- Chimera-users - RBVI Mailing Lists

Color by ramachandran probability? Or molprobity overlap?
by Oliver Clarke 19 Dec '13

19 Dec '13

Hi all, Quick question, just wondering if there is any way to color a structure by Ramachandran probability? Or by steric overlap scores for each atom as generated by mol probity? Either of these would be very handy as a way of getting a quick graphical overview of trouble spots in a structure. It seems like Chimera “knows about” Ramachandran plot data, (as one can generate such plots from the model panel) but I can’t find any convenient way to display this data on the structure. Many thanks, Oliver.

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Running Segger from a script
by Tom Goddard 19 Dec '13

19 Dec '13

Hi Rakesh, There is not Chimera command to run Segger, only a dialog. So you would have to use Python to run it and write out map files for each masked region if you wanted to script it. Segger uses several Chimera features such as Gaussian filtering, and watershed calculations that are in written in C++ and compiled against the Chimera Python. While you can get those to run in another Python if it has an identical version (e.g. 2.7.3), setting up the environment variables to find all the needed libraries is a difficult process. So I suggest using the Chimera Python. You can run Chimera scripts without the graphical interface by starting it from a shell "chimera --nogui myscript.py". The Segger Python functions are not documented so you would need to study the (complex and messy) code found in chimera/share/Segger or on Mac in Chimera.app/Contents/Resources/share/Segger Tom On Dec 18, 2013, at 5:54 PM, rakesh ramachandram wrote: > Hi, > > I would like to know if I can run Segger in a script in an automated fashion and then obtain the individual segmented regions as separate density maps. Is there a way to run chimera scripts from command line directly without using the chimera's python interpreter but using the default python interpreter after importing its libraries. > > Regards > Rakesh >

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question
by wanxiaobo＠nibs.ac.cn 17 Dec '13

17 Dec '13

Dear chimera team / users, I was looking for a way to save the content of Axis/plane/centroid information, not only the radii via command line, because I want to analyze the structure movement from MD trajectory. It is not convenient to save the information manually for each frame. Thanks Xiaobo

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Command line export to webgl
by Thomas Hrabe 17 Dec '13

17 Dec '13

Dear Chimera Team, I was curious if there was a functionality to export chimera scenes to webgl through the command line, without having to open the chimera window. Is there a set of python script commands that would do it? Thank you for your support, Thomas

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Attribute Calculator by command line?
by Hurt, Darrell (NIH/NIAID) [E] 16 Dec '13

16 Dec '13

Hi Chimera friends, I'm trying to calculate convexity as demonstrated in the Attributes tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html I can do it with the graphical tools without a problem, but when I try to do it via the command line, I run into trouble. I cannot find any documentation on running the Attributes Calculator on the command line. I've tried using "setattr": setattr a convexity atom.areaSAS/atom.areaSES This command generates a new atom attribute called "convexity" for every atom, but the value of this attribute for every atom is literally "atom.areaSAS/atom.areaSES" instead of the calculated value. Is there a way to calculate a new attribute value on the command line within Chimera? Sorry to be so demanding… Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Setting selection mode command line
by rswett＠chem.wayne.edu 16 Dec '13

16 Dec '13

Hi all, I'm interested in putting together a script that will open several large pdb files, select some very specific pieces of those files and save the output to another file. The problem is that they are large files and unwieldy in a graphics window. I have no problem generating the commands to select the regions I'm interested in, but I still need to be able to switch selection modes in between commands. Is there a way to change the selection mode at the command line without navigating the selection menu? Rebecca

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Export options for x3d2stl
by Hurt, Darrell (NIH/NIAID) [E] 16 Dec '13

16 Dec '13

Hi Chimera friends, Here's the second question of the day. Thanks for your patience with me. When I export the scene as an STL (for 3D printing), I think what happens is that Chimera outputs first an X3D file and then runs the utility program "x3d2stl" to create the STL. The X3D file is about 5 MB, but the STL is about 100 MB. I understand that much of this size inflation is because the "primitives" in X3D have to be converted to mesh objects for STL. However, when I look at the STL file, the meshes derived from the primitives are finer than I really need. I find that I can "get away with" a coarser meshification by using x3d2stl on the command line: x3d2stl -c -r 2 -o sticks.stl < sticks.x3d If I want to export the scene via the command line within Blender, is there any way to issue options to x3d2stl? Or should I just run x3d2stl outside of Blender? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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import binary format .raw file
by Carol J Hirschmugl 16 Dec '13

16 Dec '13

Hello, I am new to chimera, but have seen its capabilities for rendering 3D images of complex data sets, and think that this will be an appropriate program for excellent image analysis for my 3D tomography data sets. My data sets are in general binary format, (.raw file), 32 float, big endian, x fastest order for an x,y,z data set of 128 x 128 x 128 voxels of grey scale information. I am using AVIZO and FIJI at present. Avizo is expensive, and fiji is slow and reduces the data to 8 bit before rendering it, which I find unacceptable. TO move to Chimera - I found the web page in the Users Manual that suggested ADDING A FILE TYPE But I am lost by the description of how to proceed since I do not have prior knowledge of python and how to do the mapping to CHIMERA (x,y,z) that is suggested. I gather I need to write a python code - or numpy code maybe. Can you help or provide more context or a self-tutorial link so I can fill in the details? Thank you, Carol

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Local execution of pdb2pqr and APBS
by Hurt, Darrell (NIH/NIAID) [E] 16 Dec '13

16 Dec '13

Hi Chimera friends, Sorry to bother you again with so many questions. I'm trying to use PDB2PQR and APBS in a script to calculate an EP map. I know how to specify a local executable location for these external applications if I use the graphics interface, but the documentation that I can find does not indicate how to do this via the command line. Is it possible? How do I do it? Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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changing the rgb for stereo images
by Bala subramanian 13 Dec '13

13 Dec '13

Friends, I have a glass with a red-cyan color. When i use the Chimera stereo mode (red-cyan) under view controls. I still see some ghost images. I would like to know if there is any possibility to add a features something like a box where i can give the rgb (the light frequencies) values of the images to match my glass. Thank you, Bala -- C. Balasubramanian

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Dynamic scolor custom cmap?
by Hurt, Darrell (NIH/NIAID) [E] 13 Dec '13

13 Dec '13

Hi Chimera friends, I have a volumetric potential file loaded that I want to map onto a molecular surface. For my application, I want the color mapping to use a custom palette of at least three colors that spans the full range of surface values. I know that I can do this by simply specifying the custom colors in the Surface Color panel and then clicking "Set full range of surface values". That works for me. However, I want to do this via command line. The following line works for me (I've omitted "cmapRange full" because that is the default setting): scolor #0 volume #1 offset 1.4 cmap cyanmaroon My problem become if I want to set a custom palette: scolor #0 volume #1 offset 1.4 cmap -10,yellow:0,white:10,green This line also works, but for values lower or higher than –10 or +10, the color ramp "plateaus". And this line only works because the extents of this particular mapping happen to go from –29 to +17. Is it possible to obtain the values for the full range and specify them for a custom palette? Or is it possible to assign a custom palette and call it like the default palettes? I'm happy to clarify if needed. Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Modeling with cryo-EM
by Aurore Vaitinadapoule 13 Dec '13

13 Dec '13

Dear all, I'm would like tu use this following script to model with cryo-EM: from modeller import * log.verbose() env = environ() struct='./M60_9.pdb' map='new_map.mrc' resolution=10.2 box_size=48 # how to define the box size ?? apix=1.88 x=90; y=63; z=23 #origin steps=20 # Read in cryo-EM density map den = density(env, file=map, em_density_format='MRC', voxel_size=apix, resolution=resolution, em_map_size=box_size, density_type='GAUSS', px=x,py=y,pz=z) # Fit the PDB file into the map by MC simulated annealing den.grid_search(em_density_format='MRC', num_structures=1, em_pdb_name=struct, chains_num=[1], start_type='CENTER', number_of_steps=steps, angular_step_size=30., temperature=100., best_docked_models=1, translate_type='RANDOM', em_fit_output_file='modem.log') But i got this error message: _modeller.ModellerError: read_mrc_h_E> Density map must be cubic, and of dimension em_map_size (48): actual dimensions (40, 40, 36) What is exactly the box size? And how to define it? Thank's Aurore -- Aurore G. VAÏTINADAPOULÉ aurore <a.vaitinadapoule(a)inserm.fr>.vaitinadapoule(a)inserm.fr<a.vaitinadapoule(a)inserm.fr> a.vaitinadapoule(a)gmail.com PhD Student in Bioinformatics INSERM UMR-S665, DSIMB Team, Dynamique des Structures et des Interactions des Macromolécules Biologiques Mobile phone: +33(0) 778 18 52 07

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chimera slow
by Daniel Murin 12 Dec '13

12 Dec '13

Hi, I have been trying to use the Unit Cell function on Chimera. It works, but the graphic is so large that moving it around is nearly impossible because the program is running so slowly. It is rendered in ribbon. Is there a way to lower the quality in order to manipulate the graphic faster? Thanks! Charles Daniel Murin Ph.D. Candidate - Ward/Ollmann Saphire Labs Integrative Structural and Computational Biology Immunology and Microbial Science Kellogg School of Science and Technology The Scripps Research Institute 10550 North Torrey Pines Road, CimBio 105 La Jolla, CA 92037 Office: 858.784.3326 Lab: 858.784.7170 Fax: 858.784.8218 email: cmurin(a)scripps.edu

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(no subject)
by Danilo Di Maio 12 Dec '13

12 Dec '13

danilo.dimaio(a)gmail.com

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Launch external program from Chimera python script?
by Hurt, Darrell (NIH/NIAID) [E] 11 Dec '13

11 Dec '13

Hi Chimera friends, I am thinking of writing a script for Chimera that allows the user to map lipophilicity to the surface of protein. There are a few algorithms out there, but the easiest that I've found to use is "pyMLP": http://code.google.com/p/pymlp/ I see two ways to do this: (1) Write a wrapper script (shell, Python, etc.) to first run pyMLP to generate a DX file and then launch Chimera with its own script to generate the surface and do the mapping. (2) Write a Chimera Python script to launch pyMLP to get the DX file, generate the surface, and do the mapping. For my purposes, it might be easier in the long run to choose option 2, but that seems a little trickier starting out. Can you advise me on the best way to proceed? Also, I know that you aren't looking to add new functionality to Chimera v1, but the generation of a lipophilicity map might be a nice feature to add to Chimera at some point and pyMLP seems relatively easy to package with Chimera… Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Journal of Organic and Biomolecular Simulations: Full page charge waiver
by CompChem News 11 Dec '13

11 Dec '13

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select all side chains
by Zhou, Ming (NIH/NCI) [C] 09 Dec '13

09 Dec '13

Dear Elaine: I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? Thanks Ming Zhou

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Silhouette toggle
by Luca Pellegrini 05 Dec '13

05 Dec '13

Hi, I have set Silhouette ON in the Effects tab of the Viewing panel, and now I would like to toggle it off for one specific object. However, the Attributes window from Model Panel does not show the Silhouette option (it should feature between 'ribbon spline' and 'stick scale'). Can anyone please advice? I am using Chimera 1.9 (build 39137) for Mac . Kind regards, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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calculate buried surface area
by Bala subramanian 05 Dec '13

05 Dec '13

Friends, I have a dimer protein (say monomers 1,2). I have calculated the electrostatic potential of monomer 1 using apbs. I used volume viewer to display the electrostatic surface. I see that the elect. surface of one monomer 1, touches the vdw surface of monomer 2 at a contour level of 1. I want to calculate the total surface area of monomer 2 that is exposed/buried within the elec. surface of monomer 1. Is there any simple. If not suggestion how i can do it with a python script perhaps. Thanks, Bala -- C. Balasubramanian

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Problem of Launching Chimera Remotely on a Mac
by Anindito Sen 05 Dec '13

05 Dec '13

Dear All, I am having difficulty to launch Chimera remotely with the following Error message on my Mac. I understand that the current OS X (version 10.8.5) and the latest Xcode has some issues and cannot handle the process ?! Is there a way out of this ? Thanks and Best Wishes Andy [andy@****** ~]$ chimera Xlib: extension "NV-GLX" missing on display "localhost:15.0". Xlib: extension "NV-GLX" missing on display "localhost:15.0". X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1354 Current serial number in output stream: 1354 Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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Electrostatic potential values at each residue
by Tatsuhito Matsuo 04 Dec '13

04 Dec '13

Dear All, I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? Thank you very much in advance, T.M.

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Re: [Chimera-users] Surface area with positive electrostatic potential
by Tom Goddard 04 Dec '13

04 Dec '13

Hi T.M., To find the surface area with positive electrostatic potential would require computing the potential at surface points. Chimera does not compute solvent accessible surface (SAS) points (although it does compute total area). So there is no simple way to get the SAS area for positive potential points. Chimera does compute the solvent excluded surface (SES) using menu Actions / Surface or command "surface". For an SES surface a little Python code can give the fraction of the surface area colored red. I've attached that Python code red_area.py. You color the surface using the normal red-blue electrostatic coloring. The red_area.py code adds a command called "redarea" that computes the area of the surface that is more red than blue. Here's an example from the header of the red_area.py file. # Example use. # # menu File / Open..., red_area.py, Creates the new redarea command. # # open 1a0m # surface # coulombic -10 red 0 white 10 blue #0 # redarea #0 # # menu Favorites / Reply Log # -> "Surface MSMS main surface of 1a0m, red area 1400, total area 1888, ratio 0.7414" This script and other odd Python code for doing computations is on the Chimera developer web site: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts Tom On Dec 3, 2013, at 9:05 PM, Tatsuhito Matsuo wrote: > Dear Tom, > > Thank you very much for the reply and I'm sorry for inadequate information on what I've done (your guess is completely right). What I'd like to know is the ratio of the solvent accessible surface (SAS) with positive (or negative) potential values to the total SAS. The total SAS value is automatically calculated by the surface plot, and I need the value of SAS having positive/negative potential values. > At first, I thought the ESP value of "Attributes of Residues" is relevant to the one at the corresponding protein surface area. I now understand that this was wrong. Could you teach me how to get the SAS having positive/negative potential values? > > Best regards, > > T.M. > > On 2013/12/04, at 12:19, Tom Goddard wrote: > >> Hi T.M., >> >> I think you've left out details about what you have done -- how did you get this value_Coulombic_ESP attribute? Did you use values at atom positions? Did you use the "compute grid" option in the Coulombic Surface Coloring dialog? I guess you did that. And you say you use Attributes of Residues -- is that an average of the atom attribute obtained from the values at atom positions dialog? I can't be sure what you've done, but here's a guess at what your problem is. The Chimera Coulombic Surface Coloring dialog computes the potential at points 1.4 Angstroms out from the solvent excluded molecular surface and colors the surface points using that value. If you instead use a potential value interpolated at the center of an atom, that will give a much different value -- in fact it should tend to give an extremely large value because if the atom is charged the potential at the atom center is infinite using the simple Coulomb calculation. But because you are (I think) using a value interpolated from a grid you don't get an infinite value, just a very large value. So I think your problem is you are not considering that the electrostatic potential varies rapidly in space and you are comparing colors using potential values at different positions in space. >> >> Tom >> >> >> >> On Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote: >> >>> Dear All, >>> >>> I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? >>> >>> Thank you very much in advance, >>> >>> T.M. >>> >>> <ubiquitin.py><ubiquitin.pyc>_______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >

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request for removal from mailing list
by Aani Homeira 03 Dec '13

03 Dec '13

Thanks . . . . . . . . . . . . . . . . . . . A n i . H o m e i r a . A m i r k h a n i .

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Re: [Chimera-users] reading PDB-format alignment files
by Tom Duncan 03 Dec '13

03 Dec '13

Eric, It's not the structural info I want to extract - just the sequence alignment info. See the remarks in the file header. Thanks, Tom ----------------------------------------------------- Thomas M. Duncan, Ph.D. Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY On Dec 3, 2013, at 3:00 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > Date: Tue, 3 Dec 2013 11:27:02 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Tom Duncan <duncant(a)upstate.edu> > Cc: chimera-users BB <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] reading PDB-format alignment files > Message-ID: <9EF6E8D1-3C93-4C30-AD51-2B110CF5C813(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Dec 3, 2013, at 7:47 AM, Tom Duncan <duncant(a)upstate.edu> wrote: > >> Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file. > > Hi Tom, > Well, this "PDB" file doesn't conform to the PDB standard in a variety of ways, but the one you care about is the extra two columns on the ATOM records. The presence of those columns causes Chimera to skip those records. If you simply edit them out then Chimera displays the structure. I've attached an edited version of your file. I will open an enhancement-request ticket in our bug-tracking database for having Chimera ignore non-standard columns past the coordinate records (there are some standard columns that are supposed to be there!) and put you on the notification list for that ticket. > > --Eric

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reading PDB-format alignment files
by Tom Duncan 03 Dec '13

03 Dec '13

Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file. Thanks Tom ----------------------------------------------------- Thomas M. Duncan, Ph.D. Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY

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<< measuring areas >>
by Hatuey Hack 03 Dec '13

03 Dec '13

Hellos ChimeraUsers, It could be possible to measure different parts of a surface according to a given parameter? For example, from the electrostatic potential surface, I would like to know the respective area surface with positive and/or negative values. Best regards, Hatuey

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Information
by Mabel Guzman Rodriguez 02 Dec '13

02 Dec '13

Hello! I few days ago I tried to use your program Chimera, the reason is because I try to make a structure of a multimer protein but I need to know how can I bond the single subunits of the protein to make an hexamer. I hope you can help me. Greetings Mabel G.

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Re: [Chimera-users] Chimera- Imod file size problems
by Elaine Meng 02 Dec '13

02 Dec '13

Hi Ariane, I only know how to do it for "volume data" like MRC files and other density maps, but not for IMOD segmentation mesh (You said "imod mrc" but then it sounded like you meant a segmentation file instead.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod…> If it's a density map, you can adjust voxel size in the Volume Viewer (choose Features… Coordinates to show those settings) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu…> The same thing can also be done with the volume command, see "dimension and scale options": <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> Unless data are private, please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of only to me. Then If I don't know the answer or am away from work, others can respond. Thanks, 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 2, 2013, at 10:45 AM, Ariane Briegel <ariane.briegel(a)gmail.com> wrote: > Dear Elaine, > I have a question you might have a quick answer to. I am trying to open a model file I generated with the IMOD program. > Generally, when I open Imod mrc files in chimera the pixel size is correct in both programs. With this model the size is way off in chimera (I have never used an imod model in chimera before, just mrc files so far). > See screenshots below- the first one shows that the model has the correct pixel size when opened in IMOD, the second shows the wrong size in chimera (the blue and green layers should have the same height as the crystal structures below), and the last screenshot shows how the data opened in chimera (as a mesh). Is there a way for me to manually adjust the pixel size of a mesh? > If you have any idea how I can fix this issue I would be very grateful! > Thank you! > Ariane > <Screen Shot 2013-12-02 at 10.03.41 AM.png><Screen Shot 2013-12-02 at 10.35.06 AM.png><Screen Shot 2013-12-02 at 10.39.27 AM.png> > –––––––––––––––––––––––––––– > Ariane Briegel, Ph.D. > California Institute of Technology > Broad Center, MC 114-96 > 1200 E. California Blvd. > Pasadena, CA 91125 > > Tel: 626-395-8848 > Fax: 626-395-5730 > –––––––––––––––––––––––––––– > > >

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Query about increasing resolution for vrml export
by Darren Gowers 02 Dec '13

02 Dec '13

Dear Chimera community, Sorry to bother. I'm very interested in trying to increase the vrml export resolution (of any pdb model) so that more polygons are used to describe the curvature of the electron density more smoothly. There is a command in PyMol that does the equivalent (I think it is 'surface_quality'), but I'd rather use Chimera to generate vrml files! Does anyone have any suggestions how to make molecular surfaces much smoother please? Many thanks, Darren -- Dr Darren Gowers<http://www.port.ac.uk/departments/academic/biology/staff/title,30538,en.html> Senior Lecturer in Biochemistry School of Biological Sciences University of Portsmouth PO1 2DY +44(0)2392 842057

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Re: [Chimera-users] solvent-accessible surface area
by Amit Goyal 02 Dec '13

02 Dec '13

Hi Elaine, Today I subscribe to Chimera mailing list, but unable to get the proper way to post a query on it. So I am sending the query this way. I have been reading this post about how to get the areaSAS and areaSES values for any residues. http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002617.html Still, I think, is there any specific values/range for the areas AS to decide whether a particular amino acid residues is buried or exposed to the solvent. Hoping for Thanks for your help. Sincerely, AMIT -- AMIT GOYAL, Pusan National University, Korea south. amitgsir(a)pusan.ac.kr

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translation matrix
by Antón Vila Sanjurjo 02 Dec '13

02 Dec '13

Hi, I'm trying to get a translation matrix for two different crystal structures of ribisomal subunits. I've been trying to use the "measure rotation" command but I can only get it to display the following message "rotation angle is near zero (0 degrees)". I was wondering whether the command might be failing due to the fact that the ribosome contains numerous chains, or perhaps because the command does not deal with RNA. At any rate, how would one go about obtaining a translation matrix that can be applied to any model? best, Antón -- Antón Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Química Fundamental Facultade de Ciencias Universidade de A Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s(a)gmail.com

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colouring according to hydrophobicity
by Dieter Blaas 29 Nov '13

29 Nov '13

Hi, I am wondering whether there is any (easy) way of colouring a volume (e.g. an MRC file made from a pdb file and filtered to say, 10 A with e.g. xmipp) according to hydrophobicity (using the values derived from the amino acid residues in the pdb file)? I am aware of the way to colour the van der Waals surface but the resolution is somewhat too high not allowing to get a more general view, for example whether the molecule is more hydrophobic on one side than on another side. The same question applies to the charge distribution.... Thanks, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Overlay binding sites
by Markus Heller 28 Nov '13

28 Nov '13

Hello all, I'm pretty sure this has been done before, so before re-inventing the wheel or failing miserably and doing everything by hand, I thought I'd ask here first :) I have a protein that has been crystallized with about a dozen ligands of different sizes. I'd like to overlap the protein residues forming the binding site. My plan was to pick the 2 largest ligands, select all protein residues within say 7 A, and consider these to be the residues forming the binding site. Then, I'd like to match this set of residues for all proteins to the same reference. I suppose I could do this all manually, but I'm hoping that there is a quicker, more efficient way! Any tips are appreciated! Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image007.png@01CEEC32.879D5C80] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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features/question: stereo3d and volume rendering
by Dougherty, Matthew T 28 Nov '13

28 Nov '13

1) I have been doing S3D animations. One of things I am realizing is that I need to frequently adjust the interaxial and screen distances. Sometimes my IA might be 1mm or it might be 23 inches depending on the shot. Currently chimera does not maintain this camera metadata, so every session I need to reset the values which makes my animations slightly different. Since rendering can take several hours, one typo can trash the effort. Any suggestions on a workaround? There is also a linkage between IA, horizontal field of view, and screen distance, sometimes I think I get caught in a hysteresis loop trying to converge to the desired shot. As a note, I pretty much stopped using the zoom and have gone to dolly, keeping the scale to one. 2) when doing volume rendering of electron tomograms I am finding it useful to load the same mrc map file in multiple times, such that each model has a different transfer function relating to different densities or structures. I can currently load seven, but four must be changed from floating point to byte in order to prevent memory lockout thrashing, error messages, etc. Is there a way to load a single map file in and have multiple models and transfer functions for the solid viewing? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Protonation of selected atoms ?
by Marek Maly 28 Nov '13

28 Nov '13

Dear all, I would like to protonate just several nitrogen atoms (tertiary amines) of my hyperbranched polymer. I tried Structure "Editing -> Add hydrogens" but it protonised all my tertiary amines in the structure ignoring the fact that only few of them were selected and considered for protonation. So is there any way how to protonate only selected N atoms ? If not would be a good idea to add this possibility into Add Hydrogens panel (function). Thank you, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Automatic setting of suggested contour level
by Hurt, Darrell (NIH/NIAID) [E] 27 Nov '13

27 Nov '13

Hi Chimera team, I love how Chimera seems to intelligently and automatically choose a contour level for fetched EMDB files. However, I have noticed that most EMDB files have a "suggested contour level" associated with them. It can be obtained in the "header" XML files under the tag <contourLevel>. How much more work would it be to automatically fetch this information when fetching the map and then set the contour level to the recommended setting? Would you consider doing it? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Fwd: generate raised cosine smoothed mask with "mask ones" and "vop falloff"
by Tom Goddard 26 Nov '13

26 Nov '13

Hi Dieter, Chimera does not make masks with cosine falloff. The only mask smoothing in Chimera is "vop falloff". The algorithm is completely described in the Chimera manual (copied below) and basically amounts to a "heat equation" falloff -- the grid points outside the mask are assigned the average of the neighboring values, essentially the diffusion of heat from the masked ones region to the outside zeros region. This works for any shape. Tom "vop falloff volume-spec [ iterations M ] general-options Smooth the boundaries of a masked map by replacing the value at each grid point outside the boundary with the average of the values of its six nearest neighbors, for M iterations (default 10). All grid points with values of zero before the first iteration are taken to be outside the boundary, thus assigned a new value at each iteration. Thanks to Greg Pintilie for the initial implementation." Begin forwarded message: > From: Dieter Blaas > Subject: Re: [Chimera-users] generate raised cosine smoothed mask with "mask ones" and "vop falloff" > Date: November 26, 2013 8:34:17 AM PST > To: Tom Goddard > > Hi Tom, > > thanks for these explanations! I am still not sure whether such a mask behaves like a mask made with e.g. xmipp_transform_mask or with spider MA SOFT. I'd like to make an arbitrary mask (level 0 - 1) from a molecular volume which has a raised_cosine falloff. When comparing a spherical mask made with chimera (as given below) and with xmipp their histograms look quite different (probably also a question of the choice of parameters). The difference becomes much more striking when using a more irregular shaped molecular assembly. I found the Chimera procedure when looking for a method to make such masks as this is not provided in xmipp (only a sphere or a crown with raised-cosine but not an irregularly shaped mask). I want to use it in 3D-reconstructions...... > > Best, Dieter > > > > > > > > Am 25.11.2013 21:25, schrieb Tom Goddard: >> Hi Dieter, >> >> You should be able to generate a smooth volume mask using "mask ones" and "vop falloff" in Chimera. Here's an example making a smooth cylinder mask >> >> shape cylinder radius 100 height 100 caps true >> mask ones #0 border 10 >> vop falloff #1 iter 100 >> >> The boundary smoothing "vop falloff" is described on this web page >> >> http://www.cgl.ucsf.edu/chimera/data/falloff-sep2012/falloff.html >> >> Maybe you saw that page and got tripped up because it gave the wrong option name "step" instead of "iterations" in the vop falloff command -- I've fixed the web page. >> >> Tom >> >> >> >> On Nov 24, 2013, at 12:41 AM, Dieter Blaas wrote: >> >>> Hi, >>> I was wondering whether it is possible to generate binary raised cosine smooth masks with 'masked ones' followed by 'vop falloff' or anything alike. I'd like to generate an arbitrary mask (from a volume) with a smooth transition (over some few pixels) to 0 but I did not really find adequate parameters. Is this possible? >>> Thanks, D. >>> >>> -- >>> ------------------------------------------------------------------------ >>> Dieter Blaas, >>> Max F. Perutz Laboratories >>> Medical University of Vienna, >>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>> Dr. Bohr Gasse 9/3, >>> A-1030 Vienna, Austria, >> > > > -- > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > ------------------------------

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generate raised cosine smoothed mask with "mask ones" and "vop falloff"
by Dieter Blaas 25 Nov '13

25 Nov '13

Hi, I was wondering whether it is possible to generate binary raised cosine smooth masks with 'masked ones' followed by 'vop falloff' or anything alike. I'd like to generate an arbitrary mask (from a volume) with a smooth transition (over some few pixels) to 0 but I did not really find adequate parameters. Is this possible? Thanks, D. -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Re: [Chimera-users] Chimera-users Digest, Vol 127, Issue 22
by Boaz Shaanan 23 Nov '13

23 Nov '13

Hi Ahir, On my Dell & Nvidia dual boot (W7/linux) laptop there is the optimus feature which if it's on decides which graphics driver to use (on-board or Nvidia). You probably have a similar feature. In the system menu I switched the optimus off completely so I work only with the Nvidia driver. I did it mostly because of the linux side but keep this mode even when I'm under W7. My 2p advice. 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: Friday, November 22, 2013 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 127, Issue 22 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. Graphics Driver not switching to Nvidia (a.pushpanath(a)mail.cryst.bbk.ac.uk) 2. Re: Graphics Driver not switching to Nvidia (Tom Goddard) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Nov 2013 09:54:51 +0000 From: a.pushpanath(a)mail.cryst.bbk.ac.uk To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Graphics Driver not switching to Nvidia Message-ID: <20131122095451.15962g65x3dljxno(a)webmail.cryst.bbk.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Dear Chimera Users/Admins, I am having a sudden issue with Chimera, which refuses to pick the Nvidia GT 540M gfx card as my primary card whenever I start the program. I always get the Debug Graphics card, regardless of whether I have told the Nvidia Optimus technology to use the Nvidia card for chimera.exe. I am not entirely sure why this is happening, any help would be recommended! The intel HD graphics card is not good enough for my needs. Ahir ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ------------------------------ Message: 2 Date: Fri, 22 Nov 2013 10:07:27 -0800 From: Tom Goddard <goddard(a)sonic.net> To: a.pushpanath(a)mail.cryst.bbk.ac.uk Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Graphics Driver not switching to Nvidia Message-ID: <98429CC0-4EEE-4FB8-90D5-B67D0E27B913(a)sonic.net> Content-Type: text/plain; charset=windows-1252 Hi Ahir, Chimera does not decide which graphics card to use, your operating system decides that. The Chimera graphics debug dialog comes up every time because you set the Chimera preference "Debug OpenGL on Startup" and saved that preference setting. To turn that off use Chimera menu Favorites / Preferences?, turn the setting off and press the Save button at the bottom of the Preferences dialog. Tom On Nov 22, 2013, at 1:54 AM, wrote: > Dear Chimera Users/Admins, > I am having a sudden issue with Chimera, which refuses to pick the Nvidia GT 540M gfx card as my primary card whenever I start the program. I always get the Debug Graphics card, regardless of whether I have told the Nvidia Optimus technology to use the Nvidia card for chimera.exe. I am not entirely sure why this is happening, any help would be recommended! > > The intel HD graphics card is not good enough for my needs. > > Ahir > ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 127, Issue 22 **********************************************

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Graphics Driver not switching to Nvidia
by a.pushpanath＠mail.cryst.bbk.ac.uk 22 Nov '13

22 Nov '13

Dear Chimera Users/Admins, I am having a sudden issue with Chimera, which refuses to pick the Nvidia GT 540M gfx card as my primary card whenever I start the program. I always get the Debug Graphics card, regardless of whether I have told the Nvidia Optimus technology to use the Nvidia card for chimera.exe. I am not entirely sure why this is happening, any help would be recommended! The intel HD graphics card is not good enough for my needs. Ahir ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [Chimera-users] Chimera STL files
by Tom Goddard 20 Nov '13

20 Nov '13

Hi Julian, The problem is that you create a large density map for your protein, but then Chimera doesn't display it at full resolution, because it is so large. To make Chimera display the contour surface of the full resolution map set the "Step" value in the volume viewer dialog to 1, or use the equivalent command "volume #0 step 1" after the molmap command. Making the grid spacing 0.1 (40 times smaller than the resolution of 4 Angstroms) is likely to create a huge STL file that the printer will have trouble with, and it won't give any smoother appearance than say 0.4 I think. Tom On Nov 20, 2013, at 7:54 AM, Julian Gough wrote: > Dear Tom, > > I read what you wrote here: > > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-May/008825.html > > I am really struggling to make an STL file for a coiled coil protein for 3D printing. What I see happening in Chimera does not seem to correspond to what you say, i.e. I use "molmap #0 4 grid 0.1" which according to you should be super-smooth -being far beyond what you suggest-, but the STL file that I export still has very large and obvious triangles. > > I have played with it a great deal and I cannot find any way to control the number of triangles in the STL file. Whatever parameter I use for the grid, the output file is roughly similar in size. I can certainly fill the memory and crash it by making the grid smaller, but this is not reflected in the exported STL file. > > ANy guidance much appreciated. > > Julian > > > -- > ~~~~~~~~~~~~~~~~ > Julian Gough > Professor of Bioinformatics > University of Bristol > Department of Computer Science > Merchant Venturers building > Woodland rd, Bristol, UK, BS8 1UB > Tel: +44 (0)117 3315221 > Web: http://bioinformatics.bris.ac.uk > <owen2.py><owen2.stl>

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Set interatomic distances
by George Patargias 18 Nov '13

18 Nov '13

Hello Do you know if there is a way to set interatomic distances to a certain value in chimera (rather than measuring them)? Basically what I want to do is rotate/translate a peptide with respect to a protein so that a set of interatomic distances between the two are satisfied Many thanks! George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568

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measuring distances
by Ryan Pavlovicz 18 Nov '13

18 Nov '13

Hi, I am trying to measure the distance between two atoms from many different PDB structures using a python script. Using a command like: chimera.runCommand('distance #0:1@C1 #0:1@C2') will correctly output the distance within a tenth of an angstrom, however, i would like to output a more accurate measurement (more decimal places). Is there a way to do this when using chimera within a python script? Thanks for your help, ryan

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Commands for label formatting (font size etc)
by Andreas Göransson 18 Nov '13

18 Nov '13

Hi! How do I set font size for label / rlabel command in a command file? Can't find info in the documentation or in the mail list archive. Thanks, Andreas

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WebGL
by Hansen, Bryan (NIH/NIAID) [F] 18 Nov '13

18 Nov '13

Hi, I'm trying to export a scene using the WebGL feature within Chimera, but something seems to be going wrong. I'm attaching what opens up after Chimera saves the scene. I'm not able to rotate the output at all either. Is there a setting I need to change somewhere within Chimera? Thanks for your help and input. ************************** Bryan Hansen Microbiologist Electron Microscopy Lab NIH/NIAID/Rocky Mountain Laboratory 903 S 4th St Hamilton, MT 59840 (406) 363-9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Changing default max number of histograms shown
by Joel Meyerson 18 Nov '13

18 Nov '13

Hi, By default, Chimera displays up to 3 histograms in the "Volume Viewer". I know that this number can be increased manually in the "Data display options" after launching the program, but I would like to change the default number. Is there a built-in Chimera preference to set the default number to something higher? If not, can you perhaps suggest how this might be scripted to happen upon launching the program? Thanks, Joel

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Multi-fragment fit in map
by Paolo Swuec 18 Nov '13

18 Nov '13

Good morning, I am EM user and I was wondering wether is possible in Chimera to fit multiple pdb in the same volume (e.g. Fitting two monomers into a dimer map without overlaps and clashes). I am using Situs and the collage command, but I was wondering if there was an easy way of doing it in Chimera. Thank you very much, Paolo Paolo Swuec, Ph.D. Student Architecture and Dynamics of Macromolecular Machines London Research Institute Clare Hall Laboratories Cancer Research UK South Mimms Herts EN6 3LD, UK E-mail: paolo.swuec(a)cancer.org.uk<mailto:alessandro.costa@cancer.org.uk> NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

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Question on labeling residues on a single-chain protein
by J. David Puett 15 Nov '13

15 Nov '13

I wish to label certain residues and have these appear along with the structure. I have used the Command line to enter the following. rlabel Met_71.A What other Command(s) is required to display and later print the labeled structure? Many thanks!

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Measure buried area
by Jian Guan 15 Nov '13

15 Nov '13

Hi all, I use measure command to calculate the buried area between capsomer and Fab. My input file is pentamer.pdb and Fab.pdb. I made surface model for them respectively and use the command line as shown below: measure buriedArea #3 #2 probeRadius 1.4 However, it replied as "Surface calculation failed" I tried also delete all non-binding units in the pentamer, it still can not work. Does anyone know how to deal with that? Thank you so much. Sincerely yours, Jian

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Re: [Chimera-users] Residue selection
by Mark Girvin 14 Nov '13

14 Nov '13

Thanks for the info Eric, - Mark ________________________________ From: Eric Pettersen [pett(a)cgl.ucsf.edu] Sent: Thursday, November 14, 2013 3:43 PM To: Mark Girvin Cc: George Tzotzos ‎[gtzotzos@me.com]‎ Subject: Re: [Chimera-users] Residue selection Yeah, waters with a blank chain ID are put in chain "water" and similarly residues in HETATM records with a blank chain ID are put in chain "het". If the chain ID is non-blank, both get assigned the given chain ID rather than "water" or "het". --Eric On Nov 14, 2013, at 12:22 PM, Mark Girvin <mark.girvin(a)einstein.yu.edu<mailto:mark.girvin@einstein.yu.edu>> wrote: Got it. And no problem - just not quite expected. So then chimera sets up internal chain names (like "water") for some entries in PDB files? I don't think George's file had any internal chain entries, or HETATM lines. - Mark ________________________________ From: Eric Pettersen [pett(a)cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>] Sent: Thursday, November 14, 2013 2:50 PM To: Mark Girvin Cc: George Tzotzos; chimera List Subject: Re: [Chimera-users] Residue selection Yeah, the :127@O behavior is deliberate. If you omit the chain ID, it only matches single-character chain IDs (i.e. not chain ID "water" or "het"). This choice was made so that if your structure has a bunch of waters that so happen to have the same numbers as various polymeric residues, :127 will get the polymeric residue(s) but not the waters. This behavior was more important before the PDB remediation a few years back where such occurrences were commonplace. Now, in standard PDB files waters are frequently assigned specific chain IDs and therefore have different numbers than the polymeric residues. Chimera's behavior still matters for non-standard PDB files generated by various programs. If I were making the decision about Chimera's behavior today, given that the issue no longer affects standard PDB files, it might go the other way (it might not), but I don't feel strongly enough to change anything. A bunch of complaining could change my mind. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu<http://www.cgl.ucsf.edu/> On Nov 14, 2013, at 7:44 AM, Mark Girvin <mark.girvin(a)einstein.yu.edu<mailto:mark.girvin@einstein.yu.edu>> wrote: I don't know why that doesn't work, but: select :WAT@O seems to (if you only have the one water in your pdb file), as does: select :127.water@O (which would presumably limit the selection to the one water molecule) - Mark ________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu> [chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>] on behalf of George Tzotzos [gtzotzos(a)me.com<mailto:gtzotzos@me.com>] Sent: Thursday, November 14, 2013 8:08 AM To: chimera List Subject: [Chimera-users] Residue selection I'm attaching a pdb file of a protein ligand complex with a single conserve water molecule. The pdb file was constructed with Antechamber Leap. The water molecule is numbered as residue 127. When I try to select using: select :127 nothing happens. Selection works with: select :WAT The problem is that I need to monitor the distance between :127@O and a particular atom in the binding site of the protein during an MD trajectory. My question is if I'm doing something wrong with the residue selection. Many thanks in advance for your help Regards George _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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