- Chimera-users - RBVI Mailing Lists

robust molecular surface calculation
by Francois Berenger 21 Feb '13

21 Feb '13

Hello, Is there any plan to plug some alternative molecular surface calculation algorithm into chimera? I have seen some interesting articles about isosurface and gaussian density functions: "Yu, Z., Jacobson, M. P. and Friesner, R. A. (2006), What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. J. Comput. Chem., 27: 72–89. doi: 10.1002/jcc.20307" "What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules DOI: 10.1002/jcc.20307" http://onlinelibrary.wiley.com/doi/10.1002/jcc.20307/abstract The algorithm looks simple, robust and even parallelizable. I kind of guess that's the algorithm used in MOE when I look at their triangulation. Regards, Francois.

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A way to extract mesh data?
by Hyeong-Tae Jou 20 Feb '13

20 Feb '13

Hi list, I wonder if it is possible to extract mesh data when drawing volume data. Thanks for your help in advance. Regards, Hyeong-Tae Jou ----------------------- Korea Institute of Ocean Science and Technology

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Center
by Sebastian Mock 20 Feb '13

20 Feb '13

Hi, is it possible to center a molecule absolute? I have to molcules and want to center one in the absolute center of the other one. Or e.g. center both in coordinate system on 0.0,0.0,0.0 The "center" command only centers the camera. But I need to move the molecules, not the camera view. Greets Sebastian

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New user-visualizing coulombic
by Minor, Armond 20 Feb '13

20 Feb '13

Hello, I am just starting out using the program for a project with my Biochemistry professor. We are trying to develop a simple procedure to visualize the Coulombic surface of short DNA sequences. I have very little experience working with Chimera and do not know if I am going about it in correct way that will yield meaningful data. I have tried following the instruction but must of them seem to be for people who are more familiar with the programs than I am. Basically what I have tried is opening a pdb file, running PDB2PQR, opening the pqr file then running APBS on that. I am not sure what to do with the .dx file that comes out and how to use it to color the surface. If I use it to color the Electrostatic potential map I get a range of values that seem to be not what my professor is expecting. If I instead use the coulombic surface tool I get values like she expects but I am not sure if these are connected to the .dx file or just the pdb2pqr file. Any help would be greatly appreciated thank you. Armond Minor Student, Biochemistry, SUNY Oneonta

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Draw schemas with Chimera ?
by Benjamin SCHWARZ 20 Feb '13

20 Feb '13

Hi list, I wonder if it is possible to draw "simplified schemas", such as those that can be found in biology publications where a protein complex is represented by a superimposition of ellipses, each ellipse representing a different protein in the complex, and their 2D placement reflects their known interactions in the complex (cf, for instance http://www.erasmusmc.nl/proteomics1/files/PBAP.jpg) This question triggered several interrogations : 1.) Is it possible in Chimera to draw 2D ellipses that would always reorient towards the screen as the scene rotates the same way the labels do 2.) Is it possible to draw ellipsoids ? 3.) Is it possible to save a picture in SVG format ? Thanks for your help, and thanks once more for the wonderful tool you provide us --Ben

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Drug-Protein Interaction
by kanika sharma 20 Feb '13

20 Feb '13

Hi All, I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position? -- *Regards,* * * *Kanika Sharma*

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2. Unit of electrostatic surface coloring within Chimera
by Boaz Shaanan 19 Feb '13

19 Feb '13

Hi Florian, The units for the electrostatic surface generated by APSB (andDelphi) are kT/e, which is what Chimera uses for determining the threshold when colouring the electrostatic surface. I'm quite sure that's the case. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Tuesday, February 19, 2013 7:53 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 118, Issue 20 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Algorithm for areaSAS calculations (Korbus, Michael) 2. Unit of electrostatic surface coloring within Chimera (Florian.Capito(a)external.merckgroup.com) 3. Drug-Protein Interaction (kanika sharma) 4. Re: New user-visualizing coulombic (Elaine Meng) 5. Re: session file/HID (Tom Goddard) 6. Re: questions about modeller and task panel (Elaine Meng) 7. Re: Drug-Protein Interaction (Elaine Meng) 8. Re: Algorithm for areaSAS calculations (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Feb 2013 10:27:44 +0100 From: "Korbus, Michael" <michael.korbus(a)h-da.de> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Algorithm for areaSAS calculations Message-ID: <0781A55E8298FD4CBCAAA70C4AF2EDB6350489B0BA(a)Virgon.h-da.local> Content-Type: text/plain; charset="us-ascii" Dear Ladies and Gentlemen, I have a question concerning calculation of areaSAS with chimera. Which algorithm is used? A Shrake-Rupley based algorithm? Thank you for your help. Sincerely, Michael Korbus Michael Korbus Dipl.-Ing. Biotechnologie (FH) Hochschule Darmstadt University of Applied Sciences Fachbereich Chemie u. Biotechnologie Schnittspahnstr. 12 D-64287 Darmstadt Tel +49/6151/16-8630 Fax +49/6151/16-8404 ------------------------------ Message: 2 Date: Mon, 18 Feb 2013 14:09:24 +0100 From: Florian.Capito(a)external.merckgroup.com To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Unit of electrostatic surface coloring within Chimera Message-ID: <OF57DE4D54.6BC4EDF1-ONC1257B16.004734C6-C1257B16.004845D9(a)merck.de> Content-Type: text/plain; charset=ISO-8859-1 To whom it may concern, I am using Chimera to color surfaces of proteins according to electrostatic potential files calculated by APBS. Now, in Chimera, there is the option to select a threshold, e.g. at which value the surface should be colored in red and at which value it is colored in blue. Now i would like to know in which unit this threshold works? Is it kcal (mol?e)-1? While this has been described for the Coloumbic surface coloring within Chimera Help, I could not find any explanation for this in the help menu, when loading external APBS potential files into Chimera. Thank You very much for Your time and help!!! Mit freundlichen Gr?ssen/ With best regards Florian Capito MM-PTD-New Downstream Darmstadt Location A17/217 Postcode: A046/509 Phone: +49 6151 72-7168 Email: florian.capito(a)external.merckgroup.com Merck KGaA Frankfurter Str. 250 D 64293 Darmstadt Homepage: http://www.merck.de Pflichtangaben finden Sie unter http://mandatories.merck.de Mandatory information can be found at http://mandatories.merck.de This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. ------------------------------ Message: 3 Date: Mon, 18 Feb 2013 12:24:37 +0100 From: kanika sharma <ksharma997(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Drug-Protein Interaction Message-ID: <CAAo-yeL3vs_KH76GdFQT0iP39-K2zcYRuBvmUG8pgfTxt8ivAQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi All, I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position? -- *Regards,* * * *Kanika Sharma*

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Unit of electrostatic surface coloring within Chimera
by Florian.Capito＠external.merckgroup.com 19 Feb '13

19 Feb '13

To whom it may concern, I am using Chimera to color surfaces of proteins according to electrostatic potential files calculated by APBS. Now, in Chimera, there is the option to select a threshold, e.g. at which value the surface should be colored in red and at which value it is colored in blue. Now i would like to know in which unit this threshold works? Is it kcal (mol·e)-1? While this has been described for the Coloumbic surface coloring within Chimera Help, I could not find any explanation for this in the help menu, when loading external APBS potential files into Chimera. Thank You very much for Your time and help!!! Mit freundlichen Grüssen/ With best regards Florian Capito MM-PTD-New Downstream Darmstadt Location A17/217 Postcode: A046/509 Phone: +49 6151 72-7168 Email: florian.capito(a)external.merckgroup.com Merck KGaA Frankfurter Str. 250 D 64293 Darmstadt Homepage: http://www.merck.de Pflichtangaben finden Sie unter http://mandatories.merck.de Mandatory information can be found at http://mandatories.merck.de This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer.

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meaning of evidence in PDB/UniProt Info
by Luis M. Sánchez 19 Feb '13

19 Feb '13

In PDB/UniProt Info some features have a line with a numeric value for evidence. For example: N-linked (GlcNAc...) (complex) evidence=1 2 3 7 8 9 10 12 What do those numbers means? Thanks for a great program and best regards -- Luis M. Sánchez

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Algorithm for areaSAS calculations
by Korbus, Michael 19 Feb '13

19 Feb '13

Dear Ladies and Gentlemen, I have a question concerning calculation of areaSAS with chimera. Which algorithm is used? A Shrake-Rupley based algorithm? Thank you for your help. Sincerely, Michael Korbus Michael Korbus Dipl.-Ing. Biotechnologie (FH) Hochschule Darmstadt University of Applied Sciences Fachbereich Chemie u. Biotechnologie Schnittspahnstr. 12 D-64287 Darmstadt Tel +49/6151/16-8630 Fax +49/6151/16-8404

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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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