- Chimera-users - RBVI Mailing Lists

movie recode
by Wenda Wang 21 Jan '14

21 Jan '14

Dear List, I am trying to use UCSF chimera to make a movie after TEM reconstruction using IMOD. But an error message always pops out, even I use the script in the examples. Belows shows the error messages in the Reply Log. Can anyone take a look and give me some clue where the problem is? Thank you. ----------------------------- C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -vf crop=(in_w/2)*2:(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -vb 200.0k C:\Users\Public\Desktop\rock.mp4 An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ----------------------------- C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libvpx -f webm -vb 200.0k C:\Users\Public\Desktop\rock.webm An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ----------------------------- C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libtheora -f ogg -vb 200.0k C:\Users\Public\Desktop\rock.ogv An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: Thank you very much, Wenda Wenda Wang, PhD candidate Department of Materials Sciences and Engineering, Drexel University, Philadelphia, PA 215-6883348

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Morphing
by James Naismith 20 Jan '14

20 Jan '14

I am experimenting with the morphing feature. I know I am being very stupid but I cannot get the analysis to work. I am using a MAC OSX latest version. I have created my morph which is running nicely. What I would like to do is analyse the morph for VDW clashes. (That is in going from structure 1 to structure 2, what residues would have to move). First problem is when I run cluster (under analysis in MD movie) then generate residue interaction for cluster, up pop a new dialogue with warnings but seems to ask about calculations When I click OK or apply I get a new box residue interaction contact parameters This always generates an error “No atoms designated for clash detection’ I seem only to have four options themselves all others atoms (default) other atoms in same model second set of designated atoms Any help gratefully received (Ps I have installed the latest cytoscope but it does not have the structure.viz plugin; I keep getting errors trying to install older version) best Jim Jim Naismith The University of St Andrews is a charity registered in Scotland : No SC013532

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Re: [Chimera-users] [Chimera] #12778: failure assigning charges to FAD (was: Chimera bug report submission)
by Eric Pettersen 17 Jan '14

17 Jan '14

Hi Will, The underlying program that Chimera uses to compute charges, antechamber/sqm from AmberTools, frequently fails for molecules with regions of concentrated negative charge, such as the central phosphate connector of FAD. It not really something I can do much about. Nonetheless, the failure not only depends on the charge density but also on the specific atomic geometry. So for instance, I can compute the charges for the FAD in 4kpu, though it does take a long time (about 10 minutes). This means that there is kind of a work around. Compute the charges in a structure that works and then transfer them to your structure. You do this by bringing up the Render by Attribute tool after successfully computing charges and using it's File->Save Attributes menu entry to save the charges to a file. You should select the FAD and then restrict the save to selected atoms. Edit the resulting file and change the residue name and chain ID (in this case 401.A) to FAD so that it can be applied to all FADs in your structure. Then in the Chimera with your structure open, read in the charge-attribute file with the Define Attributes tool. To save you a lot of the effort here, I've attached the edited charge-attribute file I saved from 4kpu. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to display coordinate axes
by Michael H Peters 17 Jan '14

17 Jan '14

Hi: I have a simple question - How do I display the lab or fixed frame coordinate axes? I am using the windows 32 bit UCSF Chimera on my desktop. In rasmol the command is "axes on". I cannot find anything similar in Chimera. Thanks for your help. An axes display is critical if you need to know the spatial orientation wrt the lab frame. Best wishes, Michael Dr. Michael H. Peters mpeters(a)vcu.edu 804-828-7790 www.engineering.vcu.edu/proteinengineering

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pyroglutamate distorted in 3PFJ
by Craig Dana 17 Jan '14

17 Jan '14

I'm looking at the N-terminal pyroglutamate residue in PDB: 3PFJ. It is clearly distorted, but when I open the same PDB file in VMD, the pyroglutamate is not distorted.

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Failed to start chimera
by jupiter 17 Jan '14

17 Jan '14

Hi, I installed Chimera 1.7 on CentOS 6.4. I can run any opengl applications, but failed to run chimera , it got following error message. Appreciate any tips to fix this issue. X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 72 (X_PutImage) Serial number of failed request: 34 Current serial number in output stream: 37

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Re: [Chimera-users] rna and set shadows commands
by Elaine Meng 16 Jan '14

16 Jan '14

On Jan 9, 2014, at 12:07 PM, "pythonchemia Gazeta.pl" <pythonchemia(a)gazeta.pl> wrote: > > Hello Elaine C. Meng > > Thank you very much for your reply and sorry that I answer only now. > When it comes to command rna path and rna model your tips helped me. :) > Although I do not know how to define the path for the command operations rna duplex. : ( > > Unfortunately for me the system WinXP / Chimera 1.8 - 32bit shadows set command does not work. : ( > Chimera returns this message: > > - Unable to turn on shadows (shadows not supported) > > After opening the Chimera Reply log returns this message: > > Disabled programs because the GPU and graphics driver bug > you encountered while compiling a vertex shader. > -------------------------------------------------- ----------- > > Maybe my graphics card is inappropriate? > > The User's Guide about the Build Structure writes that the helical DNA / RNA (not yet Implemented ) > and this option is disabled. > > Sincerely, Janusz Grabowski Hi Janusz, The message suggests your computer can't do the shadows. It might help to update your graphics driver, but I don't know for certain. However, other "set" options should work, for example: set bgColor white As mentioned in the "rna duplex" description, the path file is created using the command "rna path": <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#duplex> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#path> Also, as mentioned in an earlier message you have to get a daily build (version 1.9), also available from our download page, to use the "helical DNA/RNA" option in Build Structure. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009497.html> It is recommended to send chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me directly. Thanks, Elaine

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Re: [Chimera-users] batch writing of attributes
by Eric Pettersen 14 Jan '14

14 Jan '14

Hi Jay, We thought as much really. Well, you are going to have to use a Python script. The good news is that it's a really simple Python script. Put the following in a file whose name ends in ".py": from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): from OpenSave import osOpen f = osOpen("~/surfData/%s.data" % m.name, "w") for a in m.atoms: print>>f, a, getattr(a, "areaSES", 0.0) f.close() The indentation matters, so make sure to preserve it. Then once you open your model and surface it, you can run the above script simply by opening it with the "open" command. It will create a file with a list of atoms and corresponding surface areas. The file will be named <model name>.data and it will be in the "surfData" folder in your home directory, so make sure that folder exists beforehand or modify the script to have it go to another location. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 14, 2014, at 5:56 AM, "Eifler, Jay Q. (UMKC-Student)" wrote: > Actually I'm doing ab-initio quantum mechanical calculations and need > to analyze on a atom and residue basis. I've already been able to > save the atom and residue results but can't figure out how to automate > it since you have got to click buttons in the render/select attribute. The > Chimera notes seem to imply it should be possible to save attributes to > file. However, areaSAS is supposed to be an attribute but doesn't seem > to belong to the model attributes. > From: Eric Pettersen > Sent: Monday, January 13, 2014 4:05 PM > To: Eifler, Jay Q. (UMKC-Student) > Cc: <Chimera-users(a)cgl.ucsf.edu> List > Subject: Re: [Chimera-users] batch writing of attributes > > On Jan 11, 2014, at 1:58 PM, Jay Eifler wrote: > >> >> I'm trying to automate saving the areaSAS for a bunch >> of models. I've got no problem loading the models, etc. >> The problem is simply how do I use command line >> arguments to save the areaSAS. I've tried writesel. This >> works all fine in Render/Select by attribute simply >> because it has a feature to save the areaSAS to a file. >> Thanks. > > Hi Jay, > Do you really need the values on a per-atom basis? If you just need the grand total, it's reported in the reply log so you could just open and surface your structures one by one via a script (one by one to avoid possibly running out of memory) and then afterward save the reply log contents to a file manually (there's a "Save" button on the reply log). > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu

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Problem with HEADER keyword in PDBs
by Thomas Hrabe 14 Jan '14

14 Jan '14

Hi everyone, I believe I found a problem with the >HEADER< keyword in PDB files. Some programs may create pdbs with the header keyword specifying the origin or a name of a chain or other metadata with the coordinates below. PyMol understands this keyword and colors chains that have identical chain ID (see example attached) in multiple colors while chimera interprets all as one chain. Thanks, Thomas

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MD trajectory play by commandline
by inhee park 14 Jan '14

14 Jan '14

Dear Chimera developers and users: I am using Chimera (production version 1.8 (build 38824) 2013-06-07 21:09:20 UTC). I wanted to process MD trajectories to extract their detailed H-bond information. To do so, I would like to process by script with Hbond.py file. $ chimera --script Hbond.py #---[Hbond.py] from chimera import runCommand # pr trajectory movie with open("metafile", 'w') as m: meta_input = """amber mypdb.prmtop pr_dry_netcdf.crd """ print >> m, meta_input # runCommand("open movie:metafile") runCommand("alias ^myhb hbond relax true savefile hbond.$1") runCommand("perframe myhb") runCommand("coordset #0 1,1000,10; wait 100") #----------------------- As I have many MD trajectories to be processed, I was looking for a commandline in lieu of actually clicking buttons in MD movie GUI to play. I thought that "coordset #0 1,10000,10; wait 100" may operate like automatically starting the MD movie to load frame 1 to 1000 at every 100 interval. But resulting saved H-bond files contain same information all about the first frame (because graphically displayed was the first frame without any update unless clicking the button in MD movie GUI). Is there a way to achieve an automatic play via commandline? Thank you, inhee park

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RMSD per residue NMR structure
by cantini＠cerm.unifi.it 14 Jan '14

14 Jan '14

Dear users Does anyone knows how to calculate through CHIMERA the backbone rmsd per residue of a NMR ensembles of protein structures ? thank a lot Francesca Cantini ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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batch writing of attributes
by Jay Eifler 13 Jan '14

13 Jan '14

I'm trying to automate saving the areaSAS for a bunch of models. I've got no problem loading the models, etc. The problem is simply how do I use command line arguments to save the areaSAS. I've tried writesel. This works all fine in Render/Select by attribute simply because it has a feature to save the areaSAS to a file. Thanks.

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Computing solvent accessible area without internal cavities
by Tom Goddard 13 Jan '14

13 Jan '14

Hi Numan, Chimera uses the MSMS program to compute solvent accessible surface area, and MSMS has an option to only compute for the outside surface component without internal cavities. So I think this is just what you want. Although you could script it in Chimera you might find it easier to write a script that uses the standalone program directly from Michel Sanner http://mgl.scripps.edu/people/sanner/html/msms_home.html The one trouble you may run into is the calculation failing on some molecules due to numerical instabilities. The older version of the MSMS library we use in Chimera often fails to compute the surfaces and areas for molecules larger than 10,000 atoms, and sometimes fails for much smaller molecules. The standalone program from Michel failed much less often in tests I did a few years ago, probably because it used some newer more reliable code. Tom On Jan 13, 2014, at 11:13 AM, "Oezguen, Numan" wrote: > Dear Tom, > > I am facing a problem that you have most probably already have solved and hoping you could help me out. I need to identify atoms that are solvent accessible. For this I used the program Getarea from Werner Braun’s group in Galveston Texas. It works fine, however it lists also internal cavity surface atoms as solvent exposed. Technically it is correct… but I am interested only in those surface areas that are not internal i.e. surface areas that are accessible to molecules approaching it from outside. > > Do you know of any commercial or free (preferably) program that can do this. Ideally it should be possible to call it from scripts (shell or Perl). > > Thank you very much for you time and help, > Numan > > > Numan Oezguen, Dr. rer. nat. > Instructor of Pathology & Immunology > Texas Children’s Microbiome Center > Feigin Center, Suite 830 > 1102 Bates Avenue > Houston, TX 77030

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Registration ?
by Jean-Paul Boissel 13 Jan '14

13 Jan '14

Just downloaded the new dally build. At opening got the message: Registration file "/Users/JPB/.chimera/registration" has expired. Do we have to register again for 2014 Thanks > > Dr. Jean-Paul Boissel, Team Leader > Solute Transport Through Biological Membranes/ Ellen I. Closs' group > Department of Pharmacology > University Medical Center of the Johannes Gutenberg-University > Obere Zahlbacher Strasse 67, D-55101 Mainz > Tel.: +49 6131-17 9189 > FAX: +49 6131-17 9329 > e-mail: boissel(a)uni-mainz.de > http://www.unimedizin-mainz.de/pharmakologie/research/solute-transport-thro… > -biological-membranes.html?L=1 > This e-mail contains confidential information and may also be legally > privileged. If you are not the intended recipient or received this mail by > mistake, please inform the sender immediately and delete the mail. Any > un-authorized use, copying, disclosure or forwarding of this mail and of > information contained therein is prohibited.

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displaying electrostatic field
by Bala subramanian 10 Jan '14

10 Jan '14

Friends, Kindly see the following link (Fig 22, left panel). http://www.bioscience.org/2009/v14/af/3398/fulltext.php?bframe=figures.htm Has anyone tried making the display of electric field in Chimera. Is there any way i can make the same in chimera. Thanks, Bala -- C. Balasubramanian

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running wild with Chimera :-)
by Eric Pettersen 09 Jan '14

09 Jan '14

New Year Cards in 3D

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BioPython in a Chimera Python script; PDBio?
by Hurt, Darrell (NIH/NIAID) [E] 07 Jan '14

07 Jan '14

Hi Chimera friends, I've been trying to install BioPython into the Python interpreter embedded within Chimera. I've been following the guidelines posted a couple of years ago: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000807.html This works up to a point for me. I'm using Mac OS X 10.8.5 with MacPorts installed. I'm trying to install BioPython 1.63: http://biopython.org/wiki/Download#Installation_Instructions The "build" process starts to work, but gets hung up with the error "xcrun: Error: failed to exec real xcrun. (No such file or directory)". It seems to be referencing "/Developer/SDKs/MacOSX10.6.sdk", which does not exist in recent versions of Xcode. I've been able to install the 10.6 frameworks into both Xcode 4.6.2 and Xcode 5.x, but that still doesn't work. I manually installed the MacOSX10.6.sdk from Xcode 4.2 into the appropriate location, but still no luck. I'm using BioPython because I want to pull some information out of the PDB headers. I was able to use PDBio as described in this discussion: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001291.html But the "dictionary" entries "keyed by record type" need additional cleanup/parsing before I can use them (which is why I wanted to use BioPython). Is this just a case of Apple not building in enough backwards compatibility? Or is it something that Chimera needs to fix? Do you have any additional suggestions for me about "PDBio"? The fields I want are the DOI and title information. Finally, is there an analogous "EMDBio" for EMDB records? 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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Updating coordinates without having to regenerate the depiction of an atomic model
by Mike Lawrence 07 Jan '14

07 Jan '14

Hi, Within Chimera is there any way in which the underlying coordinates of an atomic model can be updated in order to yield the same depiction but based on the new coordinates, or (equivalently) can the attributes of one model be transferred to another, assuming of course that they have the same underlying protein sequence, etc. thanks Mike Lawrence Walter + Eliza Hall Institute of Medical Research Parkville Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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the old Mac OX 10.4 can not run Chimera
by Zhang, Yinghui 06 Jan '14

06 Jan '14

Dear Sir/Madam, This is Yinghui Zhang from Massachusetts General Hospital. I am a postdoc here and my project requires me to use the Chimera often. However, the desktop I used is some old and I can not update and use Chimera right now. The Chimera installed is 1.2 version but cannot be started. The specifics of computer is as follows: Apple PowerMac G5 chip, duo core and 3G memory. The OS is Mac OX 10.4.11. The operating system very probably cannot be updated because of chip version problem. Could you please give us some information if there is some alternative we can install executable Chimera on this computer? Thank you very much! Yinghui Zhang EDR 514, Dept. of Anesthesia MGH Boston, MA 02148 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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General question about Chimera
by Lili Peng 06 Jan '14

06 Jan '14

Hi, When I load a structure of a protein into Chimera, the structure is automatically rendered in ribbon mode, with select atoms being rendered in stick mode. I am curious as to why certain atoms are rendered as sticks, and other are not. What is the selection criteria? Thank you, Lili

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How to measure the radius of density map
by Jian Guan 03 Jan '14

03 Jan '14

Hi all, I have density map of virus (mrc format) and want to measure the radius of it. I tried measure command, High-order structure-->Icosahedron surface. Both of them need me to measure it manually by eye. Are there any tools to measure the radius by chimera, so we can get more accurate result? Or does anybody know how to measure it accurately? Thank you so much. Sincerely yours, Happy New Year. Jian -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of chimera-users-request(a)cgl.ucsf.edu Sent: 2014年1月2日 15:00 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 129, Issue 1 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. rate of a reaction (Haider Abbas) 2. Error in generating sqm for FAD (Isha) 3. Re: rate of a reaction (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Jan 2014 10:51:05 +0530 From: Haider Abbas <haiderabbasphy(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] rate of a reaction Message-ID: <CAO+nnti1fDSY+i59Fa4ioQzwVF+k77OPUDLC=jHJ5m_zt-4P_g(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear all user, Could you please let me know how to calculate reaction rate of a barrierless chemical reaction in gas phase by chimera. with regards Haider Abbas

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Error in generating sqm for FAD
by Isha 02 Jan '14

02 Jan '14

Dear Sir/Mam I used antechamber in chimera to add charges to ligand "FAD" using am-bcc, amber ffo3r.1 and +5 charge (as depicted by chimera). The procedure was Tools > structure editing > add H and then add charge. The error shown is : Charge model: AMBER ff03.r1 Assigning partial charges to residue FAD (net charge +1) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/binantechamber -ek qm_theory='AM1', -i c:usersamehtaappdatalocaltemptmpjjpoaqante.in.mol2 -fi mol2 -o c:usersamehtaappdatalocaltemptmpjjpoaqante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (FAD) (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (FAD) (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (FAD) Total number of electrons: 412; net charge: 1 (FAD) (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out (FAD) Error: cannot run ""C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue FAD Please help as it is very urgent. Hope for your reply. I have also attached the ligand. Please find the attachment. With Regards, Isha C/O Dr. Raman Parkesh Protein Science & Engg. Institute of Microbial Technology Sector 39A, Chandigarh 160036 Ext: 0172-6665489

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rate of a reaction
by Haider Abbas 02 Jan '14

02 Jan '14

Dear all user, Could you please let me know how to calculate reaction rate of a barrierless chemical reaction in gas phase by chimera. with regards Haider Abbas

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Set and rna commands
by pythonchemia Gazeta.pl 30 Dec '13

30 Dec '13

Hello ! I have winXP and Chimera version 1.8. I wanted to use the commands rna and set. Unfortunately, they do not work. Why? What is it? I tried to repeat the example of the User's Guide for rna command and failed. Please help me or give me examples on the set command and rna Sincerely, Janusz Grabowski

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Find pseudo 2-fold axes relating heavy and light chain
by Jian Guan 30 Dec '13

30 Dec '13

Dear all, I am trying to find pseudo 2-fold axes relating heavy and light chains in the constant domain and variable domain respectively in Fab. I tried Define Axes, it failed. And I made artificial double heavy chain, it failed again. I can only get axis which is horizontal passing through both light chain and heavy chain. It is not what I want. Can anyone help to give some clues? Thanks Jian

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Failure of energy miminization
by Ross KK Leung 30 Dec '13

30 Dec '13

In August there was a discussion entitled "Minimization and mystery nonstandard HIS atom name" and that's the exact problem supposed to have been solved last year. What I did is similar to Jason (http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-August/009069.html) and unfortunately I'm unable to resolve the problem, giving that I'm using chimera 1.8.1 on a Win 7 32G RAM computer. I attach two files, one succeeded till completion while the other one failed early. What I did is simply "Structure editing", next, ok, next, .. Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No MMTK name for atom "HC1" in standard residue "ALA" Any suggestions to fix the problem is highly appreciated because Chimera is so impressive and I've been using it for many good analyses already. A pity to give up and switch to other programs at this very last stage.

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Reset surface programatically from python
by Thomas Hrabe 30 Dec '13

30 Dec '13

Hi everyone, I have this line of code where I want to load a density and export a negative surface of it: import chimera as ch mod = ch.openModels.open(‘./density.em')[0] mod.surface_levels = [-1,0] mod.display = True ch.exports.doExportCommand('WebGL', 'tmp.html’) However, the surface of the density is rendered for positive values. How can I refresh the display after I specify the surface_levels? Thanks, Thomas

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Re: [Chimera-users] [chimera-dev] writing in b-factor field
by Elaine Meng 30 Dec '13

30 Dec '13

On Dec 29, 2013, at 8:43 AM, MARIA VITTORIA CUBELLIS <cubellis(a)unina.it> wrote: > Dear sir/madam, > I have a file that associates to each amino acid of a protein A a given value v. > I would like to transfer this value to the b-factor field of the protein A the value v. I have a single value for each aminoacid N1,N2... I would like to transfer the value to each atom > > let say > > N1 C v1 > N1 CO v1 > N1 N v1 > .... > .... > N2 C v2 > N2 CO v2 > N2 N v2 > > and so on > > is it possible to this withe chimera? > thank you > > mvcubellis Dear M V Cubellis, Yes, you can do it, but another question is why do you want to do it? I'm guessing you want to color by those values. In Chimera you can assign the values to the atoms or residues directly as "attributes" and then do coloring to show those values. The B-factor from an input file is one atom attribute named bfactor, but you can create additional attributes with whatever names you wish, and color by any of them. The main work for you is to create an "attribute assignment file" which is mostly tab-separated columns with the atom (or residue) specifiers and values. The necessary format is described here, and there are also some example files: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defi…> Probably the trickiest part is how to specify the residues in the file, e.g. could be something like :12.a for residue 12 in chain A. See instructions on atom/residue specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> Once you have created that text file, you can read it in with Define Attribute (in menu under Tools… Structure Analysis) or command defattr. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defi…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html> Then Render by Attribute (which may automatically appear when you create the attribute, but also is in menu under Tools… Structure Analysis) can be used to show the values with colors and/or radii: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm…> If you really wanted to write a PDB file with values in the B-factor column, you would still need to create an attribute assignment file as described above, but more specifically to assign an atom attribute named bfactor. Then when you use the File menu or write command to output a PDB file, your values will be in the B-factor column. See also the Attributes tutorial for examples of coloring by attribute value. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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keyboard shortcuts
by Dougherty, Matthew T 30 Dec '13

30 Dec '13

I am writing a bunch of USB-HID keyboard shortcuts for some extensions I am writing. Usually one shortcut per def. Since my decoding of HID is integrally tied to the extension, I would like to simplify all my shortcuts coming from one device to one def. As of now if I have 100 button commands I have to 1) register 100 shortcuts, 2) create 100 defs, 3) do corresponding stuff in my extension. I would prefer to call one def that passes the actual keyboard string to my extension, thereby simplifying my user accelerators to just registration. How do I get the string within my keyboard shortcuts python file? thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

2 1

display of improper peptide bond
by Tatiana Domitrovic 30 Dec '13

30 Dec '13

Hi, I am trying to get rid of an improper bond that chimera is displaying between two nearby segments that are actually cleaved. The bond is distorted, creating long CACB bonds if B-spline mode is active. I tried to turn off the auto-chaining, but didn’t work. Because PYmol can properly display these segments as independent polypetides, I was wondering if there is other adjustment that I can try before manually deleting the bond. The PDB is 1ohf and the bond is between residue 570 and 571. Cheers,

5 7

Failure of energy miminization
by Ross KK Leung 29 Dec '13

29 Dec '13

In August there was a discussion entitled "Minimization and mystery nonstandard HIS atom name" and that's the exact problem supposed to have been solved last year. What I did is similar to Jason (http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-August/009069.html) and unfortunately I'm unable to resolve the problem, giving that I'm using chimera 1.8.1 on a Win 7 32G RAM computer. I attach two files, one succeeded till completion while the other one failed early. What I did is simply "Structure editing", next, ok, next, .. Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No MMTK name for atom "HC1" in standard residue "ALA" Any suggestions to fix the problem is highly appreciated because Chimera is so impressive and I've been using it for many good analyses already. A pity to give up and switch to other programs at this very last stage.

1 0

Sir, i donot want to recieve antomately letter from chimera, can you remove my email adress from your email list..
by 一波 28 Dec '13

28 Dec '13

2 1

How to get central cross section which pass through two asigned cross axis
by Jian Guan 27 Dec '13

27 Dec '13

Dear all, I have a density map of virus-Fab complex. I want to make a central cross section which pass through the Fab pseudo-symmetry 2-fold axis. I have measure the angle of Fab relative to the capsid. Hope someone can help me. Thank you so much. Sincerely yours, Jian -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of chimera-users-request(a)cgl.ucsf.edu Sent: 2013年12月24日 15:00 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 128, Issue 25 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. Re: saving coords from script (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Dec 2013 15:59:16 -0800 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: Tetsuro Fujisawa <fujisawa(a)gifu-u.ac.jp> Cc: "chimera-users(a)cgl.ucsf.edu Mailing List" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] saving coords from script Message-ID: <04B15E0C-844B-4594-8AE6-760588744D85(a)cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" On Dec 20, 2013, at 1:58 AM, Tetsuro Fujisawa wrote: > Hi, > > I found some strange behavior in saving pdb file by script file. > I tried to modify the orientation of pdb file ?tst.pdb? (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. > When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(?..?)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for ?Midas.write method?. > I wondered this might be a bug. > > Regards, > Tetsuro > > Sample.py: > ---------------------------------------------- > from chimera import runCommand as rc > > rc('open axis.bild') > rc('open tst.pdb') > rc('rock y 60 1 center #1 coord #0 models #1') # orientation of > tst.pdb was modified > rc('focus') > rc('write relative #0 #1 tstA.pdb') > # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened > tstA has original untransformed orientation > ----------------------------------------------- Hi Tetsuro, The issue is that unlike using the command line or IDLE or running a chimera-command script, no frames get drawn during the execution of a Python script unless explicitly requested and therefore the "rock" command in your script doesn't actually do anything until after the entire script runs, and by that time your coordinate file has already been written. To get the rock command to complete before proceeding with the rest of the script you need to append "; wait" or "; wait 1" (since you are rocking for 1 frame) to the end of your rock command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

2 1

saving coords from script
by Tetsuro Fujisawa 23 Dec '13

23 Dec '13

The following bug report has been submitted: Platform: windows Chimera Version: 1.8.1 Description Hi, I found some strange behavior in saving pdb file by script file. I tried to modify the orientation of pdb file ‘tst.pdb’ (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(’..’)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for “Midas.write method”. I wondered this might be a bug. Regards, Tetsuro Sample.py: ---------------------------------------------- from chimera import runCommand as rc rc('open axis.bild') rc('open tst.pdb') rc('rock y 60 1 center #1 coord #0 models #1') # orientation of tst.pdb was modified rc('focus') rc('write relative #0 #1 tstA.pdb') # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened tstA has original untransformed orientation -----------------------------------------------

2 1

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.

2 3

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 >

1 0

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

2 1

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

2 1

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.

3 4

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

3 5

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.

2 2

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

2 1

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.

2 2

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

2 1

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.

2 2

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

2 1

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

2 1

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

12 Dec '13

danilo.dimaio(a)gmail.com

1 0

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.

2 3

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

11 Dec '13

1 0

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

2 4

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

3 3

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

3 5

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

3 3

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.

3 3

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

2 2

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

2 2

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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Residue selection
by George Tzotzos 14 Nov '13

14 Nov '13

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

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Re: [Chimera-users] Issues with characters on command line (OS X 10.9)
by Mario Dejung 14 Nov '13

14 Nov '13

Hi Andreas, have you tried copy/paste the character from somewhere, for example Terminal, to the command line? I have “the same” problem with German keyboard layout. I am not able to type the ~ character within the command line of Chimera… But with copy paste, the character is visible and it works… Not a good workaround… by the way… Mario

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Speed problems under Mavericks
by Mario Dejung 14 Nov '13

14 Nov '13

I found Tom Goddard's post about the Mavericks bug and the change on the daily build with the disabled advanced graphics. So I am not sure, if my problem is related to the crashing of chimera. My problem is the speed of chimera under Mavericks. I work with molecules of about 20000 Atoms and rotating a PDB of this size is very painful. I didn’t had problems with Lion. I am wondering now, if I am the only person with speed problems under Mavericks, or if other people have similar issues. Is there a way to improve the speed of chimera under Mavericks? Kind regards Mario

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Re: [Chimera-users] Using runCommand outputs
by Tom Goddard 14 Nov '13

14 Nov '13

Hi Ahir, Every Chimera command has an equivalent Python function. I just didn't tell you all the places you would have to look to find them. Commands that have a separate dialog (graphical user interface) usually have their own code directory and are not in Midas/__init__.py. So for example the findclash command has the equivalent Python function "detectClash()" in directory chimera/share/DetectClash (On Mac the directory is Chimera.app/Contents/Resources/share/DetectClash). So it can be a bit tricky to find the Python. Here's what I do when I can't find the Python code. Each command is registered in Chimera code with the routine addCommand(). So I search for addCommand in all the share directories. Below is a list for Chimera 1.8. You are right that trying to save reply log output instead of directly running Python functions is not feasible for more complex scripts. Tom $ cd Chimera-1.8.app/Contents/Resources/share $ grep "addCommand(" */*.py Accelerators/ChimeraExtension.py:addCommand('ac', accel_cmd, None, help = True, changesDisplay = True) AddAttr/ChimeraExtension.py:addCommand("defattr", cmdAddAttr, help=True, changesDisplay=False) AddCharge/ChimeraExtension.py:addCommand("addcharge", cmdAddCharge, help=True, changesDisplay=False) AddH/ChimeraExtension.py:addCommand("addh", cmdAddH, help=True) Addions/ChimeraExtension.py:addCommand("adions", cmdAddions, help=True) Animate/ChimeraExtension.py:# addCommand(command, cmdFunc, revFunc=None, help=None, changesDisplay=True) Animate/ChimeraExtension.py:addCommand('scene', Animate/ChimeraExtension.py:#addCommand('transition', Animate/ChimeraExtension.py:#addCommand('animate', Animate/ChimeraExtension.py:addCommand('kfadd', Animate/ChimeraExtension.py:addCommand('kfclear', Animate/ChimeraExtension.py:addCommand('kfdel', Animate/ChimeraExtension.py:addCommand('kfmove', Animate/ChimeraExtension.py:addCommand('kfmovie', Animate/ChimeraExtension.py:addCommand('kfsave', Animate/ChimeraExtension.py:addCommand('kfshow', Animate/ChimeraExtension.py:addCommand('kfstatus', Animate/ChimeraExtension.py:addCommand('kftrans', Aniso/ChimeraExtension.py:addCommand("aniso", cmdAniso, revFunc=cmdUnaniso, help=True) BuildStructure/ChimeraExtension.py:addCommand("invert", cmdInvert, help=True) ChangeChainIDs/ChimeraExtension.py:addCommand("changechains", cmdChangeChains, help=True, changesDisplay=False) Combine/ChimeraExtension.py:addCommand("combine", cmdCombine, help=True) CrystalContacts/ChimeraExtension.py:addCommand('crystalcontacts', crystal_contacts_command, help = True) DetectClash/ChimeraExtension.py:addCommand("findclash", cmdDetectClash, revFunc=cmdUndetectClash, help=True) ESP/ChimeraExtension.py:addCommand("coulombic", wrapper, help=True) EnsembleMatch/ChimeraExtension.py:addCommand('tile', tile_cmd, tile_cmd, help = True) EnsembleMatch/ChimeraExtension.py:addCommand('cluster', cluster_cmd, None, help = True) FindHBond/ChimeraExtension.py:addCommand("hbonds", cmdHBonds, revFunc=cmdUnHBonds, help=True) FindHBond/ChimeraExtension.py:addCommand("findhbond", cmdHBonds, revFunc=cmdUnHBonds, help=True) FitMap/ChimeraExtension.py:mt.addCommand('fitmap', fit_map, unfit_map, help = True) Fly/ChimeraExtension.py:addCommand('fly', fly_cmd, help = True) IcosahedralCage/ChimeraExtension.py:Midas.midas_text.addCommand('hkcage', hkcage, help = True) Ilabel/ChimeraExtension.py:addCommand("2dlabels", doLabel2DCmd, help=True) Intersurf/ChimeraExtension.py:midas_text.addCommand("intersurf", emo.commandLine) Lighting/ChimeraExtension.py:addCommand('lighting', lighting, help=True) ListInfo/ChimeraExtension.py:addCommand("list", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listmodels", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listchains", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listresidues", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listatoms", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listselection", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listphysicalchains", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("listen", emo.command, help=True, changesDisplay=False) ListInfo/ChimeraExtension.py:addCommand("sequence", emo.command, help=True, changesDisplay=False) MMMD/ChimeraExtension.py:addCommand("minimize", emo.cmdMMMD, help=True) MMMD/ChimeraExtension.py:#addCommand("dynamics", emo.cmdMMMD, help=True) Mask/ChimeraExtension.py:Midas.midas_text.addCommand('mask', mask_cmd, help = True) MatchMaker/ChimeraExtension.py:addCommand("mmaker", cmdMatchMaker, help=True) MatchMaker/ChimeraExtension.py:addCommand("matchmaker", cmdMatchMaker, help=True) Measure/ChimeraExtension.py:addCommand('measure', measure_cmd, help = True) MeshToMolecule/ChimeraExtension.py:addCommand('meshmol', mesh_to_molecule, help = True) Midas/midas_text.py:def addCommand(command, cmdFunc, revFunc=None, help=None, changesDisplay=True): ModelClip/ChimeraExtension.py:addCommand('mclip', mclip_command, unclip_command, help = True) MoleculeCopy/ChimeraExtension.py:addCommand('mcopy', mcopy_cmd, help = True) MoleculeMap/ChimeraExtension.py:addCommand('molmap', molmap_cmd, help = True) Morph/ChimeraExtension.py:addCommand("morph", emo.cmdMorph, help=True) Movie/ChimeraExtension.py:addCommand('coordset', coordset, help = True) MovieRecorder/ChimeraExtension.py:addCommand("movie", doMovieCmd, help=True, changesDisplay=False) MultiscaleColor/ChimeraExtension.py:Midas.midas_text.addCommand('msc', msc_command, msc_undo_command, help = True) NucleicAcids/ChimeraExtension.py:addCommand('nucleotides', nucleotides, revFunc=unnucleotides, help=True) Play/ChimeraExtension.py:addCommand('play', play, reverse_play, help = ('play.html', 'Play')) RNALayout/ChimeraExtension.py:addCommand('rna', rna_cmd, help = True) Ramachandran/ChimeraExtension.py:addCommand("ramachandran", emo.cmdLine, help=True) ResRenumber/ChimeraExtension.py:addCommand("resrenumber", cmdResRenumber, help=True, changesDisplay=False) Rotamers/ChimeraExtension.py:addCommand("swapaa", cmdRotamers, help=True) Segger/ChimeraExtension.py:Midas.midas_text.addCommand('segment', segment, None, help = True) Shape/ChimeraExtension.py:addCommand('shape', shape_cmd, help = True) Solvate/ChimeraExtension.py:addCommand("solvate", cmdSolvate, help=True) SplitMolecule/ChimeraExtension.py:Midas.midas_text.addCommand('split', split_molecules, help = True, changesDisplay=False) StructureDiagram/ChimeraExtension.py:addCommand("struct2d", emo.cmdLine, help=True, changesDisplay=False) Surface/ChimeraExtension.py:addCommand('sop', sop_cmd, unsop_cmd, help = True) SurfaceColor/ChimeraExtension.py:addCommand('scolor', scolor_cmd, scolor_cmd, help = True) SurfaceColor/ChimeraExtension.py:addCommand('scolour', scolor_cmd, scolor_cmd, help = True) SurfaceZone/ChimeraExtension.py:Midas.midas_text.addCommand('bondzone', bzone, no_bzone, help = True, changesDisplay=False) SymmetryCopies/ChimeraExtension.py:Midas.midas_text.addCommand('sym', symmetry_copies, undo_symmetry_copies, Topography/ChimeraExtension.py:addCommand('topography', topo, help = True) ViewDock/ChimeraExtension.py:addCommand("viewdock", emo.cmdViewdock, help=True) VolumeFilter/ChimeraExtension.py:addCommand('vop', vop_cmd, help = True) VolumeSeries/ChimeraExtension.py:addCommand('vseries', vseries_cmd, help = True) VolumeViewer/ChimeraExtension.py:addCommand('volume', volume_cmd, help = True) Zone/ChimeraExtension.py:Midas.midas_text.addCommand('zonesel', zone_cmd, help = True) apbs/ChimeraExtension.py:addCommand("apbs", emo.cmdLine, help=True) blastpdb/ChimeraExtension.py:addCommand("blast", emo.cmdLine, help=True, changesDisplay=False) blastpdb/ChimeraExtension.py:addCommand("psiblast", emo.cmdLine, help=True, changesDisplay=False) chimera/writeSel.py:addCommand("writesel", midasCmd, help=True) pdb2pqr/ChimeraExtension.py:addCommand("pdb2pqr", emo.cmdLine, help=True) vina/ChimeraExtension.py:addCommand("vina", vinaEmo.cmdLine, help=True) $ On Nov 14, 2013, at 1:21 AM, wrote: > Thanks for the prompt reply Tom, that explains things! I took a look at the init.py file, and I can see that it's not as straight forward and as you said, some runcommand functionality is not represented by midas commands too right? For example, I cant find findclash for example. I am not beyond using runcommand ("findclash" blah blah log/savefile True) etc, but what is the easiest way to feed the output of runcommand that does not have a savefile option , i.e if the ouput goes not to the reply log but rather to IDLE, is there any way of getting this data back to a file, without manually cut and pasting it into a file and saving it? Because the saveReplyLog from tkgui does not save anything if I am running IDLE, because the output goes to IDLE (and I am using IDLE during writing/testing the script). If there is a way of doing this, then its a suitabe workaround for me! > > Thanks again > Ahir > > One thing, > > Quoting Tom Goddard > >> Hi Ahir, >> >> Unfortunately runCommand() does not return any Python objects resulting from the command -- would be convenient if it worked that way. If you want return values from a command you need to call the Python function that does that command. Most of those are in file >> >> chimera/share/Midas/__init__.py >> >> with the function name matching the command name, e.g. rmsd() for the "rmsd" command, or match() for the "match" command. So open that file in a text editor and search for the command you want. We unfortunately don't have documentation on the Python functions so this can be troublesome and I'm sure is why you prefer runCommand(). We will provide documentation for all the Python functions in our next generation Chimera that we are working on now. >> >> Tom >> >> >> On Nov 13, 2013, at 8:40 AM, wrote: >> >>> Hello all, I am getting confused by the runCommand() functionality when I am trying to run scripts. When I run my python script through IDLE(From Tools-General), the ouput of runcommand commands like rmsd etc are given the IDLE. I want to store the output from runcommand into a variable dynamically. I dont want to save from the ReplyLog (by running program without IDLE) or output to file, is there something in python itself that I am not understanding and hence, not using, or is it not possible to store the output of runcommand into a variable/list etc, as it is possible for the midas.rmsd function for example. I only ask because I prefer to use the command line functionality over the midas command. If it is only possible with the direct midas, how do I find out the equivalent command of the runcommand for the midas python formatting? >>> >>> Thank you >>> Sorry if my question is a bit confusing! >>> >>> Ahir >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. >

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Query related to chimera downloading
by akhilesh verma 14 Nov '13

14 Nov '13

Dear Sir/Madam, I am a research scholar from Cachar Cancer Hospital, India. I tried to download Chimera V-1.8.1. but could not download. It is showing insufficient permission. Kindly tell me how to set up this problem. Thanking you n anticipation -- Yours sincerely, *Dr. Akalesh Kumar Verma* *Post-Doc Research Associate* *Department of Molecular Oncology* *Cachar Cancer Hospital & Research Centre* *Mobile : +91-8471956679* *____________* *Personal Disclaimer:--* *Any information contained in this e-mail and/or any attachments is confidential and only intended for reception and use by the specified person. If you are not the intended recipient, please return the email to the sender and delete it afterwards. In this case any copying, forwarding, printing, disclosure and use is strictly prohibited.* *_____________________________*

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chimera multiple sequence alignment
by Covell, David (NIH/NCI) [E] 13 Nov '13

13 Nov '13

Dear Chimera Help, I have used NCBI's COBALT to align the active site residues for the ~400 kinases in the 'kinome tree'. This fasta alignment can be exported and read into chimera. Once loaded, tools > sequence > multialign/viewer > info > percent identity gives me the % identity for a pair of sequences. Since I have ~400 sequences, I would like to know whether the upper-triangular matrix of percent identities can be done automatically. If so, can a weight matrix for scoring (BLOSUM62) be used? Thanks in advance for your help. David Covell, Ph.D.

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Issues with characters on command line (OS X 10.9)
by Andreas Göransson 13 Nov '13

13 Nov '13

Hi everybody! I am experiencing a strange issue with the command line. I have OS X 10.9 and Chimera 1.8.1. I can't type tilde sign (~) in the command line - nothing comes up. Other Alt-combinations to produce special characters as @ works fine. Have any of you the same problem / any suggestions for solution? Thanks, Andreas

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Using runCommand outputs
by a.pushpanath＠mail.cryst.bbk.ac.uk 13 Nov '13

13 Nov '13

Hello all, I am getting confused by the runCommand() functionality when I am trying to run scripts. When I run my python script through IDLE(From Tools-General), the ouput of runcommand commands like rmsd etc are given the IDLE. I want to store the output from runcommand into a variable dynamically. I dont want to save from the ReplyLog (by running program without IDLE) or output to file, is there something in python itself that I am not understanding and hence, not using, or is it not possible to store the output of runcommand into a variable/list etc, as it is possible for the midas.rmsd function for example. I only ask because I prefer to use the command line functionality over the midas command. If it is only possible with the direct midas, how do I find out the equivalent command of the runcommand for the midas python formatting? Thank you Sorry if my question is a bit confusing! Ahir ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Mapping Change in Surface Exposed Residues on Model
by Joshua Carter 12 Nov '13

12 Nov '13

Hello, My name is Josh Carter and I am an undergraduate at MSU working on some modeling. I am working in particular on a ribo-nucleo-protein complex that undergoes a conformational change upon target binding. I am trying to find a good way to map the change in surface exposed residues after this conformational change occurs. I have a morph model of the two states and was just wondering if there was a way to map using chimera which models are surface exposed or not? Thanks, Josh

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Re: [Chimera-users] set attribute coil/helix/sheet in chimera
by Tom Goddard 12 Nov '13

12 Nov '13

There is no isCoil attribute. If a residue is not helix and not sheet then it is coil. So to set residues 106-121 to coil use setattr r isHelix 0 :106-121 setattr r isSheet 0 :106-121 Tom On Nov 11, 2013, at 3:58 AM, Puey Ounjai wrote: > Dear Tom, > > I am wondering if there is any way to set attribute to coil for particular residue just for rendition? > I tried command "setattr" it works perfectly for helices and sheet but I dont know if option isCoil do exist > > Thanks, > Puey

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suggestion: stereo3D
by Dougherty, Matthew T 12 Nov '13

12 Nov '13

Hi, I would recommend an option to lock the focal plane to the min clipping plane. having that track will make first pass stereography easier to create the stereo3D parallax budget. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Automatic mutations
by James Starlight 12 Nov '13

12 Nov '13

Dear Chimera users! I'm looking for the possible python script which using the Chimera's source would introduce selected mutations in the defined PDB file and produce PDB output containing such protein with the selected substitution residues. It would be also good if rotamers for mutation residues would be backbone dependent or taken from the existing rotamer libraries (although its not essence because I can run minimization on the mutants) Previously I've done such tasks with selectivity mutations via Chimera-GUI rotamer plugin but now I'd like to obtain big series of the mutant of studied protein for further examinations of such mutants by means of molecular dynamics simulation. Could someone provide me with such script if it could not be very complicated to make it? Thanks for help, James

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Re: [Chimera-users] Problems with binding site representation
by Elaine Meng 12 Nov '13

12 Nov '13

Hi Vigneshwari, The CASTp approach is great in that it automatically figures out for you where the pocket boundaries are (where the pocket ends and the outside begins), and provides volume and other measurements. CASTp works with apo structures as well as liganded. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html> <http://sts-fw.bioengr.uic.edu/castp/calculation.php> Another tool that can be used with Chimera is the Voss Volume Voxelator (3V) web server, which will create "density"-type maps of the pockets and tunnels in a structure. In Chimera, you can open the resulting map, adjust the isosurface level as desired in Volume Viewer, then measure the volume enclosed in the isosurface with the "Measure and Color Blobs" tool (in menu under Tools… Volume Data). <http://3vee.molmovdb.org/> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblo…> These do not display different inside and outside colors, but they use other ways to locate the pocket boundaries. The complicated procedure in Chimera to generate the pockets with different inside and outside coloring is because we currently don't have 2-sided coloring on a single surface. The map from 3V could be shown with two different isosurfaces slightly offset from each other in two differen colors, but I don't know how useful that would be. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> You may need to use a different program if none of the above suffice. Best, 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 Nov 11, 2013, at 11:14 PM, vigneshwari subramanian <vignesh.bioinfo(a)gmail.com> wrote: > Hi Elaine, > Thanks for your email. > > Our aim is to show the differences in the volume of binding cavities when an agonist and antagonist binds. We also want to show the ligand free state of the cavity. The reason for having 2 different colors is to clearly see if the volume marks the inner or outer surface of the cavity. > > Since this doesn't work very well, I thought I could solvate the cavity and display that surface. I am not sure if there better ways to represent the volumes of binding cavities. > > regards, > vigneshwari >

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Re: [Chimera-users] Problems with binding site representation
by Elaine Meng 11 Nov '13

11 Nov '13

Hi Vigneshwari, You can see the manual page by using command "help measure" or you can see it on our website here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contact…> Best, 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 Nov 9, 2013, at 3:31 AM, vigneshwari subramanian wrote: > Hi Elaine, > > Thank you so much for your timely help. I could actually make the same figure. I need to do the same for our dataset. > > It would be really helpful if you can tell me what each of these parameters mean. I think you gave an overview. But I would like to know what each of these mean. > > 3 slab -.1,0 > > measure contactArea #0.2 #0.1 3 slab -.1,0 color tan > measure contactArea #0.2 #0.1 2.99 slab -.11,-.01 color cornflowerblue > > I checked the manual. But I couldn't find any information about measure contactArea. > > I am there in the chimera list. > > regards, > vigneshwari

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Change line width of stick representation?
by Amy Davenport Migliori 08 Nov '13

08 Nov '13

Does anyone know if it is possible to change the line width of stick representations? Either that or add the ability to have depth in wire representations (i.e. shading, etc)? I would greatly appreciate any help. Thanks Amy Migliori, UCSD

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Problems with binding site representation
by vigneshwari subramanian 08 Nov '13

08 Nov '13

Dear all, I have been trying hard to make a figure similar to the one shown in this web page. http://www.cgl.ucsf.edu/chimera/ImageGallery/ I would like to have 2 different colours to represent the inner and outer surfaces of binding site. I opened 2 different structures of the same protein and adjusted the surface parameters (probe radius and vertex density) . But that doesn't seem to work. I would be really happy if someone can help me to sort out this issue. thanks, vigneshwari

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