- Chimera-users - RBVI Mailing Lists

selection line-width
by Daniel Gurnon 15 Dec '10

15 Dec '10

Hi everyone, Two requests that would help with interactive demonstrations to large audiences: In preferences/background, the selection mode can be "fill" or "outline". Is it possible to add a line-width option for outline? I want to increase the thickness of a selection outline to make it easier for my students to see when I'm projecting an image, but I don't want to use the fill option and lose residue color information. I suspect that's an easy fix, but this one might be more difficult: Transparent surfaces are very informative when combined with underlying ribbons or stick representations of atoms. But if a residue is visible beneath a transparent surface, selecting it (via the command line) does not show the selection outline. Is it possible to make that work? Thanks, Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] [Chimera-announce] Chimera 1.5 release
by Elaine Meng 15 Dec '10

15 Dec '10

Hi Surendra, Yes, if you are doing map-in-map fitting, it calculates the correlation values, in 1.5 and also in earlier versions. You have the choice of calculating the correlation about zero or about the mean. If you are doing atoms-in-map fitting, it does not give correlation values UNLESS you turn on the "Use map simulated from atoms" option, and in that case you also need to enter a resolution value for the simulated map. If you click the Help button on the dialog it will show the manual page with more detailed explanations, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht…> 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 Dec 15, 2010, at 9:33 AM, Negi, Surendra S. wrote: > Hi Elaine, > In EM fit, Is it possible to calculate the Correlation? I am using current version 1.5 of UCSF chimera. > Thank you. > Surendra > ps: the snapshot is available at : http://img221.imageshack.us/img221/2492/screenshotpt.png

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Maximum surface areas for each amino acid
by Boaz Shaanan 15 Dec '10

15 Dec '10

Hi Elaine, The values in the table you mentioned seem to correspond to side-chain accessibility only, if I compare them to those for Gly-X-Gly peptide as in the classical paper by Miller et al. (1987), 196, 641-656. Their table can also be found in the book by Creighton: Proteins, 2nd edition, p. 142. Best regards, Boaz ----- Original Message ----- From: chimera-users-request(a)cgl.ucsf.edu Date: Tuesday, December 14, 2010 21:11 Subject: Chimera-users Digest, Vol 92, Issue 11 To: chimera-users(a)cgl.ucsf.edu > 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. Maximum surface areas for each amino acid (Tom > Goddard) 2. Center of segmentation regions (Tom Goddard) > 3. Chimera Error (Kshatresh Dutta Dubey) > 4. Re: Chimera Error (Elaine Meng) > 5. Re: Maximum surface areas for each amino acid > (Elaine Meng) > 6. 3D-Stereo. (ayassin(a)wadsworth.org) > 7. merging 3D volumes (Marlovits,Thomas) > 8. Re: merging 3D volumes (Elaine Meng) > > > ----------------------------------------------------------------- > ----- > > Message: 1 > Date: Mon, 13 Dec 2010 18:08:11 -0800 > From: Tom Goddard <goddard(a)sonic.net> > Subject: [Chimera-users] Maximum surface areas for each amino acid > To: iropson(a)psu.edu > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4D06D18B.7040806(a)sonic.net> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Ira, > > I don't know of any table of maximal solvent > accessible surface areas > for each residue type when bounded by glycines. Maybe > someone on the > Chimera mailing list will know. > > A Chimera Python script could run through the PDB > and accumulate > per-residue surface area statistics. One trouble with that > would be > that surface calculation fails in Chimera in some percentage of > cases > (~5%) due to numerical problems. > > Tom > > > Hi Tom, > > > > Love the software. Do you have a table for calculating the > maximum > > available surface area for amino acids eg.(Gly-Xxx-Gly) so > that I can > > get a relative percentage exposed surface area from the > calculations? > > Do you know how to find one in the literature? Has anyone > written a > > program that describes the possible surface exposure for a > residue in > > a particular secondary structure and/or a particular sequence? > This > > maximal value would certainly be different depending on the > local > > sequence and structure. For example, a residue in the middle > of a > > helix would have to be shielded from the solvent by the i+4 > and i-4 > > residues, and the size of those residues would matter. > > > > Thanks, > > Ira > > > > > > On 12/10/10 2:41 PM, Tom Goddard wrote: > >> Hi Sumitro, > >> > >> I made a Chimera video tutorial showing how to > determine which > >> residues are on the surface. > >> > >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html > >> > >> Tom > >

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delete named selection
by S. Shunmugasundararaj 14 Dec '10

14 Dec '10

Hi, How do I delete the "Named selection" from the chimera file? I could not get the info from the archive or by searching the web. Thanks in advance Raj

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3D-Stereo.
by ayassin＠wadsworth.org 14 Dec '10

14 Dec '10

Hello, Will the sequential stereo work with the Nvidia 3D vision kit available with the Toshiba 3DV series laptops? if not, What would be the best option for sequential stereo? Thank You. Aymen Yassin. IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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merging 3D volumes
by Marlovits,Thomas 14 Dec '10

14 Dec '10

Hi, I was wondering, whether a 3D map can be placed into a box with a user defined number or x/y/z planes ? Ideally, I would like to place several 3D maps into boxes of the same dimensions and would like then to merge all maps into one 3D map file. Is this possible ? Tx for your fast answer, Best, -Thomas Thomas C Marlovits Research Group Leader marlovits(a)imp.ac.at

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Chimera Error
by Kshatresh Dutta Dubey 14 Dec '10

14 Dec '10

Dear All, When i am trying to assign partial charge on a molecule, it is giving error something like this- AttributeError: '_chimera.Atom' object has no attribute 'gaffType' File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py", line 289, in writeMol2 atomType = atom.gaffType I am using chimera 1.5 on linux 64-bit Kindly help to resolve this problem Thanks in advance kshatresh

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Maximum surface areas for each amino acid
by Tom Goddard 14 Dec '10

14 Dec '10

Hi Ira, I don't know of any table of maximal solvent accessible surface areas for each residue type when bounded by glycines. Maybe someone on the Chimera mailing list will know. A Chimera Python script could run through the PDB and accumulate per-residue surface area statistics. One trouble with that would be that surface calculation fails in Chimera in some percentage of cases (~5%) due to numerical problems. Tom > Hi Tom, > > Love the software. Do you have a table for calculating the maximum > available surface area for amino acids eg.(Gly-Xxx-Gly) so that I can > get a relative percentage exposed surface area from the calculations? > Do you know how to find one in the literature? Has anyone written a > program that describes the possible surface exposure for a residue in > a particular secondary structure and/or a particular sequence? This > maximal value would certainly be different depending on the local > sequence and structure. For example, a residue in the middle of a > helix would have to be shielded from the solvent by the i+4 and i-4 > residues, and the size of those residues would matter. > > Thanks, > Ira > > > On 12/10/10 2:41 PM, Tom Goddard wrote: >> Hi Sumitro, >> >> I made a Chimera video tutorial showing how to determine which >> residues are on the surface. >> >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html >> >> Tom

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Center of segmentation regions
by Tom Goddard 13 Dec '10

13 Dec '10

Hi Tyler, The Chimera Segger segmentation tool currently doesn't report the geometric center of segmentation regions or the principal axes. I've attached a Python script that will do that. Select the regions in Chimera then open the script (File / Open). The results will appear in the reply log (menu Favorites / Reply Log). The results are in physical coordinates (taking account of volume grid spacing), not grid index units. Tom > Dr. Meng, > > I am using Segger in Chimera and displaying the principal axes for > some of my segmentations. I am wondering if there is a way to find > the XYZ coordinates of the origin of the principal axes for each of my > segments. Is there a way to put the coordinates for these axes in a > text file? > > Thank you, > > Tyler Steele >

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Inatallation Location
by Stephen P. Molnar 13 Dec '10

13 Dec '10

Chimera 1.5 (32-bit) on OpenSuSE 64-bit v11.2 I have just installed 1.5 on my syustem.. The installer insists on an installation in /home/computation/.local in spite of my attempts to install in a location of my choice. This is rather annoying as I prefer to install software on a hard drive that will not be overwritten when I upgrade the OS. Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivarate http://www.FoundationForChemistry.com

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Chimera Error
by יוכבד 13 Dec '10

13 Dec '10

---------- Forwarded message ---------- From: יוכבד <ybaime(a)gmail.com> Date: Mon, Dec 13, 2010 at 11:44 AM Subject: Chimera Error To: chimera-users(a)cgl.ucsf.edu Hi I'm trying to open a density map file using chimera and for some reason the file won't open. The opening is followed by an error message regarding the file size being too small for the grid size. The same error appears also in the old version (1.4.1) and also in the newest version. How can I solve this problem? How can I change the grid size? The same file opens successfully on a friends computer with the 1.4.1 version and so I assume the file is not corrupted. Attached is an image of the error message. I'd appreciate your response. Thank you Yocheved Baime Bar-Ilan univ.

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Calculating Solvent Accessible Surface of individual residue in a model
by Sumitro Harjanto 10 Dec '10

10 Dec '10

Hi Meng, I would like to find out if I can use Chimera to calculate the solvent accessible surface(SAS) of each residue in a model..? I would like to find out, basically, if I show the surface of the molecule, which are the residues buried (SAS = 0) and which are the ones contributing to the surface contour (SAS > 0). Thanks! =] Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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Measuring the volume enclosed by a complex
by Anindito Sen 10 Dec '10

10 Dec '10

Dear All This question may have been answered before but will be helpful if you can let me know - How can I measure the volume enclosed by a protein complex. Thanks Andy Dr. Anindito Sen (Ph.D) School of Biological Sciences University of Auckland 3A Symonds Street Room 420 Auckland City. New Zealand. Tel: +64 -9- 373-7599 ext: 87593

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Recommended HW for Chimera 3D
by Marek Basler 07 Dec '10

07 Dec '10

Hi, what would be recommended HW and OS for trouble free 3D using glasses with new 120Hz LCDs? Linux or Win? What is the best graphics card? I don't care about money but nothing crazy either. Any suggestions? Thanks a lot! Marek

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Re: [Chimera-users] Query regarding Fit in Map
by Tom Goddard 07 Dec '10

07 Dec '10

Hi Arun, So you just want to measure the correlation for a selected atoms in a map, no fit optimization. This can be done without Python. Make a simulated map with the Chimera "molmap" command, and report the correlation with "measure correlation". molmap sel 12.5 modelId #5 measure correlation #5 #0 Here the map is #0, selected atoms are referred to using "sel" and a simulated map for those atoms is created as model #5. Results with be in Chimera reply log (menu Favorites / Reply Log). I don't think you want to turn off the "use only data above contour level". If you do it will measure the correlation of the entire box of simulated data including all the zeros far from the atom, which probably will not match the non-zeros in your map. If you really want that use option "aboveThreshold false" with the measure correlation command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat… Tom > Hi Tom, > > Thank you very much for your kind reply. It is quite helpful to know. > I am able to run the script and fit a map on to a map. But the problem > at had is slightly different. I have got the fits done already with > Flex-EM and I am actually trying to measure (ideally automate it with > the Chimera script) the correlation for the currently selected atoms > in the given map using the 'Update' option available in the Fit in Map > dialog. I would also like to specify the following option in the script. > > Real-time correlation / average update (turn off within the script) > Use map simulated from atoms, resolution = value > use only date above contour level from the first map (turn off within > the script) > optimize correlation > correlation calculates about mean data value (turn off within the script) > rotation (turn off within the script) > shitf (turn off within the script) > Move whole molecule (turn off within the script) > > I am not sure how to put all this options in a script and calculate > the correlation for the currently selected atoms with the Update > option. I would greatly appreciate if you could provide me with some > more insight on how to change the code specifically. Thanking you. > > with kind regards, > Arun Prasad > > > Tom Goddard wrote: >> Hi Arun, >> >> Yes you can use Fit in Map in a script. I've attached an example >> Python script. This script comes from the Chimera Python scripts web >> page but that web site is down right now. It is necessary to use >> Python rather than a simpler Chimera command script because there is >> no Chimera command to use Fit in Map. There probably should be, but >> since Fit in Map only does a local optimization you need some way to >> initially position the molecule or map you are fitting. That is the >> hard part and so there hasn't been much demand for the fitting command. >> >> The Python code for the Fit in Map dialog is included in all >> Chimera distributions in the directory >> >> chimera/share/FitMap >> >> You could look at the __init__.py and gui.py to learn what the >> available functions are. The gui.py (graphical user interface) file >> shows how those functions are called by the dialog. >> >> Tom >> >>> Hi all, >>> >>> I would like to know whether its possible to automate the operations >>> available with 'Fit in Map' tool and its options within a script. >>> Actually I would like to calculate the correlation for certain segments >>> of the atomic structure and it would be help if I could do it with a >>> script rather that the GUI. Any suggestion is greatly appreciated. >>> >>> Thank you, >>> Arun Prasad >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> >

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problem in showing disulfide bonds
by Pardeep kumar 06 Dec '10

06 Dec '10

Hi, I am unable to show disulfide bonds in my final structure. It has at least five disulfide bonds. Please tell me how can I do that???and how can I save the image as a post script file....I tried it by save as .ps file but then the save file was not there in the designated folder though other formats (eg jpeg) were easily saved....

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"Surface calculation failed, mscalc returned code 5"
by Sumitro Harjanto 06 Dec '10

06 Dec '10

Hi Meng, I've run into this problem a few times when I wanted to calculate and show the surface of a pdb model. I got the following on my reply log: C:\Chimera\bin\mscalc.exe 1.400000 2.000000 1 Calculation of some surface components failed. Falling back to single-component calculation. C:\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 Sometimes I managed to go around it by resaving the pdb file in Chimera, or removing some irrelevant chains. but other times it just doesn't work. Any suggestions? One particular file that gives me the problem is 1IGT from PDB. I've tried removing all the heteroatoms and water molec, for I only need the chains A, B, C and D. but still the problem persists. Thanks! Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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Query regarding Fit in Map
by Arun Prasad Pandurangan 03 Dec '10

03 Dec '10

Hi all, I would like to know whether its possible to automate the operations available with 'Fit in Map' tool and its options within a script. Actually I would like to calculate the correlation for certain segments of the atomic structure and it would be help if I could do it with a script rather that the GUI. Any suggestion is greatly appreciated. Thank you, Arun Prasad

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need examples of Chimera crash on Mac OS X 10.6.5
by Greg Couch 03 Dec '10

03 Dec '10

There have been occasional reports of Chimera crashing in the graphics driver on Mac OS X 10.6.5. However, the reports have not included enough information to allow us to reproduce the problem and debug it. If you observe this crash, please report it to Apple (a dialog to do this will appear when the crash happens). The next time you start Chimera after the crash, another dialog will appear with the option to send us a bug report too. Please go ahead and do that, including a description of what you were doing before the crash, and your email address in case we need to request further details. Thank you, Greg

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how to product a color scale bar
by C.J. 03 Dec '10

03 Dec '10

Dear all, I am writing to ask how to product a scale bar to indicating different radius with different color when I visualizing a spheric structure with Chimera. Thanks. Regards! C.J.

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unable to show disulfide bonds
by Mahlawat, Pardeep 02 Dec '10

02 Dec '10

Hi, I am unable to show disulfide bonds in my final structure. It has at least five disulfide bonds. Please tell me how can I do that???and how can I save the image as a post script file....I tried it by save as .ps file but then the save file was not there in the designated folder though other formats (eg jpeg) were easily saved....

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display angle label
by Gesa Volkers 02 Dec '10

02 Dec '10

Dear all, I measured an angle (or better torsion) between four atoms. How can I display the angle with a label? I only found how to diplay measured distances with a label, but not angles/torsions. Thanks in advance, Gesa -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

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Re: [Chimera-users] Exporting .stl
by Greg Couch 01 Dec '10

01 Dec '10

Forgot to reply to list as well. -------- Original Message -------- Subject: Re: [Chimera-users] Exporting .stl Date: Tue, 30 Nov 2010 13:33:23 -0800 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: Dennis Kolva <dk429(a)cornell.edu> On 11/25/2010 06:29 PM, Dennis Kolva wrote: > I have been using Chimera to export .stl files of proteins and RNA for 3D printing. The surface models print OK, but sticks or ribbons choke the printer. I looked close at the output meshes, and they have many extra surfaces which should be removed to make "legal" .stl format. > > Is that portion of the code open source? I'd like to take a closer look and see if it's possible to fix. It would be much easier to rectify the bad surfaces upon creation, rather than trying to remove them by post-processing. > > Thanks, > > Dennis Kolva > Cornell U. Presumably , you don't have a Z-Corp printer and their ZPrint software, otherwise you would output VRML from chimera and have ZPrint do the proper conversion to STL. So yes, the source code is available at http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/apps/x3d2/stl, and we would welcome improvements. I believe that the problem is that chimera does not output manifold geometry and that the X3D to STL converter would need to perform CSG operations on all of the geometry, especially the spheres and cylinders, to eliminate interpenetrating surfaces. Another issue to consider is what to do about ribbons and cylinders that are too thin for the printer you're using. Feel free to contact me directly with questions about the code or use the chimera developers mailing list, chimera-dev(a)cgl.ucsf.edu, Greg

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pythonw.exe error
by Hunmin JUNG 01 Dec '10

01 Dec '10

Hi, Whenever I open the chimera after the installation, it gives me an error 'pythonw.exe has stopped working'. It didn't matter the version of the chimera. Please what I need to do to resolve the problem. Thanks, Hunmin (Mike) Jung Department of Chemistry Texas A&M University (979)862-7639

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Closest Waters
by Beale, John 30 Nov '10

30 Nov '10

I am working with a protein in explicit water. Using AMBER tools, I have selected the 100 closest water molecules in and around the protein. Is there a way in Chimera to identify which amino acid residues that the waters are hydrogen bonded to? Or, is there a way to visualize which amino acids the water molecules are closest to? Thanks! John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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