April 2012 - Chimera-users - RBVI Mailing Lists

remote session
by Hernando J Sosa 23 Apr '12

23 Apr '12

Hi I used to be able to run chimera remotely from a machine with an X- windows server (the one that comes with Cygwin in this case). But now I get the following error: Xlib: extension "NV-GLX" missing on display "localhost:10.0". X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 148 (GLX) Minor opcode of failed request: 181 () Serial number of failed request: 12779 Current serial number in output stream: 12784 I t does work fine if run directly from the computer where chimera is installed. Any idea what the problem could be? Thanks Server computer: Chimera v 1.5 (similar problem with 1.6) OS: Linux OpenSuse 11.3 64b Client computer: OS: Windows 7 64. Graphics: ATI Radeon HD 5450

2 1

Displaying atoms within a distance
by Nikolay Igorovich Rodionov 21 Apr '12

21 Apr '12

Hi everyone, I am trying to display waters within a set distance from a solvated protein. Can someone please tell me how I can use the display or show commands to selectively show only the residues that are within a specific distance from a residue type? I've looked at the chimera manual and I am still confused on how these commands function. Thank you, Nikolay Rodionov

3 3

Charge calculations PDB2PQR
by Nikolay Igorovich Rodionov 20 Apr '12

20 Apr '12

Hi all, Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem? Sincerely, Nikolay Rodionov

3 7

Volume Viewer Mesh
by Terry Lang 20 Apr '12

20 Apr '12

Hey Guys, I am using the Volume Viewer to look at some electron density for a figure. I'd like to use the mesh option but when I generate the figure, the mesh is too fine, even at the starting default values. Is there a way to make the mesh coarser? Thanks, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

3 4

modeller interface
by Sadler, Evan 19 Apr '12

19 Apr '12

Hi, I'm trying to construct what I think should be a simple homology model and it's failing as below whether I use the web server or run modeller locally: Target seq: VWF_CK Template structures: 2TGI.pdb (#0)Run locally, the Modeller binary location: /Library/modeller-9.10/bin/mod9.10 Now, modeller is running locally... <type 'exceptions.UnboundLocalError'> Exception in Tk callback Function: <function command at 0x17982770> (type: <type 'function'>) Args: () Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 700, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerDialog.py", line 579, in Apply veryFast=self.veryFastVar.get(), tempPath=self.pathTempOpt.get().strip(), **kw) File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 247, in model if loopData: <type 'exceptions.UnboundLocalError'>: local variable 'loopData' referenced before assignment UnboundLocalError: local variable 'loopData' referenced before assignment File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 247, in model if loopData: See reply log for Python traceback. My version of Chimera is alpha version 1.7 build 36205, running under Mac 10.6.8. Do you have any advice? Thanks, Evan Sadler -- J. Evan Sadler, M.D., Ph.D. Chief, Division of Hematology Department of Medicine Washington University 660 S. Euclid Ave., Box 8125 St. Louis, MO 63110 Tel: 314-362-9067 FAX: 314-454-3012 email: esadler(a)wustl.edu

2 1

How to save high resolution image?
by Yogendra 19 Apr '12

19 Apr '12

Dear Sir, I am a new user of Chimera software. I am using this software for academic purposes (i.e. research publications). I am trying to save the image with more then 600 dpi but every time i am ending up with an image of 96 dpi. I am using the POV-Ray method for image improvement but everything is going to the drain when taking the final print of the document. Can you please help me ho can i save a high resolution image? I am briefly describing my protocol of image generation: 1) I am making a density map of particular PDB file. 2) loading in the Chimera and adjusting the volume by volume viewer option 3) Coloring it using described colors 4) Using Pov-Ray for increasing effects on plane 5) Increasing the pixels to about 5000 in the pixel option 6) finally trying to save an image with 600 or 1200 dpi. But at the end of this, i am just getting an image of 96 dpi every time. Can you please help me out to make an image of higher dpi (600, 1200 or more if possible). It will be very much helpful for me if can do it. I am stuck at this point.I am badly waiting for your reply whether i can do it or should i look for some another software. Regards Yogendra S Rathore Research Scholar ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202

4 6

Methanesulfinamide Stability and Synthesis
by Nancy 19 Apr '12

19 Apr '12

Hello All, I would greatly appreciate it if anyone has information on the stability of methanesulfinamide (SMILES: C[S](=O)N([H])[H]), as well as it's stability in water. Thank you.

3 2

Command line "Render by attribute"
by rswett＠chem.wayne.edu 19 Apr '12

19 Apr '12

So, I"m wondering if there's a way to call "Render by Attribute" command line for movie making purposes. I have several Defined Attributes and i'd like to be able to recolor surfaces by the various attributes at different points in a movie. What would the format for that type of command be? Thanks for any help you guys have! ~Rebecca

2 1

Check Marks in 2D Labels
by Paul Cernek 17 Apr '12

17 Apr '12

Hello, I'm having trouble inserting a check mark (Unicode page here: http://www.fileformat.info/info/unicode/char/2713/index.htm) into a 2D label, using the Chimera Daily Build from April 10 2012 on Windows Vista. I know that you can reference a special character via its Unicode escape sequence (in this case \u2713). Indeed, when I specify such text from the command line, or when I copy/paste the check mark into the text box of the 2D Labels window, it displays exactly what I want IN THE 2D LABELS WINDOW. However, in the main Chimera model display window the check mark is NOT properly depicted in the label. Instead, I get that empty square you get whenever a program encounters an unrecognized character. Other more conventional symbols (such as the Greek letter 'alpha') display normally. Why would the "2D Labels" window display the check mark properly, while the main display window does not? Any assistance in this matter is very much appreciated. Thanks, -Paul

3 2

APBS maps
by Rebecca Swett 12 Apr '12

12 Apr '12

Hey guys, i'm working with some electrostatic potential maps and am interested in doing a difference map. Two nearly homologous proteins with nearly identical surface shapes, and radically different electrostatics. I"m thinking a difference map would illustrate the differences well, but in looking at the APBS output I have no idea how to do that manually. Does anyone here have an idea about how to do that in chimera?

4 7

Chimera-users April 2012