreting the chimera backtrace, you can send it to me. HTH, Greg On 02/05/2013 12:48 PM, chris.wood(a)stfc.ac.uk wrote: > > Hello all, > > I'm trying to run Chimera on VirtualBox. The installation completes > fine, but when I try and run the program (|cd| to the bin directory > and run |./chimera|) I see > > X Error of failed request: BadDrawable (invalid Pixmap or Window > parameter) > > Major opcode of failed request: 72 (X_PutImage) > > Resource id in failed request: 0x480006a > > Serial number of failed request: 1382 > > Current serial number in output stream: 1388 > > I've tried enabling / disabling hardware virtualization & 3D > acceleration, but to no avail. Although people do seem to have > problems with chimera on a virtualbox, it normally seems to be a > problem with OpenGL, which this doesn't seem to be. > > Has anyone seen this error before? Is there anything else I'm missing? > I can't even work out if it's a hardware, VirtualBox, or OS problem... > > ** > > *System:* > > VirtualBox 4.2.4 > Guest additions 4.2.4 > > Guest OS: Ubuntu 12.04 > Host OS: Windows 7 professional > > Thanks in advance! > > Chris > > ------------------- > > Dr Chris Wood > > STFC Rutherford Appleton Laboratory > > Didcot > > OX11 0QX > > chris.wood(a)stfc.ac.uk > www.ccpem.ac.uk > > > Tel: +44(0)1235 567864 > > Tel: +44(0)7909 586624 > Fax: +44(0)1235 567801 > > > -- > Scanned by iCritical. >

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color spill
by Yadong Yu 05 Feb '13

05 Feb '13

Hi there, I have a color spill problem when drawing a few figures of a hexamer. The coordinates of 6 protomers were saved into a PDB file. I wanted to color chain A red and the rest gray, so I selected chain A and colored it with red. The red color strangely spilled to an N-terminal segment of the next chain. I think there is some problem with the format of my PDB file, but don't know exactly what is wrong. Here's the end of A and begin of B where spill happend: ATOM 2657 C ASP A 418 74.297 91.204 65.520 1.00 0.00 P1 C ATOM 2658 OT1 ASP A 418 73.965 91.654 66.693 0.00 0.00 P1 O ATOM 2659 OT2 ASP A 418 73.731 91.612 64.449 0.00 0.00 P1 O ATOM 2660 N ASP A 418 74.565 88.894 65.731 1.00 0.00 P1 N ATOM 2661 CA ASP A 418 75.338 90.111 65.514 1.00 0.00 P1 C ATOM 2662 CB ASP A 418 76.099 90.113 64.183 1.00 0.00 P1 C ATOM 2663 CG ASP A 418 77.091 91.332 64.042 1.00 0.00 P1 C ATOM 2664 OD1 ASP A 418 76.837 92.210 63.175 1.00 0.00 P1 O ATOM 2665 OD2 ASP A 418 78.018 91.382 64.875 1.00 0.00 P1 O ATOM 2666 N LEU B 87 68.825 113.707 134.628 1.00 0.00 P2 N ATOM 2667 CA LEU B 87 68.215 113.786 133.272 1.00 0.00 P2 C ATOM 2668 CB LEU B 87 67.055 114.822 133.239 1.00 0.00 P2 C ATOM 2669 CG LEU B 87 66.068 114.738 134.402 1.00 0.00 P2 C ATOM 2670 CD1 LEU B 87 65.132 115.985 134.379 1.00 0.00 P2 C ATOM 2671 CD2 LEU B 87 65.430 113.355 134.203 1.00 0.00 P2 C ATOM 2672 C LEU B 87 69.159 114.128 132.171 1.00 0.00 P2 C ATOM 2673 O LEU B 87 69.384 113.413 131.199 1.00 0.00 P2 O Any suggestion? Thank you! Yadong

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Modeller
by Hernando J Sosa 05 Feb '13

05 Feb '13

Hi, I am trying t use modeller within chimera but it always end with an error: .... Kind, OS, HostName, Kernel, Processor: 4, Linux watson.cgl.ucsf.edu 2.6.32-279.14.1.el6.x86_64 x86_64 Date and time of compilation : 2012/08/29 11:36:00 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2013/02/05 13:11:37 check_lice_E> Invalid license key: Go to http://salilab.org/modeller/ to get a license key, and then set the 'license' variable to it in the file /usr/lib/modeller9.11/modlib//modeller/config.py I have installed modeller in my computer and have a license to it. I also verified that the license number was set in the config.py file. So I am not sure what the problem could be ?? System details: Chimera v. 1.7 Modeller v. 9.11 OS: Windows 7 64bits Thanks, Hernando

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Chimera on a virtualbox
by chris.wood＠stfc.ac.uk 05 Feb '13

05 Feb '13

Hello all, I'm trying to run Chimera on VirtualBox. The installation completes fine, but when I try and run the program (cd to the bin directory and run ./chimera) I see X Error of failed request: BadDrawable (invalid Pixmap or Window parameter) Major opcode of failed request: 72 (X_PutImage) Resource id in failed request: 0x480006a Serial number of failed request: 1382 Current serial number in output stream: 1388 I've tried enabling / disabling hardware virtualization & 3D acceleration, but to no avail. Although people do seem to have problems with chimera on a virtualbox, it normally seems to be a problem with OpenGL, which this doesn't seem to be. Has anyone seen this error before? Is there anything else I'm missing? I can't even work out if it's a hardware, VirtualBox, or OS problem... System: VirtualBox 4.2.4 Guest additions 4.2.4 Guest OS: Ubuntu 12.04 Host OS: Windows 7 professional Thanks in advance! Chris ------------------- Dr Chris Wood STFC Rutherford Appleton Laboratory Didcot OX11 0QX chris.wood(a)stfc.ac.uk www.ccpem.ac.uk Tel: +44(0)1235 567864 Tel: +44(0)7909 586624 Fax: +44(0)1235 567801 -- Scanned by iCritical.

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MatchMaker
by Mock, Sebastian 05 Feb '13

05 Feb '13

Hi, I am facing a problem with Matching! Is there any possibility to match two structures, without losing the coordinates of e.g. a dimer unit. In this case, I want to match a homo-dimer to another similar structure. When I match all of the above mentioned dimers (chains), Chimera will match it all at the same place, so I will have two identical positions. In this case I am losing the steric information about the assembly of the homo-dimer. Is there any method, to treat the dimer as one molecule, which cannot be splitted and can be matched on another structure without losing the biological assembly? It is hard to explain, I hope you get me. Thanks in advance Sebastian

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Modification of COX Demo
by Noel Pace 05 Feb '13

05 Feb '13

To whom it may concern, I am a university student in his final year following a course in Pharmacy at the University of Malta. Currently, under the supervision of my tutor, I am working on a dissertation entitled " The Development of Computational Chemistry Practicals". During my research I came across your software UCSF Chimera and found out the DEMO section. I would like to make use of the editing function to edit the COX demo present with the software to represent Beta-Receptors instead. I will write down that the demo has been based on the COX demo present. Is the above request possible? I really find your software to be suited for my needs and would be honored to have your support in the fulfillment of my dissertation. I thank you in advance Noel Pace M. Pharm Student (Malta)

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Blast protein
by Bobo Dang 05 Feb '13

05 Feb '13

Hi guys, I was trying to build homology model using chimera. The uniprot ID of the molecule I want to build is Q9X2V8, when I was trying to blast to find the homologs which have structures. It returns "no BLAST matches found". Does this mean there is no Q9X2V8 homolog from PDB? how does Chimera judge one molecule could match (could be the homolog)? thanks bobo

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pseudo bond reader in command line
by M. Elizabeth Stroupe 04 Feb '13

04 Feb '13

Hi, I am trying to make a figure with pseudo bonds - the figure is fairly complicated and it will be a frame in a movie of related shots, so I need to call the pseudo bonds in from the command line. How do I read in a text file that defines the pseudo bonds (as if from the pseudo bond reader) and then alter their attributes (to make them into dotted rather solid lines)? Thanks much, Beth

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Add hydrogens to DNA
by sette＠uniroma2.it 02 Feb '13

02 Feb '13

Hi, I used the addH to add hydrogens to a DNA pdb file generated with 3DNA but most of the atoms are not protonated. Is addH used for DNA or just for proteins? Thanks, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

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Re: [Chimera-users] Problem with Chimera 1.7 on Linux OS
by Greg Couch 01 Feb '13

01 Feb '13

Those errors are coming from Chimera asking the graphics driver about multisampled visuals. You might be able to avoid the problem by starting up chimera with the --debug-opengl flag and turning off multisampling. But the fact that you are getting an error means that you need to update the graphics driver on your Linux production computer. For Linux computers, we recommend installing the proprietary NVIDIA or AMD graphics driver depending on which brand of graphics hardware you have. If you have Intel graphics, the only easy way to get updates is to update to a newer version of Linux. If you are running Chimera inside a virtual machine, then updating the graphics driver means updating the virtual machine software, but chimera would perform better without that intervening layer. Also note that on some newer versions of Linux, eg., Ubuntu 12.10, the default setup interferes with OpenGL applications, in particular, opening the SideView tool causes Chimera to crash. The workaround is to switch to a non-compositing window manager like xfce. HTH, Greg On Fri, 1 Feb 2013, Stephen P. Molnar wrote: > I have downloaded, and installed, the 64 bit linux version 1.7, in 64 bit > Debian Testing running in Oracle VirtualBox v4.2.6r82870 before loading it > onto my Linux production computer. The installer ran smoothly without > generating any warnings or errors. > > > > However, when I run the executable I get the following messages: > > > > computation@debian:~/Apps/chimera/bin$ ./chimera > > OpenGL Warning: glXChooseVisual: bad attrib=0x186a0, ignoring > > OpenGL Warning: glXChooseVisual: bad attrib=0x186a1, ignoring > > OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your > SPU > > > > I have the win version open in MS Win 7 on the same computer as I compose > this message. > > > > Stephen P. Molnar, Ph.D. Life is a fuzzy > set > > Foundation for Chemistry Stochastic and > multivariate > > www.FoundationForChemistry.com > > (614)312-7528 (c) > > Skype: smolnar1 > > > > > _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Problem with Chimera 1.7 on Linux OS
by Stephen P. Molnar 01 Feb '13

01 Feb '13

I have downloaded, and installed, the 64 bit linux version 1.7, in 64 bit Debian Testing running in Oracle VirtualBox v4.2.6r82870 before loading it onto my Linux production computer. The installer ran smoothly without generating any warnings or errors. However, when I run the executable I get the following messages: computation@debian:~/Apps/chimera/bin$ ./chimera OpenGL Warning: glXChooseVisual: bad attrib=0x186a0, ignoring OpenGL Warning: glXChooseVisual: bad attrib=0x186a1, ignoring OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU I have the win version open in MS Win 7 on the same computer as I compose this message. Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1

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