- Chimera-users - RBVI Mailing Lists

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

2 2

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

2 1

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

3 5

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

3 3

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*

3 5

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*

1 0

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.

2 1

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

2 2

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

2 1

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).

2 1

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

2 2

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

1 1

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

2 1

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

3 9

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> >> **> >> >> >>

1 0

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

2 1

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> >> >>

1 0

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

2 1

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

2 1

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

2 2

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

1 0

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

2 1

(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

3 2

Re: [Chimera-users] Chimera on a virtualbox
by Greg Couch 06 Feb '13

06 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. >

2 1

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

2 3

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

2 2

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.

1 0

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

3 2

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)

2 1

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

2 2

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

2 4

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

1 1

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

1 0

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

1 0

Write DMS missing from Tools->Structure Editing menu? (v 1.6.2 and v 1.7)
by Duncan Napier 31 Jan '13

31 Jan '13

Hi, My first posting here, and I have come here after google searching high and low about this. I understand that Write DMS is now a standard part of Chimera, but I am (or more correctly, the users I support) not able to access or use it from the Tools->Structure Editing menu. I installed the binaries (x86_64 and x86) from the UCSF Chimera site, but none of them seem to have Write DMS functionality. I am running Ubuntu 12.04.1 LTS (Precise) on a Dell Vostro 486 PC, Intel Core i7-2600 3.4 gHz, 8 Gb RAM, 1 Tb SATA HDD, Video AMD Radeon HD 6450 1GB DDR3. What am I doing wrong? You can click on this link for a screenshot of what I see (its an XMing screenshot, but the view is the same in Ubuntu) http://www.sfu.ca/~dgnapier/post/chimera-DMS.jpg Any suggestions much appreciated! -- Thanks, Duncan.

2 2

1.7 production release
by Eric Pettersen 31 Jan '13

31 Jan '13

Hello everybody, The official 1.7 production release of UCSF Chimera is now available: http://www.cgl.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). Note: 1.6 was the last version to support Mac PPC and OS X 10.5. New features include faster loading and graphics, improvements in lighting and interactive shadows, "click-to-center" mouse mode, map display as orthogonal planes, interface to Modeller for building missing loops, Animation timeline, enhanced commands for animation, interfaces to PDB2PQR, APBS, and AutoDock Vina single-ligand docking. More details are given below; see release notes for the full list: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.7.html Graphics, Depiction: * faster loading of large molecules * faster graphics on many systems; target frame rate raised to 60 fps * interactive shadows: finer quality; available on more systems * glossy default lighting, better control over contrast * users can create custom presets * 2D Labels can have backgrounds (colored rectangles beneath) * PipesAndPlanks can color SSEs uniquely, show arrowheads * Actions...Color menu works on axis, plane, and centroid objects * CASTp pocket display omits small surface fragments * "surface" and "sop" command options to hide small fragments Animation: * Animation tool allows placing scenes and simple actions (rock, roll) along a timeline to define a movie * new output movie formats H.264, VP8/WebM, Theora * "play" command to animate complex motions like radial explosion * "transparency" command to set transparency of atoms, ribbons, etc. without otherwise changing their colors, can be applied gradually * "movie" command usability improvements * "perframe" allows embedding other commands directly, substituting variables other than frame count, executing at multiframe intervals * "roll" and "turn" command options for precession motion Structure Analysis and Modeling: * AmberTools updated to v12, default charges etc. now Amber ff12SB * "click-to-center" mouse mode (default Ctrl-right button) * "show distances to nearby residues" added to atom context menu * interface to Modeller for building missing segments * interface to APBS Poisson-Boltzmann electrostatics calculations * interface to PDB2PQR charge and radius assignment * interface to AutoDock Vina single-ligand docking * ViewDock support for AutoDock/Vina .pdbqt, GOLD .mol2 files * MD Movie can calculate average structures, plot RMSD vs. frame, read GROMACS .xtc format; occupancy calculation can treat atoms as VDW spheres (as opposed to points only) * Build Structure bond length slider, bond angle control * Multalign Viewer can use a subset of the existing sequences (rather than all) to guide alignment of a new sequence; the Region Browser lists individual-sequence regions separately (now that a sequence can have many UniProt annotations) Density Maps: * Volume Viewer orthogonal planes feature * Volume Tracer default mode includes placing markers on planes * "fitmap" option to fit multiple models independently * "vop cover" can extend a map using its symmetries Enjoy! On behalf of the Chimera team, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Measure inertia?
by Yen-Ting Lai 31 Jan '13

31 Jan '13

Hi, What's the formula that's used by "measure inertia"? I found a paper: An ellipsoidal approximation of protein shape. J. Mol Graph (1983) Does the "measure inertia" use the same method? Thank you! Yen

3 3

Command Patch problem
by mahad iou muddei addò 30 Jan '13

30 Jan '13

Hi, i'm working with chimera for the first time. I need to patch 2 structures that i have the PDBs. I've already read the user guide and try to follow the instructions for making a controlled superimposition of the two structures. These are my two sequence: 1)RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFR 2)DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/ I need to create a structure like this: RKYVYSLYWSTLTLTTIGETPPPVRDSEYFFVVADFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHF *RD*SSRRQYQEKYKQVEQYMSFH KLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQP GDYIIREGTIGKKMYFIQHGVVSVLTK-NKEM--KLSDGSYFGEICLLT------RGRRTASVRADTYCRLYSLSVDN FNEVLEEYPMMRRAFETVAIDRLDR/ I know the position of the aa involved but after i launch the command trough command line it gives me errors like match #0:422 #1:442 Unequal numbers of atoms chosen for evalutation What am i doing wrong? Thanks, sincererly Mahad

2 7

Selection and deleting
by Zhixue Zhu 29 Jan '13

29 Jan '13

Dear Sir/Madam: I just installed Chimera 1.7. However, I can not select individual atom or a group of atoms and then delete them. Please give some advice and instructions. Regards Zhixue

2 1

placement of metal ion in the protein model
by si yang 25 Jan '13

25 Jan '13

Good day to you, currently i am using Chimera to do some bioinformatics analysis, i want to put zinc ion into my predicted protein structure at the known binding sites, but i try to insert :Tools/structure editing/add ion/, but the option did not consists of zinc ion, hence may i know what are the alternative ways to introduce the zinc ion in order to facilitate the downstream application such as docking?? Hopefully can hear from you as soon as possible.... thank you -- Zhao Yang

2 2

Using Select with multiscale models
by Peter.Durr＠csiro.au 24 Jan '13

24 Jan '13

Hi I am using Chimera to try to visualise and then highlight the position of several amino acid mutations on a virus capsid. I have managed to use the Multiscale module to build the capsid from a PDB file. My next step is to select the residues of interest. I am able to use the Select command to find the residue within the icosahedral asymmetric unit - e.g. "select #0:14.A" However, when I apply the same command to the modelled surfaces, it doesn't work. More specifically when I run "select #1:14.A" at the command line - nothing happens - not even an error message. However, I can hunt around in the modelled surfaces on the screen and then use the mouse to interactively select the residue of interest - so Chimera seems to know which residues are which on the modelled surfaces. Thanks in advance for any guidance on how to deal with this problem. Peter Durr

2 1

Chimera 1.7 release candidate
by Elaine Meng 23 Jan '13

23 Jan '13

Hello, A Chimera production release candidate (version 1.7) is available; please try it and report any problems: <http://www.cgl.ucsf.edu/chimera/download.html> New features include faster loading and graphics, improvements in lighting and interactive shadows, "click-to-center" mouse mode, map display as orthogonal planes, interface to Modeller for building missing loops, Animation timeline, enhanced commands for animation, and interfaces to PDB2PQR, APBS, and AutoDock Vina single-ligand docking. See the release notes for details: <http://www.cgl.ucsf.edu/chimera/1.7/docs/relnotes/1.7.html> Mac PowerPC and OS X 10.5 are no longer supported. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

4 3

periodic shift of data in a Cryo EM map
by Benjamin SCHWARZ 23 Jan '13

23 Jan '13

Hi list, Sorry for the inaccurate vocabulary, I am not really from the field. I'll try to be as descriptive as I can. My problem is that I have a cryo EM map of a protein complex with the information somehow "shifted" in the "outline box". It looks like the center of my complex was placed on one corner of the outline box, and that the whole complex is thus spread over the 8 corners of the box… All the information is thus present in the map but should be periodically translated in order to place the center of my complex in the center of the box. I can think of two ways to solve my problem, and for both I need your help : 1. how to shift periodically the content of a map ? 2. how to create a new (and bigger) map by repeating and translating one map in the 9 surrounding directions ? Thanks in avance --Ben

2 2

selection using mouse
by francesco oteri 22 Jan '13

22 Jan '13

Dear Chimera's users, I downloaded and installed version 1.7 build 38047 and I noticed that is no longer possible to select atoms through mouse. Previously, I used the 1.6 and it was still possible using mouse for selecting atoms. I am wondering whether this function has been removed or I miss something? Francesci

2 1

(no subject)
by Jean-Francois Menetret 18 Jan '13

18 Jan '13

Hi, I am trying to restore sessions I saved about 4 months ago but I keep getting the following message: python2.7: ../../nouveau/nouveau_pushbuf.c:274: nouveau_pushbuf_flush: Assertion `0' failed. Aborted (core dumped) PS: I am currently using chimera version 1.7 (build 38083) J-F

2 1

colour with coulombic potential
by giulia zanetti 18 Jan '13

18 Jan '13

Hi all, I am trying to colour with coulombing potential only a portion of the surface I generated, and show it together with the rest of the surface, coloured in grey. The way I've done it is to create a duplicate of the pdb model, generate surface1 from the full model, and surface2 from the selected area, and colour with coulombic potential only surface2. The issue is that sometimes surface1 is "in front" of surface2, and the only way to see surface2 is to hide surface1. This is not related to the order I create the surfaces apparently, but rather to the order I created the models. Is there a way to "bring to front" or " send to back" surfaces or models for display purposes, rather than copying models (and re-doing the selection for the residues that I want coloured?). Or a way to colour with potential only the selected area of a surface? Thanks! Giulia

2 4

Re: [Chimera-users] Homology Modeling
by Elaine Meng 17 Jan '13

17 Jan '13

Hi CE, Different or missing chain IDs are not a problem, unless they somehow cause your specification to indicate different numbers of atoms in the two structures. The example command I gave in the previous message had one structure with chain A and the other with no chain ID. Different residue numbering is also not a problem, because you enter the numbers yourself in the match command. > match #1:482-513.A@ca #0:212-243@ca However, a structure without chain IDs could cause a problem if it contains multiple chains and thus more than one residue with the same residue number. Other common reasons for an error message like this: (a) the specification syntax is simply wrong (b) one structure has "alternate locations" (for example, 2fma residue 170.A) and thus multiple instances of the same atom/residue/chain name. If I run into this, I usually delete the alternate locations (e.g. command "delete @.b" would delete all alternate locations B) and try again. You can see how many atoms each specification generates with commands like: select #1:482-513.A@ca select #0:212-243@ca It is impossible to guess without having the actual structure and seeing the exact command that you used, sorry. However, if you think it is related to chain ID, that can be changed using "Change Chain IDs" (in menu under Tools... Structure Editing) or command "changechain" <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechai…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html> 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 Jan 17, 2013, at 2:26 PM, Chinaza Egbuta wrote: > Hi Elaine, > > Thank you for your prompt response. Yes, the question is actually about 3D superposition. I used the match command following the atom specification syntax described in <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>. However, I have been getting the following error message "Unequal number of atoms chosen for evaluation". > > The two models I am comparing both have the same model number but the chains are different (one is "chain A" and the other is "principal chain"). This could be because the actual homology modeling was performed on the MOE platform (chemical computing) and the chain numbers are assigned differently. Please could you let me know if I the error message is as a result of this nomenclature? If yes, please could you provide me with information on how to change the chain number? > > Thank you! > > CE

1 0

copy file command
by Rachel Kramer Green 17 Jan '13

17 Jan '13

Hi, I am trying to save an image using the cmd line in Chimera. The command that I am using is: copy file testimage.jpg jpeg width 500 height 500 It looks like it is working. The bottom bar of the display screen says "rendering high resolution image" and then "Finished saving image(s)." However, then I cannot find a created file anywhere. Any idea what is happening to the saved file? Thanks! -- ------------------------------------------------------------------------ Rachel Kramer Green, Ph.D. RCSB PDB kramer(a)rcsb.rutgers.edu

2 1

Re: [Chimera-users] Homology Modeling
by Chinaza Egbuta 17 Jan '13

17 Jan '13

I have a protein with multiple modules that are homologous to each other. I have generated a homology model of one module based on the structure of another. However, I need to align a specific peptide that is identical between my two modules. Is there a way to do this? Thank you. CE

2 1

Structure minimization
by Bobo Dang 15 Jan '13

15 Jan '13

Hey All, I am trying to use Chimera to minimize a small protein with a special structure, the model has nonstandard amino acid, Also the N-terminal is connected to cyclized to one Asp side chain, is it possible to minimize this modified structure by Chimera? Thanks bobo

3 6