- Chimera-users - RBVI Mailing Lists

Showing more than a single centroid trace
by Francesco Pietra 18 Aug '11

18 Aug '11

Hello: I would like to show several centroid traces for model 0, 1, 2, .. Actually, it is the same model, differing, in the movies, for the protein fluctuations. What I did, was to superimpose movie for model 1 to the already done movie for model 0, hiding the protein for model 1 and choosing a different color for the centroid. Doing that, the instant position of the centroid can only be color-highlighted for model 0. I wonder whether there is a better procedure to show the various centroid traces above a single protein model. thanks francesco pietra

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XPLOR volumetric data not shown as a volume
by matthias.gutmann＠stfc.ac.uk 18 Aug '11

18 Aug '11

Dear all, having succeeded in writing an XPLOR data file and importing it into CHIMERA, I was expecting to see a cube like volume. Instead, I'm only seeing a thin plane. Is this to be expected? The header for the XPLOR file is as below: 1 SXD2001reciprocal_space_volume 301 0 300 301 0 300 301 0 300 30.10000 30.10000 30.10000 90.00000 90.00000 90.00000 ZYX 0 0.57280 0.05125 0.25826 0.23192 0.47232 0.40565 0.28667 0.06406 0.13678 0.22750 0.22332 0.11380 -0.02432 0.32358 0.22395 0.06303 0.22736 0.27504 0.30512 0.21062 0.26810 0.15033 0.25180 0.39434 0.85280 0.25197 0.07160 0.22430 0.28253 0.11386 0.34160 0.32177 -0.03150 0.22739 0.47072 -0.00241 0.26013 0.20844 0.20823 0.30089 0.40608 0.23863 -0.13479 0.28377 0.08277 0.25996 0.23550 0.09638 How can I get the entire volume to display as a volume rather than a single plane? Is the XPLOR format not a good one to use for this purpose? Many thanks and best wishes, Matthias ---------------------------------------------------------------------------------------------- Matthias Gutmann Instrument Scientist SXD Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397 ISIS Facility Fax: +44 (0)1235 44 5200 Chilton Didcot Office : R3, 1.28 Oxfordshire OX11 0QX Email: Matthias.Gutmann(a)stfc.ac.uk UNITED KINGDOM -- Scanned by iCritical.

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Unrecognized command: "minimize"
by Viachaslau Bernat 18 Aug '11

18 Aug '11

Dear Chimera developers, I've got a problem with scripting in chimera. By analogy with your example I've written a python script for geometry optimization of small library of ligands. In GUI mode all commands run smoothly as I type them into chimera command line. Nevertheless, when I try to run a script containing the same commands I get the error `unrecognized command: "minimize"`, no matter if I run it from GUI interface menu or with --nogui parameter. Here is my testing script (test.py): import os import chimera from chimera import runCommand as rc from chimera import replyobj os.chdir("/home/viachaslau/sybyl/sublib/") fn = "lib1.mol2" rc("open " + fn) rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") rc("write format pdb 0 min/" + fn + ".pdb") rc("close all") rc("stop now") And here is the output from Python: ~/sublib> ~/chimera/bin/chimera --nogui test.py Executing test.py... Opening lib1.mol2... UNQ1 opened Traceback (most recent call last): File "/home/viachaslau/chimera/share/chimeraInit.py", line 677, in init chimera.openModels.open(a, prefixableType=1) File "/home/viachaslau/chimera/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/home/viachaslau/chimera/share/chimera/__init__.py", line 973, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 8, in <module> rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") File "/home/viachaslau/chimera/share/chimera/__init__.py", line 2235, in runCommand makeCommand(*args, **kw) File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand 'Unrecognized command: "%s"' % cmd MidasError: Unrecognized command: "miminize" Error while processing test.py: MidasError: Unrecognized command: "miminize" File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand 'Unrecognized command: "%s"' % cmd See reply log for Python traceback. I run SUSE 11.3 as operating system and chimera is installed into ~/chimera/ I also tried to run commands row by row in IDLE window of chimera and found out that python suspends on runCommand("minimize ...") command -- Viachaslau Bernat, PhD-student Department Chemistry and Pharmacy Schuhstrasse 19, 91052 Erlangen -- Germany Phone: +49-9131-8522588 www.medchem.uni-erlangen.de

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delete volume densities
by Hernando J Sosa 17 Aug '11

17 Aug '11

A while ago I remember using a Chimera function to delete map densities that were outside a given distance from selected atoms in a structure. I can't seem to find this utility anymore. Can somebody please remind me where to find it. Is this utility still there in the new chimera versions? Thanks Hernando

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Re: [Chimera-users] suggested feature/model panel
by Eric Pettersen 17 Aug '11

17 Aug '11

On Jan 22, 2009, at 3:15 PM, Eric Pettersen wrote: > On Jan 21, 2009, at 5:05 PM, Matthew Dougherty wrote: > > > 1) ability to create folders in the model panel so models can be > > grouped > > 2) ability to have a model in multiple folders > > 3) ability to show/hide in a folder by a a single checkbox > > 4) ability to name the folder > > These are good suggestions, and we have discussed adding some kind of > grouping mechanism in Chimera given that there are a lot of situations > where you want to treat a set of models as a single entity (e.g. > multiple structures fit into a EM map). > > I think #2 and #3 are in conflict though. Really, I don't think you > want #2 -- it's too confusing. Say a model is in two groups: you > close one group -- what happens? You hide one group -- what happens? > You deactivate one group and move the other -- what happens? Perhaps > if you elaborated on the motivation for putting a model in multiple > groups then some other alternative could be devised that provides what > you need. > > I'll open a change-request in our Trac database for "grouping > mechanism" and include the above. I don't really want to promise a > timeline, but the issue is a concern of ours. Seems like I never opened that ticket, at least I can't find it searching the database. A year later I did open a very similar ticket (#8253) which has now been implemented. So the Model Panel now supports grouping (and ungrouping) models in the current daily build, which at least minimally satisfies points 1, 3, and 4 above. The groups can be named as you wish, and changing active/shown/color/etc. for a group changes the corresponding attribute of all the models in the group. Right now if multiple models are opened from a single data source they are automatically grouped. This comes into play most often when opening NMR ensembles. If anyone has any strong opinion as to whether this is a good default behavior or not, please speak up! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Calculation of Hydrophobicity
by Magnus Andersson 17 Aug '11

17 Aug '11

Hi, I'm a new user to Chimera and found it very useful really fast. I have a question however, is possible to make a calculation of the hydrophobicity of a surface or the electrostatic potential, not only show it visually? Best regards Magnus ------------------------------------------------------------ Magnus Andersson, PhD Assistant Professor Department of Physics Umeå University SE-901 87 Umeå, Sweden Phone: +46 90 786 63 36 Mobile: +46 706 460 602 Email: magnus.andersson(a)physics.umu.se<mailto:magnus.andersson@physics.umu.se> ------------------------------------------------------------

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Problem with volumetric data in XPLOR format
by matthias.gutmann＠stfc.ac.uk 17 Aug '11

17 Aug '11

Dear all, I'm trying to write volumetric data in XPLOR format in order to import it into Chimera for displaying. The volumetric data set is a general volume data set, not necessarily an electron density map. However, it keeps on failing as Chimera keeps on thinking there are only 262 data values, whilst expecting 90601 numbers (which is the correct number). I'm trying to write the XPLOR file in the format given on the CNS web page: Format of CNS maps The grid size of the map is determined by the GRID parameter in the FFT statement. The following lines show the beginning of a typical electron density map file: 2 !NTITLE REMARKS FILENAME="" REMARKS DATE:18-Jun-98 12:24:08 created by user: 30 4 12 15 5 10 16 2 12 0.40960E+02 0.18650E+02 0.22520E+02 0.90000E+02 0.90770E+02 0.90000E+02 ZYX 0 -0.97086E+00-0.49927E+00-0.82774E+00-0.13491E+01-0.57034E+00-0.71253E-01 -0.19491E+00 0.61017E+00 0.10064E+01-0.22888E+01-0.94020E+00 0.77451E+00 0.57539E+00-0.31211E-01-0.27430E+00-0.36526E+00 0.34772E+00 0.81884E+00 -0.19954E+01-0.10117E+01 0.18038E+01 0.19008E+01 0.11886E+00-0.41646E+00 0.47560E-01 0.48855E+00 0.57606E+00-0.22320E+00-0.12787E+01 0.47590E+00 .... -9999 0.2044E-09 0.9999E+00 Is this correct or is Chimera expecting a different format? Looking forward to your replies! Many thanks and best wishes, Matthias ---------------------------------------------------------------------------------------------- Matthias Gutmann Instrument Scientist SXD Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397 ISIS Facility Fax: +44 (0)1235 44 5200 Chilton Didcot Office : R3, 1.28 Oxfordshire OX11 0QX Email: Matthias.Gutmann(a)stfc.ac.uk UNITED KINGDOM -- Scanned by iCritical.

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suggestion
by Dougherty, Matthew T 16 Aug '11

16 Aug '11

It would be good to have a session description window that I could type text into. The typical method is to generate a session file name that is the description, but as the complexity of a session file increases it would helpful to be able to write a couple sentences/paragraph as to the subtle differences it has over a near identical session file. It would also allow me to pass messages/instructions in the session file to other users so they can properly implement the session file on their computer (e.g., "be sure to change the directory name and update your density files", "the related command files that work with this session file are ....") Later on such information could be extracted in mass from closed session files, allowing for searches using database-like queries. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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BIOMT
by Ludovic Autin 16 Aug '11

16 Aug '11

Hi there, I am wondering if its possible to access the matrices computed by the sym command and/or if its possible to save the multiscale structure as a PDB with the BIOMT fields instead of the full structure? thanks in advance Ludovic

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Residue.uniprotIndex
by Eric Pettersen 16 Aug '11

16 Aug '11

I thought some of the script writers out there might want to know that in the latest daily builds residues have a "uniprotIndex" attribute which gives the position of the residues relative to their UniProt sequence, if the correspondence can be determined. To determine the correspondence the structure must have valid PDB HEADER and SEQRES records, and the PDB web site must be reachable (to use their UniProt mapping service). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Surface point types in WriteDMS
by Ken Shimo 11 Aug '11

11 Aug '11

Hello, When I use WriteDMS, a surface point is defined by the 7th field, which should start in 'S'. In the format definition, next to it, should be an 'S', for saddle, 'C', for contact, 'R', for reentrant, that defines de surface type. But in Chimera's WriteDMS the surface points are always set as 'C' (contact). How can I create a DMS file with the correct surface types? I'm thankful for any help, -- Helder Ken Shimo BSc in Biomedical Informatics (University of São Paulo - Brazil) MSc candidate in Bioinformatics (University of São Paulo - Brazil) -- "When I get sad, I stop being sad and be awesome instead." (Neil Patrick Harris as Barney Stinson)

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Large size display system
by jens j birktoft 10 Aug '11

10 Aug '11

Subject: Large size display system: I am looking for some advice regarding a presentation system that permit the display in high definition of interactive molecular graphic sessions (incl. Chimera) to our research group (10-12 people). Ideally we would like a 32"-36" LCD monitor coupled to a computer equipped with the proper graphics card for the large display as well as 24" monitor . Any suggestions would be greatly appreciated Cheers Jens +++++++++++++++++++++++++++++++++++++++++++++++++++++++*/ Jens J. Birktoft, Department of Chemistry, New York University e-mail: birktoft(a)nyu.edu <mailto:jens.knold@gmail.com> slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057

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Problem with a script calculating distance between residues in a single pdb file with several models
by Damien Larivière 09 Aug '11

09 Aug '11

Dear all, Here is a single pdb file called modetest_14.pdb. It contains 6 structures: 1 protein MutS (only chain B) with 5 different conformations + another protein MutL (chains A and B). In Chimera, the protein with the 5 different conformations is displayed as model 0.1 to 0.5. The other protein is model 0.6. I would like to calculate the distance between the residue 239 of MutS chain B (for the 5 conformations) and the residue 169 of MutL chain A. I wrote this script which reports this error message: expected an indented block (scriptdistance.py, line 4) *from chimera import runCommand as rc rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\New_filtering\Eucl_Dist_S246-L297\Top solutions\SL0265B\dockLH248\NMA\Test\modetest_14.pdb") for i in range(1, 6): rc("distance #0.%d:239.B@N #0.6:169.A@N" % i)* May you tell me what is wrong? the script correctly opens the file so I suppose it is the python string #0.%d (intended to specify 0.1, 0.2,... 0.5)!? Thanks for your help Damien

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python and MD
by Daniel Gurnon 08 Aug '11

08 Aug '11

Hi everyone, I have a question for the python experts: Suppose I have opened an MD trajectory using MD movie. I want a script that will capture images along the trajectory spaced by user-defined timespans. Problem is, I don't know how to use a script to go to a specific frame in MD movie. As I understand it, coordset, as employed in the following example, requires the user to first play through the entire trajectory. With a million frames, that's not practical. Here's what I have so far, cobbled together from examples and my own limited understanding of Python. ---------------------------- from chimera import runCommand timestep=input ("How many picoseconds pass between frames?") spacing=input ("What spacing, in ps, do you want between structures?") start=input ("Which frame do you want to start with?") end=input ("What frame do you want to end with?") runCommand("coordset #0" + start) runCommand("focus") runCommand("copy file C:\Users\Dan\Desktop" + "\\" +start + ".png" + " width 2000 width 2000 supersample 3") ---------------------------- So in place of coordest, what could I use to jump to frames within MD movie? And while I'm at it, How can I generically specify the desktop in a windows environment (so that I could give this to a student and they wouldn't have to change "Dan" in c:\users\Dan\Desktp") How can I change the filename for the image to reflect framenumber? Thanks as always for your help. Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Python command SaveReplyLog
by Damien Larivière 08 Aug '11

08 Aug '11

Dear all, Within a loop for i in range(1, 5), I would like to save the Reply Log in text file in a specific location. My script fails when I use such syntax, saying Unrecognized command: *from chimera.tkgui import saveReplyLog rc("saveReplyLog('C:\Program Files (x86)\Hex 6.3\examples\replyLog%d.txt')" % i)* I looked at old posts saying the syntax to be saveReplyLog('path') but it does not work. May you tell me what is wrong with it? I can post the whole script if necessary. Many thanks for your help Damien

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MD setup from command line?
by Dr. techn. Thomas Mitterfellner 04 Aug '11

04 Aug '11

Hello! I'm using Chimera to view DFT optimizations and vibrational modes. I split the large xyz files into multiple small xyz files and load them with the MD tool. Now my question is: can I do the last step from the command line so I could write a script which sets the first and the last frames automatically? Also, is it possible to create the respective movie (as mpeg) in an automated fashion? Thank you, Thomas

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Fwd: [3DEM]asymmetric unit segmentation
by C.J. 03 Aug '11

03 Aug '11

Dear all, I post here for the suggestion of Steven Ludtke in the 3DEM list. best regards! C.J. ---------- Forwarded message ---------- From: C.J. <biocjh(a)gmail.com> Date: 2011/7/13 Subject: [3DEM]asymmetric unit segmentation To: 3dem(a)ncmir.ucsd.edu Dear all, Any one have a experience on segmentation of asymmetric unit from icosahedron virus structure volume? I wonder whether there is any programme could process that automatically? Any comment would be appreciated! -- Regards! C.J. -- Regards! C.J.

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Torsion adjust causes weird behavior
by Greg Friedland 03 Aug '11

03 Aug '11

Hi, I'm attempting to adjust a side chain torsion by hand for an asparagine residue but when I change it in the 'adjust torsion' panel, another residue (only one) 5 angstroms or so away is rotated around the bond axis as well. I made sure that the dihedral bond vector in the panel is pointing away from the backbone pointing in the direction and that only one torsion is selected. Is there a way I can change this behavior to only adjust the relevant residue? Thanks, Greg

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Announcement: Release of DOCK 6.5
by Scott Brozell 01 Aug '11

01 Aug '11

We are pleased to announce the release of DOCK 6.5. DOCK is a suite of programs for molecular docking. In version 6.5 a new scoring function Descriptor Score is available. It reports van der Waals and Coulombic energies, hydrogen bonds, and per-residue energy decomposition comparisons with a reference molecule. DOCK continues to provide a variety of other scoring methods including grid based, PB/SA, and GB/SA, as well as a simple interface to the AmberTools MD engine that enables receptor flexibility and a complete MM force field. For full information on what is new in DOCK 6.5, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.5.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

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centroid trace problems
by Francesco Pietra 01 Aug '11

01 Aug '11

hello: "centroid" works fine to me in getting the trace of a moving molecule in and out of a protein, using command define centroid radius 0.2 color red :residuename when the residue is unique. In fact, the method has produced extraordinarily illustrative (I am using the words of the referee) in a paper that will appear shortly on Chemistry & Biodiversity. Now I have three diatomic molecules, only one of which is made moving around. In this case define centroid radius 0.2 color red :residuename:residuenumber for the moving residue does not work. What happens is that "red balls" for the specified residue are being accumulated at the place of origin of the residue, while the residue is leaving the protein as a short bar, not a ball. Could that be fixed in the above command? thanks francesco pietra

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hide a peptide in Chimera
by C.J. 29 Jul '11

29 Jul '11

Hi,all, I have a pdb file containing several peptides. And I want to hide some of them when visualizing the file in Chimera. Anyone would like to help me to that? I'm appreciated of any suggestions. -- Regards! C.J.

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Hbond in CLI + cacheDA
by Maciek Wójcikowski 28 Jul '11

28 Jul '11

Hello everyone, I'm trying to compute hbonds for quite large molecular database, so i do it in CLI. I've added cacheDA parameter which speeds up whole process at first by 10 times, although after time cache is getting bigger and bigger operations slows down as one can expect, because Chimera is caching every compound. Is there a way to limit the size of a cache, or even better to tell chimera to cache only protein donors and acceptors? ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek(a)wojcikowski.pl

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Chimera 1.5.3, nvidia quadro 4000 and stereo
by Veli-Pekka Kestilä 26 Jul '11

26 Jul '11

Hello, I found following problem when trying to use Chimera 1.5.3 with stereo in Nvidia Quadro 4000. When starting the chimera in windows I will get error: Error Initializing OpenGL: Couldn't configure togl widget When stating in OpenGL debug mode it starts without any problem. Nvidia driver is 275.65 and everything works in linux without problem. In Manage 3D settings I have put on Stereo Enable. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

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gtx-470 GeForce cards
by Francesco Pietra 26 Jul '11

26 Jul '11

With GeForce2 MX200 / Debian GNU-Linux i386 wheezy I have no problems in running movie with "define centroid". In contrast, with GeForce gtx-470 (two such cards and PhenomII 1075T (six cores)/ Debian amd64 wheezy, on running movie to get the trace of the centroid, the X server hangs and the keyboard is no more sensed. I have to restart the computer from a ssh-linked desktop. In both cases chimera 1.5.3. Chimera was started as the only application, just after booting the OS (I am saying that because, to run molecular dynamics, I have first to command # nvidia-smi -L # nvidia-smi -pm 1 Any experience to this regard? thanks francesco pietra

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castp .poc file is not opened in restored session (plain text version)
by Boaz Shaanan 26 Jul '11

26 Jul '11

Hi, I save a session in which I used castp .poc file (very nice indeed!). However, after saving the session, the restored session does not open the .poc file. Is that how it's supposed to be? Cheers, Boaz P.S. sent again in plain text format since it seems the previous html version has been mangled up 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

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Query regarding Ksdssp assignment
by Arun Prasad Pandurangan 25 Jul '11

25 Jul '11

Dear Users and Developers, I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera? Looking forward for the advices. Thank you. with best regards, Arun Prasad

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Display of bond between CA's
by Greg Friedland 25 Jul '11

25 Jul '11

Hi, I'm trying to prepare an image from a structure in which I'd like to hide the backbone atoms except the CAs. When I do this for two neighboring residues however a long bond is drawn between the CAs. How can I hide this without hiding the CAs? Thanks, Greg

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creating multimeric units
by ALEXANDER MUCHUGIA 25 Jul '11

25 Jul '11

Hi, My name is Alexander Muchugia, I am a Bioinformatics student at Rhodes University, South Africa and I am working on modelling HIV protease. It is a dimer but Its modelled as a monomer. I was trying to look for software than can convert it as a dimer. I am enquiring if it is possible to use chimera to do it and how can I do it. Regards. Alexander.

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Chimera for Mac OSX Lion
by Victoria James 22 Jul '11

22 Jul '11

Hi there! I was just wondering if you know if the latest build of Chimera will run on Mac OSX Lion? If not, will you be releasing another build soon that will be able to? Many thanks and kind regards Victoria

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Re: [Chimera-users] Structure -> Match in a script
by Eric Pettersen 20 Jul '11

20 Jul '11

On Jul 20, 2011, at 2:09 PM, Sierk, Michael wrote: > Eric, > > Thanks for the script! It works but I have a couple of issues still: > > 1) The second sequence in the alignment is not automatically being > associated with the second structure. (It looks like the first > sequence/structure association is done automatically, but not the > second.) I can do it manually with Structure->Associations (with > zero mismatches), and then the script works. Is there a way to > create the second association via either the Chimera command line or > using python? Is that association supposed to occur automatically > as well? AFAIK the second sequence should associate. If you send me the alignment and the structures (or tell me their PDB codes if they're standard PDB entries) I can investigate (send them off-list!). > 2) What I am trying to do is load in two molecules and 3 different > sequence alignments of the two molecules. In my Chimera script I > make 2 copies of the 2nd molecule (using "combine") and color them > differently. I would like to then do the Structure->Match process > for each of the 3 alignments. Does the "findMAV" function in the > mavMatch.py script return all instances of MAVs or just one? I know > the titles so could I perform 3 different mav.match statements, one > for each MAV instance? Well, this is a more complicated scenario than what the script I wrote really handles -- since you have multiple MAV instances and only want certain open structures to associate with each instance despite the fact that those structures are identical. So it needs two scripts! Here's the approach: In your Chimera script: 1) Open the three alignments. 2) Open the first Python script (no-auto-assoc.py) to turn off auto- association in the MAV instances. 3) Open your two structures, "reference" structure first (more specifically, in a lower model number than the matching structures) 4) Make the two copies, or just open the second structure two more times. 5) Run the second Python script (assoc-and-match.py) to associate the reference structure with the first sequence in all the alignments, and one copy of the matching structure with the second sequence in each alignment, and then match them. --Eric

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problem with a script calculating distance between residues
by Damien Larivière 20 Jul '11

20 Jul '11

Dear all, The script below has been validated for me by the Chimera team sometimes ago. In fact this script does not work each time I run it: When reaching the pdb dockSL0007.pdb, or dockSL0010.pdb, or dockSL0020.pdb,... Chimera can remained fixed on the current PDB file as if it faces problem to open it. I'm forced to close Chimera which does not respond anymore. The exit code is 805306369. I attached dockSL0009.pdb and dockSL0010.pdb. What can I do to report this bug (which may be due to something external to Chimera; my Chimera version is 1.5.2 Build 32411; my plateform is Windows 7 64 bits) since I have to brutally stop Chimera, and know more about this problem? Many thanks for your help Damien from chimera import runCommand as rc #from chimera.tkgui import saveReplyLog for i in range(1, 101): rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\dockSL%04d.pdb" % i) rc("distance :246.C@CB :297.A@CB") rc("distance :246.C@CB :297.B@CB") rc("close all") #rc("saveReplyLog('replyLog%04d.txt')" % i)

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Structure -> Match in a script
by Sierk, Michael 20 Jul '11

20 Jul '11

All - I would like to write a command file that will automatically read in two structures and a corresponding alignment file, then perform the superposition (and coloring, etc.). I can read in the pdb and pir files using the command line, and I can do the superposition in the Multalign Viewer using Structure->Match, but I cannot figure out how to do the superposition based on the sequence using the command line. I think if there was a way to select the residues that are aligned in the sequence alignment I could use the "match" command, but I don't see a way to do that. Is there an attribute analogous to mavPercentConserved that corresponds to "aligned"? Or is there an automatically generated region based on the sequence alignment? Thanks, Mike Sierk +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Michael Sierk Email: michael.sierk<AT>email<dot>stvincent<dot>edu Assistant Professor of Bioinformatics Phone: (724) 805-2367 Saint Vincent College Office: Physics 205 ----------------------------------------------------------------------------------------------------------------------------------------- "There is something fascinating about science. One gets such wholesome returns of conjecture out of such a trifling investment of fact." -- Mark Twain. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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Re: [Chimera-users] Listing hydrogen bond geometries
by Elaine Meng 18 Jul '11

18 Jul '11

Hi Greg, For FindHBond, Chimera "imagines" the possible locations of hydrogens given the atom types (element, hybridization state) of the heavy atoms. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon…> "When there are no explicit hydrogens on a potential donor atom, FindHBond will use the donor atom type to infer their presence. For functional groups where the hydrogen positions are well-determined by the positions of the nonhydrogen atoms, the H-bonds detected in the presence and absence of explicit hydrogen atoms should be virtually identical. For functional groups where the hydrogen position is not well-determined (such as rotatable hydroxyls), the presence of an explicit hydrogen atom will limit the detected H-bonds to those appropriate for the observed position, instead of all of its possible positions." If you want explicit hydrogens, you could use Chimera's AddH tool (under Tools... Structure Editing) or addh command. By default, it will look at the surroundings and try to place hydrogens to make hydrogen bonds. However, it does not exhaustively optimize the H-bonding network of the whole structure. The goal is to determine reasonable positions based on immediate surroundings in a fairly short time. However, if you add explicit hydrogens and then use FindHBond, there will be fewer possibilities listed, as explained above. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> For the next level of computational intensity in adding hydrogens, we recommend the "Reduce" program from the Richardson lab. From the bottom of the AddH page, "When a more intensive approach is desired, the program Reduce (developed by the Richardson Laboratory) is a good alternative. Reduce places hydrogens to optimize local H-bonding networks and avoid steric overlaps, while flipping certain sidechains 180 degrees as deemed appropriate to fulfill these criteria. Asparagine and glutamine sidechains may be flipped to switch their terminal N and O atoms, and the imidazole ring of histidine may be flipped to switch N and C identities. The protonation state of histidine is adjusted based on the local environment. Reduce is available free at http://kinemage.biochem.duke.edu: • for on-line use as part of the MolProbity service, on a file uploaded or chosen by PDB code (individual sidechain flips can be accepted or rejected) • for download (from the Software section) to run on most platforms and is described in: Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. Word JM, Lovell SC, Richardson JS, Richardson DC. J Mol Biol. 1999 Jan 29;285(4):1735-47. " I hope this helps, Elaine On Jul 18, 2011, at 2:16 PM, Greg Friedland wrote: > Hi Elain, > Thanks very much for you response and sorry for the delay in getting back to you. > > I am trying to determine the potential hydrogen bonding potential (i.e. the ability to form these bonds) from hydrogen-less structures (they are from the PDB). I have been trying to model in the hydrogens but it is not trivial since there are many hydroxyls, which can rotate about their dihedrals. (if you have suggestions on how to model these hydrogens it'd be great to know about them). > > So until I can get a good model with the hydrogens attached I am wondering how Chimera is able to determine potential hbonds from heavy atom positions only. Any insight you can provide would be appreciated. > > Cheers, > Greg

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Listing hydrogen bond geometries
by Greg Friedland 14 Jul '11

14 Jul '11

Hello, I would like to list the hydrogen bond geometries between two models. I have found the feature to do this in the FindHBond panel but it only lists the distances not the angles. This information appears to be used in identifying the hydrogen bonds however, so is it possible to extract this information as well? If not, can you suggest another tool that could do this? Thanks, Greg

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(no subject)
by efratk＠techunix.technion.ac.il 14 Jul '11

14 Jul '11

Hello, I am a Phd student at the Technion, I use the program- DMS and I would like to know what is the numeration of the columns of the first six fields in the output format of the dms. Thanks in advance, Efrat

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(no subject)
by efratk＠techunix.technion.ac.il 14 Jul '11

14 Jul '11

Hello, I am a Phd student at the Technion, I use the program- DMS and I would like to know what is the numeration of the columns of the first six fields in the output format of the dms. Thanks in advance, Efrat

1 0

saving coordinates from a session and re-opening them in another one
by Boaz Shaanan 14 Jul '11

14 Jul '11

Hi I save selected & displayed coordinates (using save pdb) from a session, in order to incorporate them into another session. It’s a selected zone around the active site. When I open them in the new session they look strange. Also, the saved coordinates don’t always contain the full set of displayed coordinates (I’ve done this several times on different structures and it seems particularly but not just on pdb’s with aniso card). I’m attaching the session whose coordinates I saved + the saved coordinates (I hope that’s OK with the BB policy). Please help me figure out the problem. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail:bshaanan@bgu.ac.il Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan

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DMS output format
by Efrat Kligun 13 Jul '11

13 Jul '11

Hello, I am a Phd student at the Technion, I use the program- DMS and I would like to know what is the numeration of the columns of the first six fields in the output format of the dms. Thanks in advance, Efrat

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3D chimera
by Bigley, Andrew 11 Jul '11

11 Jul '11

Dear Chimera Developers, The recent advances in 3D technology is affording some unique opportunities to people interested. I have recently seen advertisements for new glasses free 3D smart phones. Can you adapt chimera for such a platform and hence convert a smart phone into a portable 3D protein viewer that would allow manipulation of the view through typical touch screen commands? Andrew N. Bigley, Ph.D.

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Curved helical filaments
by Tom Goddard 11 Jul '11

11 Jul '11

Hi Andy, The "vop unbend" command can straighten the density from a curved filament. The tricky part is you need a center-line path. You could define that by placing 3 markers. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#unbend Bending a straight filament map to follow a curve is not available. This is the inverse of the vop unbend operation. You can do a fake version of this by making a helical curve around the straight density map and then using vop unbend. That won't center the filament on the helical path, but it will create something similar by straightening the helix which I think will twist the density. Tom > Hi Tom- > > Not sure if there is an option for this - > > 1. can we bend an electron density map of a filament/tube by an small > angle ? > > 2. Can we generate an helix using a density map of a filament. > An example will be that of the bacterial flagella - it has the local > helical arrangement of the flagellin molecule and then thAT > ARRANGEMENT extends over several micrometers like a "sinusoidal wave" > with different helical arrangement to the filament axis. > > Best > Andy > > > Dr. Anindito Sen (Ph.D) >

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Tear-off menus in Chimera 1.5.3 for Mac OS X
by Jeff Lawton 11 Jul '11

11 Jul '11

Hi, I am running the native aqua version of Chimera 1.5.3 on Mac OS X 10.6, and it seems that the "tear off" feature of the menus is not available, though I was previously able to do that when running the X window version of Chimera. Is there a way to use the menu "tear off" feature in the native aqua version? Thanks! Jeff -- Associate Professor of Biochemistry Department of Chemistry Eastern University 1300 Eagle Road St. Davids, PA 19087 (610) 341-1545

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Re: [Chimera-users] distance between 2 residues
by Dedan Githae 11 Jul '11

11 Jul '11

how is the problem solved in chimera? i want to measure distance between 2 residues

2 2

Invitation à se connecter sur LinkedIn
by Vincent Zoete 07 Jul '11

07 Jul '11

LinkedIn ------------ J'aimerais vous inviter à rejoindre mon réseau professionnel en ligne, sur le site LinkedIn. Vincent Vincent Zoete Associate group leader chez Swiss Institute of Bioinformatics Région de Genève, Suisse Veuillez confirmer que vous connaissez Vincent Zoete https://www.linkedin.com/e/vxh6i1-gpupen7z-1e/isd/3469346511/KWdfhuHl/ -- (c) 2011, LinkedIn Corporation

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Problem with multiple monitors and NVidia 3D Vision - any suggestions ?
by Steven Ludtke 07 Jul '11

07 Jul '11

Hi. I just set up a 3-D vision compatible stereo monitor as a second display on my desktop. I have a Quadro 4000 video card and am running 64 bit linux (Ubuntu 11.04) with the latest 270.41.06 Nvidia driver. If I only have one monitor (the stereo capable one) attached to the machine, I can get stereo working (looks very nice), but if I have the second non-stereo capable monitor connected at the same time, it will not initialize the stereo display mode (on either display). I have it configured using Xinerama, so the 2 displays are on separate X-servers. Even when I disable Xinerama, and the second display is running on a completely independent Screen, it still won't go into stereo mode. Here are the relevant lines from the Xorg log file: [ 9016.284] (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 [ 9016.284] (==) NVIDIA(0): RGB weight 888 [ 9016.284] (==) NVIDIA(0): Default visual is TrueColor [ 9016.284] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) [ 9016.285] (**) NVIDIA(0): Option "TwinView" "0" [ 9016.285] (**) NVIDIA(0): Option "MetaModes" "nvidia-auto-select +0+0" [ 9016.285] (**) NVIDIA(0): Option "TwinViewXineramaInfoOrder" "DFP-2" [ 9018.424] (II) NVIDIA(GPU-0): Display (DELL3007WFPHC (DFP-0)) does not support NVIDIA 3D [ 9018.424] (II) NVIDIA(GPU-0): Vision stereo. [ 9018.466] (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 [ 9018.466] (==) NVIDIA(1): RGB weight 888 [ 9018.466] (==) NVIDIA(1): Default visual is TrueColor [ 9018.466] (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) [ 9018.467] (**) NVIDIA(1): Option "Stereo" "10" [ 9018.467] (**) NVIDIA(1): Option "TwinView" "0" [ 9018.467] (**) NVIDIA(1): Option "MetaModes" "1920x1080_120 +0+0" [ 9018.467] (**) NVIDIA(1): USB IR emitter stereo requested [ 9019.116] (II) NVIDIA(GPU-1): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision [ 9019.116] (II) NVIDIA(GPU-1): stereo. [ 9019.117] (II) NVIDIA(1): NVIDIA GPU Quadro 4000 (GF100GL) at PCI:2:0:0 (GPU-1) [ 9019.117] (--) NVIDIA(1): Memory: 2097152 kBytes [ 9019.117] (--) NVIDIA(1): VideoBIOS: 70.00.37.00.03 [ 9021.570] (II) NVIDIA(1): USB emitter - Copyright (c) 2009 NVIDIA Corporation NVIDIA [ 9021.570] (II) NVIDIA(1): stereo controller [ 9021.598] (II) NVIDIA(1): Setting mode "1920x1080_120+0+0" So, the logfile seems to indicate that it's initialized correctly, but when chimera tries to open a Stereo window, it raises an error :^( Here are the relevant xorg.conf sections: Section "ServerLayout" Identifier "Layout0" Screen 0 "Screen0" 0 0 Screen 1 "Screen1" 2560 0 InputDevice "Keyboard0" "CoreKeyboard" InputDevice "Mouse0" "CorePointer" Option "Xinerama" "1" Option "XineramaStereoFlipping" "0" EndSection Section "Device" Identifier "Device0" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Tesla C2070" BusID "PCI:131:0:0" EndSection Section "Device" Identifier "Device1" Driver "nvidia" VendorName "NVIDIA Corporation" BoardName "Quadro 4000" BusID "PCI:2:0:0" EndSection Section "Screen" Identifier "Screen0" Device "Device0" Monitor "Monitor0" DefaultDepth 24 Option "TwinViewXineramaInfoOrder" "DFP-2" Option "TwinView" "0" Option "metamodes" "nvidia-auto-select +0+0" SubSection "Display" Depth 24 EndSubSection EndSection Section "Screen" # Removed Option "metamodes" "nvidia-auto-select +0+0" Identifier "Screen1" Device "Device1" Monitor "Monitor1" DefaultDepth 24 Option "TwinView" "0" Option "metamodes" "1920x1080_120 +0+0" Option "Stereo" "10" SubSection "Display" Depth 24 EndSubSection EndSection Section "Extensions" Option "Composite" "Disable" EndSection Anyone else have a Stereo configuration with dual monitors working ? cheers ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging Dept of Biochemistry and Mol. Biol. Baylor College of Medicine sludtke(a)bcm.edu stevel(a)alumni.caltech.edu

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Re: [Chimera-users] Regarding adding plane surfaces....
by Elaine Meng 07 Jul '11

07 Jul '11

On Jul 6, 2011, at 11:23 PM, chinmaya joshi wrote: > Hi Elaine, > > I have three objects in the chimera image. > All these objects are in different planes. > How to add surfaces to each of these so that they can be shown to lie in diff planes? > I have attached a typical image herewith. > > Regards, > Chinmaya Hi Chinmaya, There is a tool to define planes from sets of atoms, but I don't know if you have atoms. The "objects" (your image included below) look like isosurfaces in one volume data set. If you had atoms to start with, for example if you made the volume from atoms using the command "molmap", you could go back to those atoms use them to define planes. It could be done with the "define" command or "Axes/Planes/Centroids" (under Tools... Structure Analysis). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> I don't know any way to define planes for isosurface blobs directly, without atoms. However, if you can calculate the plane coordinates yourself from these blobs, you can create plane objects with those coordinates in the BILD format. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> The last idea is that you can use the Volume Viewer tool, Features menu entry "Planes" to view only certain slices of your data at a time, but this does not draw a plane object. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum…> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of directly to me. 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

2 1

Chimera function
by Flora Ieong 07 Jul '11

07 Jul '11

To whom it may concern, I am a chimera user and am currently doing a glycan research using Chimera 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. Sincerely, Pek Ieong

2 2

movie script
by Jean-Francois Menetret 06 Jul '11

06 Jul '11

Hello, I am trying to make a movie to illustrate a conformational change between two PDBs; I would like to turn the objects while switching from one to the other. Could you give me some pointers ? Thank you J-F

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Re: [Chimera-users] Drug-Metal Complexation Modeling
by Mickey Branham 06 Jul '11

06 Jul '11

Thanks Elaine, I did check out the CCL website; a great resource. Mickey >>> Elaine Meng 07/05/11 6:25 PM >>> Hi Mickey, I don't have experience in this area, but you might try asking on the Computational Chemistry List (www.ccl.net) as to what programs might be suitable for predicting the structure of your complex. One way is to use their web form http://www.ccl.net/cgi-bin/ccl/send_ccl_message 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 Jul 2, 2011, at 1:46 AM, Mickey Branham wrote: > Thanks Elaine, > Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. > > So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. > > We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty. > > Don't know if this seems interesting but any comments from you would be appreciated. > > Thanks again for your response. > > Cheers > Mickey Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/

1 0

Not Responding
by Chad Junkermeier 05 Jul '11

05 Jul '11

Hello, I have been having strange behavior lately with opening coordinate files. I am using xyz format files with up to 500 atoms. When I tell Chimera to open one of these files the computer sits for a moment and then starts reporting that Chimera is "Not Responding." I have tried this on three different Mac computers, one using OS X 10.6.7 (iMac Core i7, 8 GB Ram, ATI Radeon HD 4850) with all of the latest updates, one using OS X 10.6.7 (iMac Core 2 Duo, 4 GB Ram, NVIDIA GeForce 9400), and one 3 or 4 year old Macbook that has (4GB RAM, and I don't know anything else). On each of these machines I have tried using a variety of different versions of your code, and I continually find that I have the same problem. I also just installed Chimera on a Windows XP machine and it has similar issues. The xyz files are the product of relaxing a graphene sheet in Quantum Espresso, and then copying and pasting the final configuration out of the QE output file into a xyz file. Here are a few of the things that puzzle me. First, if I place the input configuration of atoms into a xyz file, Chimera will read in the structures without any problems. The output xyz files work in VMD and in iMol. I thought that it might be an issue with the xyz data structure and transformed it to PBD and it still wouldn't load. I also wondered if it was an issue of too many decimal points (higher precision than the input file), but after reducing the number of decimal points of each coordinate on all of the atoms, it still wouldn't work. I have looked through some of the output files and there doesn't appear to be any weirdness in any of the files. Further complicating this issue is that sometimes, after if I let it sit for a while, the program magically starts working. Again, I have no problem opening other files. Does anyone have any ideas on what to do to fix this problem? Chad

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Re: [Chimera-users] Drug-Metal Complexation Modeling
by Mickey Branham 05 Jul '11

05 Jul '11

Thanks Elaine, Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty. Don't know if this seems interesting but any comments from you would be appreciated. Thanks again for your response. Cheers Mickey >>> Elaine Meng 06/23/11 6:23 PM >>> Hello Mickey, Chimera has a "Metal Geometry" tool for assessing the coordination geometry within metal complexes, for example, identifying a protein complexation site as octahedral vs. pentagonal bipyramidal. It is intended for use with existing coordinates, such as from crystallography or output by other computational methods. Chimera does not include QM calculations, and would not replace the programs you mention if you are primarily interested in generating the coordinates in the first place. You can build structures with Chimera, but optimization is rather limited to only a few metals, and those that are handled are treated as point-charge VDW spheres (only minimization, no MD, and no QM to incorporate orbital directionality). It could be useful modifying existing metal complex structures, and as mentioned above, analyzing those structures output from other programs. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 22, 2011, at 11:11 PM, Mickey Branham wrote: > Dr. Meng > Our group is interested in drug-metal complexation modeling. We have ongoing MM and MD studies using Gaussian or COSMO, with mixed results. Before we embark on a new voyage into Chimera can you tell us its capacity for elucidating drug-metal complexes e.g. tetracycline-M+2. > > Cheers > Mickey > > Michael Lee Branham, PhD. > University of KwaZulu-Natal > School of Pharmacy and Pharmacology > Durban, South Africa > > Please find our Email Disclaimer here-->: http://www.ukzn.ac.za/disclaimer > Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/

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System requirements
by יוכבד 04 Jul '11

04 Jul '11

Hi I'm looking into upgrading my computer and I was wondering whether Chimera runs properly on Windows7 and with a NVIDIA GT430 1GB graphic card. Thank you Yocheved

2 1

Coordinates
by George Tzotzos 01 Jul '11

01 Jul '11

Hi everybody, Is there a way to find out the coordinates of the centre of mass of (a) protein; (b) a specific residue in a protein; (c) a ligand bound on a protein. I searched the Chimera documentation but didn't find anything appropriate. Maybe that my search terms were wrong. Many thanks and best regards George

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Re: [Chimera-users] Stereo vision with Quadro 600
by William Joseph Allen 29 Jun '11

29 Jun '11

Hi Greg, I was finally able to figure out what I was doing wrong. On the Nvidia control panel, I was changing the following settings: Stereo - Enable: 'On' Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D vision)' For only specific programs (VMD, MOE, Chimera). That worked for VMD and MOE, but not for Chimera. As soon as I made those settings global, I was able to use stereo in Chimera. There must be other programs, like python.exe or something, that must also be stereo-enabled for this setup to work. Thanks again for your help, William Allen On 6/28/11 10:38 AM, Greg Couch wrote: > So according to the wglinfo output, your driver is not configured for stereo. > Check out the st/ro column, it is always a '.' and there should be some 'y's. > So no OpenGL stereo program should work. I did try the 275.36 driver with our > Quadro FX 3700, and stereo did work, so it is unclear why stereo isn't working > for you. To confirm that the driver configuration is working, try one of the > passive stereo options for the "Stereo - Display mode" and rerun wglinfo (or > Chimera) to see if stereo is supported. You also might want to go over the > driver settings with a colleague to see if either of you can spot anything, > and if that doesn't work, try an earlier version of the driver. > > Good luck, > > Greg > > On 6/27/2011 3:01 PM, William Joseph Allen wrote: >> Hi Greg, Here are the results: Thanks for your help! >> >> ########## >> C:\Users\William\Desktop>wglinfo.exe >> OpenGL vendor string: NVIDIA Corporation >> OpenGL renderer string: Quadro 600/PCI/SSE2 >> OpenGL version string: 4.1.0 >> OpenGL extensions (GL_): >> GL_ARB_blend_func_extended, GL_ARB_color_buffer_float, GL_ARB_compatibility, >> >> GL_ARB_copy_buffer, GL_ARB_depth_buffer_float, GL_ARB_depth_clamp, >> GL_ARB_depth_texture, GL_ARB_draw_buffers, GL_ARB_draw_buffers_blend, >> GL_ARB_draw_indirect, GL_ARB_draw_elements_base_vertex, >> GL_ARB_draw_instanced, GL_ARB_ES2_compatibility, >> GL_ARB_explicit_attrib_location, GL_ARB_fragment_coord_conventions, >> GL_ARB_fragment_program, GL_ARB_fragment_program_shadow, >> GL_ARB_fragment_shader, GL_ARB_framebuffer_object, GL_ARB_framebuffer_sRGB, >> GL_ARB_geometry_shader4, GL_ARB_get_program_binary, GL_ARB_gpu_shader5, >> GL_ARB_gpu_shader_fp64, GL_ARB_half_float_pixel, GL_ARB_half_float_vertex, >> GL_ARB_imaging, GL_ARB_instanced_arrays, GL_ARB_map_buffer_range, >> GL_ARB_multisample, GL_ARB_multitexture, GL_ARB_occlusion_query, >> GL_ARB_occlusion_query2, GL_ARB_pixel_buffer_object, >> GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_provoking_vertex, >> GL_ARB_robustness, GL_ARB_sample_shading, GL_ARB_sampler_objects, >> GL_ARB_seamless_cube_map, GL_ARB_separate_shader_objects, >> GL_ARB_shader_bit_encoding, GL_ARB_shader_objects, GL_ARB_shader_precision, >> GL_ARB_shader_subroutine, GL_ARB_shading_language_100, >> GL_ARB_shading_language_include, GL_ARB_shadow, GL_ARB_sync, >> GL_ARB_tessellation_shader, GL_ARB_texture_border_clamp, >> GL_ARB_texture_buffer_object, GL_ARB_texture_buffer_object_rgb32, >> GL_ARB_texture_compression, GL_ARB_texture_compression_bptc, >> GL_ARB_texture_compression_rgtc, GL_ARB_texture_cube_map, >> GL_ARB_texture_cube_map_array, GL_ARB_texture_env_add, >> GL_ARB_texture_env_combine, GL_ARB_texture_env_crossbar, >> GL_ARB_texture_env_dot3, GL_ARB_texture_float, GL_ARB_texture_gather, >> GL_ARB_texture_mirrored_repeat, GL_ARB_texture_multisample, >> GL_ARB_texture_non_power_of_two, GL_ARB_texture_query_lod, >> GL_ARB_texture_rectangle, GL_ARB_texture_rg, GL_ARB_texture_rgb10_a2ui, >> GL_ARB_texture_swizzle, GL_ARB_timer_query, GL_ARB_transform_feedback2, >> GL_ARB_transform_feedback3, GL_ARB_transpose_matrix, >> GL_ARB_uniform_buffer_object, GL_ARB_vertex_array_bgra, >> GL_ARB_vertex_array_object, GL_ARB_vertex_attrib_64bit, >> GL_ARB_vertex_buffer_object, GL_ARB_vertex_program, GL_ARB_vertex_shader, >> GL_ARB_vertex_type_2_10_10_10_rev, GL_ARB_viewport_array, GL_ARB_window_pos, >> >> GL_ATI_draw_buffers, GL_ATI_texture_float, GL_ATI_texture_mirror_once, >> GL_S3_s3tc, GL_EXT_texture_env_add, GL_EXT_abgr, GL_EXT_bgra, >> GL_EXT_bindable_uniform, GL_EXT_blend_color, GL_EXT_blend_equation_separate, >> >> GL_EXT_blend_func_separate, GL_EXT_blend_minmax, GL_EXT_blend_subtract, >> GL_EXT_compiled_vertex_array, GL_EXT_Cg_shader, GL_EXT_depth_bounds_test, >> GL_EXT_direct_state_access, GL_EXT_draw_buffers2, GL_EXT_draw_instanced, >> GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_framebuffer_blit, >> GL_EXT_framebuffer_multisample, GL_EXTX_framebuffer_mixed_formats, >> GL_EXT_framebuffer_object, GL_EXT_framebuffer_sRGB, GL_EXT_geometry_shader4, >> >> GL_EXT_gpu_program_parameters, GL_EXT_gpu_shader4, GL_EXT_multi_draw_arrays, >> >> GL_EXT_packed_depth_stencil, GL_EXT_packed_float, GL_EXT_packed_pixels, >> GL_EXT_pixel_buffer_object, GL_EXT_point_parameters, >> GL_EXT_provoking_vertex, GL_EXT_rescale_normal, GL_EXT_secondary_color, >> GL_EXT_separate_shader_objects, GL_EXT_separate_specular_color, >> GL_EXT_shader_image_load_store, GL_EXT_shadow_funcs, >> GL_EXT_stencil_two_side, GL_EXT_stencil_wrap, GL_EXT_texture3D, >> GL_EXT_texture_array, GL_EXT_texture_buffer_object, >> GL_EXT_texture_compression_dxt1, GL_EXT_texture_compression_latc, >> GL_EXT_texture_compression_rgtc, GL_EXT_texture_compression_s3tc, >> GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp, >> GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, >> GL_EXT_texture_filter_anisotropic, GL_EXT_texture_format_BGRA8888, >> GL_EXT_texture_integer, GL_EXT_texture_lod, GL_EXT_texture_lod_bias, >> GL_EXT_texture_mirror_clamp, GL_EXT_texture_object, >> GL_EXT_texture_shared_exponent, GL_EXT_texture_sRGB, GL_EXT_texture_swizzle, >> >> GL_EXT_texture_type_2_10_10_10_REV, GL_EXT_timer_query, >> GL_EXT_transform_feedback2, GL_EXT_vertex_array, GL_EXT_vertex_array_bgra, >> GL_EXT_vertex_attrib_64bit, GL_IBM_rasterpos_clip, >> GL_IBM_texture_mirrored_repeat, GL_KTX_buffer_region, GL_NV_alpha_test, >> GL_NV_blend_minmax, GL_NV_blend_square, GL_NV_complex_primitives, >> GL_NV_conditional_render, GL_NV_copy_depth_to_color, GL_NV_copy_image, >> GL_NV_depth_buffer_float, GL_NV_depth_clamp, GL_NV_explicit_multisample, >> GL_NV_fbo_color_attachments, GL_NV_fence, GL_NV_float_buffer, >> GL_NV_fog_distance, GL_NV_fragdepth, GL_NV_fragment_program, >> GL_NV_fragment_program_option, GL_NV_fragment_program2, >> GL_NV_framebuffer_multisample_coverage, GL_NV_geometry_shader4, >> GL_NV_gpu_program4, GL_NV_gpu_program4_1, GL_NV_gpu_program5, >> GL_NV_gpu_program_fp64, GL_NV_gpu_shader5, GL_NV_half_float, >> GL_NV_light_max_exponent, GL_NV_multisample_coverage, >> GL_NV_multisample_filter_hint, GL_NV_occlusion_query, >> GL_NV_packed_depth_stencil, GL_NV_parameter_buffer_object, >> GL_NV_parameter_buffer_object2, GL_NV_path_rendering, >> GL_NV_pixel_data_range, GL_NV_point_sprite, GL_NV_primitive_restart, >> GL_NV_register_combiners, GL_NV_register_combiners2, >> GL_NV_shader_buffer_load, GL_NV_texgen_reflection, GL_NV_texture_barrier, >> GL_NV_texture_compression_vtc, GL_NV_texture_env_combine4, >> GL_NV_texture_expand_normal, GL_NV_texture_lod_clamp, >> GL_NV_texture_multisample, GL_NV_texture_rectangle, GL_NV_texture_shader, >> GL_NV_texture_shader2, GL_NV_texture_shader3, GL_NV_transform_feedback, >> GL_NV_transform_feedback2, GL_NV_vertex_array_range, >> GL_NV_vertex_array_range2, GL_NV_vertex_attrib_integer_64bit, >> GL_NV_vertex_buffer_unified_memory, GL_NV_vertex_program, >> GL_NV_vertex_program1_1, GL_NV_vertex_program2, >> GL_NV_vertex_program2_option, GL_NV_vertex_program3, >> GL_NVX_conditional_render, GL_NVX_gpu_memory_info, GL_OES_depth24, >> GL_OES_depth32, GL_OES_depth_texture, GL_OES_element_index_uint, >> GL_OES_fbo_render_mipmap, GL_OES_get_program_binary, GL_OES_mapbuffer, >> GL_OES_packed_depth_stencil, GL_OES_rgb8_rgba8, GL_OES_standard_derivatives, >> >> GL_OES_texture_3D, GL_OES_texture_float, GL_OES_texture_float_linear, >> GL_OES_texture_half_float, GL_OES_texture_half_float_linear, >> GL_OES_texture_npot, GL_OES_vertex_array_object, GL_OES_vertex_half_float, >> GL_SGIS_generate_mipmap, GL_SGIS_texture_lod, GL_SGIX_depth_texture, >> GL_SGIX_shadow, GL_SUN_slice_accum, GL_WIN_swap_hint, WGL_EXT_swap_control. >> >> WGL extensions: >> WGL_ARB_buffer_region, WGL_ARB_create_context, >> WGL_ARB_create_context_profile, WGL_ARB_create_context_robustness, >> WGL_ARB_extensions_string, WGL_ARB_make_current_read, WGL_ARB_multisample, >> WGL_ARB_pbuffer, WGL_ARB_pixel_format, WGL_ARB_pixel_format_float, >> WGL_ARB_render_texture, WGL_ATI_pixel_format_float, >> WGL_EXT_create_context_es2_profile, WGL_EXT_extensions_string, >> WGL_EXT_framebuffer_sRGB, WGL_EXT_pixel_format_packed_float, >> WGL_EXT_swap_control, WGL_NVX_DX_interop, WGL_NV_DX_interop, >> WGL_NV_DX_interop2, WGL_NV_copy_image, WGL_NV_float_buffer, >> WGL_NV_gpu_affinity, WGL_NV_multisample_coverage, >> WGL_NV_render_depth_texture, WGL_NV_render_texture_rectangle, >> WGL_NV_swap_group, WGL_NV_video_capture. >> >> visual x bf lv rg d st ge ge r g b a ax dp st accum buffs ms >> id dep cl sp sz l ci b ro ne ac sz sz sz sz bf th cl r g b a ns b >> ----------------------------------------------------------------------- >> 0x01 32 wn . 32 . r . . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x02 32 wn . 32 . r . . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x03 32 wn . 32 . r . . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x04 32 wn . 32 . r . . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x05 32 wn . 32 . r . . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x06 32 wn . 32 . r . . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x07 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x08 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x09 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x0a 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x0b 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x0c 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x0d 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x0e 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x0f 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x10 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x11 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x12 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0xf5 32 wn . 32 . r . . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0xf6 32 wn . 32 . r . . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0xf7 32 wn . 32 . r . . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0xf8 32 wn . 32 . r . . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0xf9 32 wn . 32 . r . . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0xfa 32 wn . 32 . r . . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0xfb 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0xfc 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0xfd 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0xfe 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0xff 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x100 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x101 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x102 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x103 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x104 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x105 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x106 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x16f 32 wn . 32 . r . . y . 8 8 8 . . 32 8 16 16 16 . 0 0 >> 0x170 32 wn . 32 . r . . y . 8 8 8 . . 16 8 16 16 16 . 0 0 >> 0x171 32 wn . 32 . r y . y . 8 8 8 . . 32 8 16 16 16 . 0 0 >> 0x172 32 wn . 32 . r y . y . 8 8 8 . . 16 8 16 16 16 . 0 0 >> 0x173 32 wn . 32 . r . . y . 8 8 8 8 . 32 8 16 16 16 16 0 0 >> 0x174 32 wn . 32 . r . . y . 8 8 8 8 . 16 8 16 16 16 16 0 0 >> 0x175 32 wn . 32 . r y . y . 8 8 8 8 . 32 8 16 16 16 16 0 0 >> 0x176 32 wn . 32 . r y . y . 8 8 8 8 . 16 8 16 16 16 16 0 0 >> 0x177 32 wn . 32 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x178 32 wn . 32 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x179 32 wn . 32 . c y . y . . . . . . 32 8 . . . . 0 0 >> 0x17a 32 wn . 32 . c y . y . . . . . . 16 8 . . . . 0 0 >> 0x17b 24 bm . 24 . r . . y . 8 8 8 . . 32 8 16 16 16 . 0 0 >> 0x17c 24 bm . 24 . r . . y . 8 8 8 . . 16 8 16 16 16 . 0 0 >> 0x17d 24 bm . 24 . r . . y . 8 8 8 8 . 32 8 16 16 16 16 0 0 >> 0x17e 24 bm . 24 . r . . y . 8 8 8 8 . 16 8 16 16 16 16 0 0 >> 0x17f 24 bm . 24 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x180 24 bm . 24 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x181 16 bm . 16 . r . . y . 5 5 5 . . 32 8 11 11 10 . 0 0 >> 0x182 16 bm . 16 . r . . y . 5 5 5 . . 16 8 11 11 10 . 0 0 >> 0x183 16 bm . 16 . r . . y . 5 5 5 8 . 32 8 8 8 8 8 0 0 >> 0x184 16 bm . 16 . r . . y . 5 5 5 8 . 16 8 8 8 8 8 0 0 >> 0x185 16 bm . 16 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x186 16 bm . 16 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x187 8 bm . 8 . r . . y . 3 3 2 . . 32 8 11 11 10 . 0 0 >> 0x188 8 bm . 8 . r . . y . 3 3 2 . . 16 8 11 11 10 . 0 0 >> 0x189 8 bm . 8 . r . . y . 3 3 2 8 . 32 8 8 8 8 8 0 0 >> 0x18a 8 bm . 8 . r . . y . 3 3 2 8 . 16 8 8 8 8 8 0 0 >> 0x18b 8 bm . 8 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x18c 8 bm . 8 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x18d 4 bm . 4 . r . . y . 1 1 1 . . 32 8 5 6 5 . 0 0 >> 0x18e 4 bm . 4 . r . . y . 1 1 1 . . 16 8 5 6 5 . 0 0 >> 0x18f 4 bm . 4 . r . . y . 1 1 1 8 . 32 8 4 4 4 4 0 0 >> 0x190 4 bm . 4 . r . . y . 1 1 1 8 . 16 8 4 4 4 4 0 0 >> 0x191 4 bm . 4 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x192 4 bm . 4 . c . . y . . . . . . 16 8 . . . . 0 0 >> ----------------------------------------------------------------------- >> visual x bf lv rg d st ge ge r g b a ax dp st accum buffs ms >> id dep cl sp sz l ci b ro ne ac sz sz sz sz bf th cl r g b a ns b >> ----------------------------------------------------------------------- >> ########## >> >> >> >> >> >> On 6/27/11 4:42 PM, Greg Couch wrote: >>> Those settings should work for Chimera too. Please download >>> http://www.cgl.ucsf.edu/home/gregc/wglinfo.exe, run it in a terminal window >>> (eg., All Programs / Accessories / Command Prompt), and send the results >>> directly back to me. wglinfo lists all of the possible OpenGL framebuffer >>> configurations and should confirm if OpenGL is reporting that stereo is >>> available and with which graphics capabilities. I'll summarize what I find >>> to chimera-users. >>> >>> -- Greg >>> >>> On 06/27/2011 12:34 PM, William Joseph Allen wrote: >>>> Hi Greg, >>>> >>>> Thank you very much for your quick reply. >>>> >>>> I had actually already changed those settings in the Nvidia control panel. >>>> They are as follows: >>>> >>>> Stereo - Enable: 'On' >>>> Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D vision)' >>>> >>>> The display mode you mentioned in your reply was not an option in my Nvidia >>>> control panel. Although, this is the only setting that really makes sense >>>> for what I am doing, and I tried most of the other settings without >>>> success. I also tried toggling some of the other features in a non-random >>>> way, but without success. >>>> >>>> These two settings, however, are the changes that made stereo in VMD and >>>> MOE start working (both of which use OpenGL). But, for whatever reason, >>>> Chimera still gives those previously mentioned errors when I try to turn on >>>> stereo. If it helps, the monitor is an Asus 120 Hz LCD display connected by >>>> a dual-link DVI cable directly to the graphics card. No DIN connector is >>>> involved. >>>> >>>> Thanks again, >>>> >>>> William Allen >>>> >>>> >>>> >>>> On 6/27/11 1:42 PM, Greg Couch wrote: >>>>> It's should be a driver configuration issue. There are two different 3D >>>>> graphics APIs on Windows, Direct3D and OpenGL, and most Windows >>>>> applications use the former and Chimera uses the latter (because it works >>>>> on Linux and Mac OS X too). To configure OpenGL stereo in the Quadro >>>>> driver on Windows, bring up the NVIDIA Control Panel, navigate to 3D >>>>> Settings, then Manage 3D Settings. And in those options, set "Stereo - >>>>> Enable" to on, and "Stereo - Display mode" to the appropriate type of >>>>> stereo, in your case, my guess would be "On-board DIN connector (with >>>>> NVIDIA 3D Vision)". >>>>> >>>>> HTH, >>>>> >>>>> Greg >>>>> >>>>> On 06/27/2011 08:02 AM, William Joseph Allen wrote: >>>>>> Hello Chimera Users, >>>>>> >>>>>> I am trying to view molecules in sequential stereo in Chimera (v 1.5.3). >>>>>> When I >>>>>> choose Camera -> Sequential Stereo, I get an error that says: "Unable to >>>>>> turn on >>>>>> stereo viewing (Unable to find hardware support / couldn't choose pixel >>>>>> format / >>>>>> Couldn't configure tool widget)". >>>>>> >>>>>> Here is a little bit of the background: >>>>>> >>>>>> The machine is a new Dell desktop running 64-bit Windows 7. I installed a >>>>>> Quadro >>>>>> 600 graphic cards, and I am using the Nvidia 3D vision wireless glasses >>>>>> kit. The >>>>>> version of the Nvidia driver is 275.36, which I believe is the latest >>>>>> version. I >>>>>> should also note that I was able to successfully configure VMD and MOE to >>>>>> work >>>>>> in Stereo with set up described, so I know that 3D should work, I just >>>>>> can't get >>>>>> it to work in Chimera. >>>>>> >>>>>> Previous messages in the mailing archive seem to indicate that the >>>>>> specific type >>>>>> of graphics card or the version of the driver is usually the problem. >>>>>> From what >>>>>> I have read, the Quadro 600 should be compatible. I guess my only concern >>>>>> is the >>>>>> version of the driver. It seems there was some bugs in the 197.x, 258.x, and >>>>>> 259.x versions of the driver, and 266.45 was reported to work. I have >>>>>> version >>>>>> 275.36, should I be worried about a bug or is there something else I missed? >>>>>> >>>>>> Than you for your help, >>>>>> >>>>>> William Allen >>>> >>>> >>> >>> >> > > -- William Joseph Allen, Ph.D. Robert C. Rizzo Research Group Department of Applied Mathematics and Statistics Stony Brook University http://rizzo.ams.sunysb.edu/~wjallen/

2 1

creating a peptide bond between two fragments
by Glenn Millhauser 28 Jun '11

28 Jun '11

Hi Folks, I am trying to add a four amino acid segment to the N-terminus of a protein in the pdb. I can generate the four residue stretch and move its C-term close to the N-term of the structured protein. I can then select the C' and N atoms, which are about 1.0 Angstrom apart. At that point, I am stuck. Not sure how to add a bond and then create a proper structure. I've played around with Join Models, but no luck. Without a peptide bond recognized by Chimera, ribbons are discontinuous. Any ideas? Many thanks, glenn Glenn L. Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 566 3337 cell 831 459 2935 fax 831 824 4645 google voice glennm(a)ucsc.edu http://chemistry.ucsc.edu/~glennm http://www.chemistry.ucsc.edu/faculty/millhauser.html

4 6

Capping a clipped sphere representation
by Michelle E. McCully 28 Jun '11

28 Jun '11

Hi, I would like to create an image of a protein shown in van der Waals spheres with a clipped surface. I'd like each individual sphere/atom to be capped and colored the same color as the atom. Is this possible? I can show the protein in spheres and clip it using the side view dialog, but the clipped spheres show up as shells instead of solid balls. I also have found directions for capping and coloring surfaces, but I don't see a way to make the clipped surface colored by atom. It seems that building my protein out of sphere shapes and clipping that would give me the desired effect, but I was hoping there was something easier and built-in that I'm missing. Thanks for your help, Michelle

4 5

Stable 64bit version
by Guy Hughes 28 Jun '11

28 Jun '11

Hello, I am an MPhil researcher at the University of Manchester based in laboratory of Professor Bob Ford. I have been using cryo-electron tomography to build a 3D volume containing mucins (High Mr heavily glycosylated polypeptides) which are what my research focusses on. We use a Tecnai 300kV Polara and Gatan's Digital Micrograph software to create tomograms of our samples and then IMOD to view them. Recently I was told that Chimera would be a very useful tool when married with the data from IMOD so I downloaded a copy from your website. I regret to admit that I had several problems with the programme and eventually had to delete. The main problem was that my computer continued to blue-screen and perform very slowly if at all. The labtop I was using has the following spec.; CPU: Intel Core i5 VGA: NVIDIA Geforce 310M/1GB DDR3 RAM: DDRIII 4GB (2GB*2) OS: Windows 7 64-bit Is my PC inadequate or is it possible I downloades a corrupted/unstable version of Chimera? I would very much like to try and start using Chimera again but would first like some advice on what the original problem may have been. Any suggestions or help would be greatly appreciated. Thanks, Guy Hughes.

2 1

chimera setup
by yp sun 28 Jun '11

28 Jun '11

Dear sir, I want to setup the chimera 1.5.3 program on windows XP system, but the setup cannot be finished, it retures a error information that says: "Unable to excute file: C:/program file/chimera 1.5.3/bin/pythonn.exe." How can I solve the problem? Thanks. Best regards Yeping Sun PhD CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

2 1

preserving the serial numbering
by George White 28 Jun '11

28 Jun '11

Hi, I am wondering is there any way to write a pdb from Chimera that preserves the original atom serial numbering of the input pdb. Chimera seems to apply its own renumbering (i.e. making the number of the 1st atom #1 etc.) . Thanks in advance, George

3 2

ViewDock compound state
by S. Pea 27 Jun '11

27 Jun '11

Hello, I was wondering if there is an option in ViewDock to create more bins (flags) in the "change compound state"? Currently there is an option to change the compound state from Viable, to either Deleted or Purged but is there an option to put extra user defined states. Thanks, Magdalena

2 2

Stereo vision with Quadro 600
by William Joseph Allen 27 Jun '11

27 Jun '11

Hello Chimera Users, I am trying to view molecules in sequential stereo in Chimera (v 1.5.3). When I choose Camera -> Sequential Stereo, I get an error that says: "Unable to turn on stereo viewing (Unable to find hardware support / couldn't choose pixel format / Couldn't configure tool widget)". Here is a little bit of the background: The machine is a new Dell desktop running 64-bit Windows 7. I installed a Quadro 600 graphic cards, and I am using the Nvidia 3D vision wireless glasses kit. The version of the Nvidia driver is 275.36, which I believe is the latest version. I should also note that I was able to successfully configure VMD and MOE to work in Stereo with set up described, so I know that 3D should work, I just can't get it to work in Chimera. Previous messages in the mailing archive seem to indicate that the specific type of graphics card or the version of the driver is usually the problem. From what I have read, the Quadro 600 should be compatible. I guess my only concern is the version of the driver. It seems there was some bugs in the 197.x, 258.x, and 259.x versions of the driver, and 266.45 was reported to work. I have version 275.36, should I be worried about a bug or is there something else I missed? Than you for your help, William Allen

2 3

Select
by George Tzotzos 27 Jun '11

27 Jun '11

Can anyone provide some help. I'm trying to select two specific oxygen atoms in different residues (98 and 142). The command select :142@O1 :98@O1 selects only 1 atom (that of residue 142). I tried select :98@O1 only. The output is "selection" cleared. I'm rather puzzled. Any help would be greatly appreciated Regards George

2 1

pdb to xml
by Damien LARIVIERE 24 Jun '11

24 Jun '11

Dear all, WritePDB enables to save a displayed structure in the pdb format. Is there a way to save the structure into the PDBML format? If not, do you know a (simple) way to do that? Many thanks Damien

2 1

Water Ice Structures
by Matthew Thompson 24 Jun '11

24 Jun '11

I am looking for the crystal structures of "normal" ice (Ih), ice(VI), and ice(VII). I have found the .cif file for ice(VI), but I can't seem to get it to load properly into Chimera. I am really only familiar with using pdb's in Chimera. These would be used in a presentation given this coming weekend at the National School for Neutron and X-ray Scattering. Any help in this would be greatly appreciated Thanks Matt _ Matthew K. Thompson, PhD North Carolina State University Raleigh, NC 27695 Office: 919-515-2105 Cell: 919-455-1775

4 7

Re: [Chimera-users] Drug-Metal Complexation Modeling
by Elaine Meng 23 Jun '11

23 Jun '11

Hello Mickey, Chimera has a "Metal Geometry" tool for assessing the coordination geometry within metal complexes, for example, identifying a protein complexation site as octahedral vs. pentagonal bipyramidal. It is intended for use with existing coordinates, such as from crystallography or output by other computational methods. Chimera does not include QM calculations, and would not replace the programs you mention if you are primarily interested in generating the coordinates in the first place. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeo…> You can build structures with Chimera, but optimization is rather limited to only a few metals, and those that are handled are treated as point-charge VDW spheres (only minimization, no MD, and no QM to incorporate orbital directionality). It could be useful modifying existing metal complex structures, and as mentioned above, analyzing those structures output from other programs. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.…> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 22, 2011, at 11:11 PM, Mickey Branham wrote: > Dr. Meng > Our group is interested in drug-metal complexation modeling. We have ongoing MM and MD studies using Gaussian or COSMO, with mixed results. Before we embark on a new voyage into Chimera can you tell us its capacity for elucidating drug-metal complexes e.g. tetracycline-M+2. > > Cheers > Mickey > > Michael Lee Branham, PhD. > University of KwaZulu-Natal > School of Pharmacy and Pharmacology > Durban, South Africa > > Please find our Email Disclaimer here-->: http://www.ukzn.ac.za/disclaimer >

1 0

computer advice
by Ryan Woltz 21 Jun '11

21 Jun '11

Dear Chimera, We are looking at getting a new computer for our lab to used for only modeling. We are planning using chimera, pymol, and dock 6.4 as primary programs for this. What specifications i.e. graphic cards, ram, do you recommend us getting? Thank you, Ryan Woltz UC Davis Cardiology

2 1

Segmentation fault
by Jean-Francois Menetret 20 Jun '11

20 Jun '11

Hello, I have installed chimera (chimera-alpha-linux_x86_64.bin) on my Ubuntu laptop. The session crashes with segmentation fault without apparent reasons (30% memory usage; 0% swap) and even when doing nothing ... How can I debug this situation ? Jean-Francois

2 1

Manual placement of ligand into the receptor binding site
by George Tzotzos 20 Jun '11

20 Jun '11

Hi everybody, I'm trying to simulated ligand binding by molecular dynamics. I'd like to place a ligand into the binding site of a receptor molecule downloaded from the Protein Data Bank. The ligand has not been co-crystalised with the protein and its coordinates do not match those of the protein. Is there a way that I can achieve a coordinate "translation" manually by using Chimera? Thanks in advance for any suggestions Regards George

2 1

custom residue label
by Sasha Tkachev 20 Jun '11

20 Jun '11

How to programmatically set a residue label to an arbitrary text, e.g. to say something like: rlabel :656.E "Lys-57" What happens in some structures, like for instance 1U35 structure that contains H3 proteins, is that residue numbers in a PDB file is different from residue number of the sequence. In this particular example Lys57 of H3 on chain E maps to PDB residue number 656. So if I use default labeling I am getting wrong results...

2 2

Inner Cavities
by Mueller, Juergen-Joachim 20 Jun '11

20 Jun '11

Dear helper, I know the general pathway to get an inner cavity with CHIMERA 1.5.2 e.g. tools surface surfnet #0 MESH Apply control click on mesh (all bubbles selected) commandline:ac Sc control click on bubble of interest (select only 1 bubble) select invert (selected models) all wrong bubbles are selected action surface hide .... My problem is, there is no inner bubble detected in my molecule but there is one! There were ligands which have been removed before. What happens? Is there a probe sphere too large? Where can it set smaller? Thank you for help, Juergen

2 2

opening image stack
by chinmaya joshi 17 Jun '11

17 Jun '11

Can you help me how I can open a stack of .png images using a command line in chimera. I will have a set of images and I want to open the stack in chimera using the command line. Is there any python script for this? Waiting for replies

2 1

Sequence aligment
by Simon Sham 17 Jun '11

17 Jun '11

Hi, Is it possible that to do a sequence alignment in Chimera given only a text file with 2 protein amino acid sequences? I have the pdb files but there are some missing amino acids in them. Thanks for your help. Simon

2 1

Chimera-1.5.3 on RHEL 5 Linux workstation does not display surface
by Starr Hazard 15 Jun '11

15 Jun '11

Folks, I recently upgraded my LINUX to RHEL 5 (its an old machine and RHEL 6 did not recognize my old graphics card so I settled for RHEL5). I have installed xterm (eg yum install xerm). I downloaded Chimera 1.5.3 build 33475 2011-5-24 17:23 When I read in a PDB file and then try to display a surface, the calculation finishes but the display of the surface is fragmented with only a few of the triangular surface components displayed. The issue is not confined to a particular PDB. A windows version 1.5.3 works nominally with respect to surface display. So I am wondering if I have my xterm properly installed. Can you suggest some things for me to examine? Thanks Starr

3 2

Chimera API question
by Jonathan Rodgers 15 Jun '11

15 Jun '11

Hello, After looking through the Chimera documentation and examples, I couldn't find any mention of working with volumes. Is that data currently accessible through the API? Thanks, Jonathan Rodgers

5 8

help
by chinmaya joshi 14 Jun '11

14 Jun '11

Hello, I want to write a script in python to open a set of images in chimera set a viewpoint(rotate, translate,etc). and make a movie out of them all through command line for my project. Can someone please let me know how it can be done. I am new to python. Can anyone tell me any good links for these? The documentation on chimera ucsf is a bit confusing. Thanks. Chinmaya

3 11

Biological dimer shows up as a monomer
by James Ferrell 13 Jun '11

13 Jun '11

I'm new to Chimera and trying to create a figure panel for a paper. I'm running Chimera on a Mac from the graphical interface. The protein is a a yeast topoisomerase II. Its PDB ID is 2RGR. If I view the protein with Cn3D I can see the whole biological unit, in which the protein is present as a symmetrical dimer (with some DNA strands too). If I view it with Chimera I see a protein monomer. The problem is I want to illustrate a particular intermolecular salt bridge, which is present in the dimer but isn't present in the monomer. Is there some preference to toggle to allow Chimera to display the whole biological unit? Or would I have to artificially build a dimer out of two monomer models? Thanks, Jim -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- James E. Ferrell, Jr., M.D., Ph.D. Professor and Chair of Chemical and Systems Biology Stanford University School of Medicine

2 1

Protein Design
by Jared Adolf-Bryfogle 13 Jun '11

13 Jun '11

2 1

Re: [Chimera-users] [chimera-dev] Protofibril model
by Elaine Meng 09 Jun '11

09 Jun '11

Dear Lihong and others, The Multiscale Models tool in Chimera is meant for this purpose --- it shows low-resolution surfaces, which are often preferred for large complexes. In Chimera I tried opening 1ei3, then started Multiscale Models (in menu under Tools... Higher-Order Structure), then clicked the "Make models" button at the bottom of the multiscale dialog. This shows the structure with low-resolution surfaces and automatically uses different colors for the different chains. You can adjust the colors, surface resolution, etc. in the dialog. Click the dialog's Help button to see its manual page. There is also a copy here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu…> I also tried it with 1m1j, which also worked fine on my computer. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 9, 2011, at 12:13 PM, Russell M. Taylor II wrote: > Dear Lihong, > I am glad to hear that Chimera let you start down this path. > I'm CCing the Chimera developer mailing list in case they know of a better solution. > You can also join the chimera users list at http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html and then post a query there. > > The following is a somewhat convoluted path to get where you want to go. Hopefully someone on one of the above mailing lists will know a better one. If you need to go down this path, we should probably set a time for us to sit down together and go through this. > > Download MGLTools from http://mgltools.scripps.edu/downloads. I ran the Windows installer. > This launched the Python Molecule Viewer. > Select Compute/Coarse Molecular Surface. Kept the default parameters. This produced a surface that was near the outside of the molecule. > Clicked to turn off the red dot under the CPK label so that we only see the surface. > Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL file. > > I was able to load the resulting .wrl file back into Chimera. This should provide you with a simplified model. You should be able to adjust the parameters for the coarse saving to get different model quality. > > I attach the resulting coarse model (inside a Zip file) to this email. > Russ > > [Things below I tried that didn't work] > > (Fine surface) > Select File/Read Molecule. Opened 1EI3.pdb (when I used 1M1J.pdb, it crashed trying to make the surface). > Compute/Molecular Surface/Compute Molecular Surface. Used the default parameters (other parameters caused it to crash). This produced a fine molecular surface. This could be used directly or simplified. > > VMD uses a program called MSMS, but can't run it. When I go to the MSMS home page, it eventually redirects me to MGLTools from Scripps. > > NOPE: > > You can load the PDB file into the VMD program (File/New, select the file name and click Load on the Molecule File Browser). Then select Graphics/Representations from the VMD Main menu. Then pull down Drawing Method and select Surf. Turn off the "Apply Changes Automatically" control and then set the Probe Radius to 4.0 and click Apply. > To turn off the little axes display, select Display/Axes/Off > To save the resulting geometry, select File/Render from the main menu. Pull down "Render using" and select Wavefront. Change the .obj file name to one that is useful to you (I named id protofibril.obj). Click the "Start Rendering" button. > > Open Blender (available from blender.org) Press delete to get rid of the cube that is created by default. > Select File/Import/Wavefront to load the model. Pick the file name and then click "Import a Wavefront OBJ" > > At 10:18 AM 6/7/2011, lihong huang wrote: >> Dear Dr. Taylor, >> >> I am postdoc working in Dr. Susan Lord's lab. According to your suggestion, we set up the protofibril model using UCSF Chimera program which is very nice. Now we want to move on to make small fiber model, however, the program run very slowly when we add more fibrinogen molecules. We are thinking if we could make the fibrinogen molecule lose more details, maybe the program could run easily. Do you know which program could do this? We just want to show the basic shape of fibrinogen, no needs to show very detailed part, such as alpha, beta and gamma chains. Thanks a lot for your help. >> >> Lihong Huang, >> Postdco >> Pathology and lab medicine > > --- > Russell M. Taylor II, Ph.D. taylorr(a)cs.unc.edu > CB #3175, Sitterson Hall www.cs.unc.edu/~taylorr > University of North Carolina, Voice: (919) 962-1701 > Chapel Hill, NC 27599-3175 FAX: (919) 962-1799 <protofibril.zip>_______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

2 1

Contacts
by George Tzotzos 07 Jun '11

07 Jun '11

Hi everybody, I'm trying to analyse AMBER trajectories of protein/ligand complexes. The objective of my exercise is to find out contacts/interactions between the ligand and the receptor in the course of the trajectory. Is there a way of doing this DIRECTLY in Chimera? Or one has to first perform clustering of structures and then work out clashes/contacts on the representative structures that are dumped from the trajectory. Best regards George

2 1

mac default directory
by Dougherty, Matthew T 06 Jun '11

06 Jun '11

Hi- Where is the default directory for movie images on the mac? thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

2 1

coordinate rotation measuring
by Jeffrey Hu 06 Jun '11

06 Jun '11

Hi, I'm currently working on a gp140 model and have docked coordinates for 2 different conformations. I am trying to measure the rotation between the docked coordinates using the method in the EM-fit tutorial and i had a few questions. How does the "measure rotation #1 #3 showslab true" command measure the rotation? How does it determine the axis of rotation? Is it possible for me to create my own axis? Is there any way to increase the size of the slabs (they are too small visually)? -Thanks!

3 2

Smooth edge when masking volume data
by Tom Goddard 03 Jun '11

03 Jun '11

> Thanks, Tom. That helped a lot. However, is there anyway to smooth out the masked edge? I end up with chopped voxels (looks like stair-steps), rather than getting an interpolated smooth surface at the edge. This is true whether I am masking directly, or the inverted view. > > Kelly Hi Kelly, When you mask volume data in Chimera using Volume Eraser or the mask command it sets the density values to zero outside the surface. In places where high density crosses the surface the masked result looks horrible -- volume contour surface is jagged with stair-steps following the pattern of the volume grid. I don't have any trick to make that surface look smooth. I have two ideas about how to approach the problem. One is to not have the density fall to zero immediately outside the surface. If it rolled off gradually the contour surface of the masked data would look better. I'm not optimistic that that will produce a good result. The second approach is to do something different from masking. Instead clip the volume surface with the sphere surface and cover the resulting holes with patches of the actual smooth sphere surface. I think this would look very nice and the patches of sphere could be a different coloring which would give a nice visual indication that you have cut through high density. I have not implemented either of these two ideas. Just last week I had a lengthy discussion on this problem with Greg Pintilie and Ernesto Arias. Greg said he might try the gradual fall-off technique. I include that email discussion below. Tom -------- Original Message -------- From: Greg Pintilie To: Tom Goddard Date: 5/24/11 6:10 PM > Right - it's numpy to the rescue; I'll give it a shot... I think if we > use a smoothing filter with relatively high width the staircase effect > may not be as bad as you think... though then the boundaries may > become exceedingly smooth; so it will be a fine balance. Will let you > know how it goes! > > Greg > > > > On Tue, May 24, 2011 at 7:42 PM, Tom Goddard wrote: >> Hi Greg, >> >> It's an interesting idea. But it seems to me there will still be a >> discontinuity in map values. For example imagine you have a box shaped >> region with density values 1 inside and 0 outside. The Gaussian filter of >> that will give values approximately equal to 0.5 at the surface (if the >> Gaussian is half in the 1 region and half in the 0 region). So I think the >> drop from 1 to 0.5 on the surface is likely to give the same ugly artifacts. >> That said, implementation would be trivial. Just compute the Gaussian >> smoothing and copy it only where the original map has zeros (can be done >> with a line or two of tricky numpy Python code). >> >> You know Gaussian smoothing is what the heat equation produces. If you >> modify your idea so the non-zero density points are fixed temperature >> sources, and the heat flows to the zero grid points (by averaging neighbor >> temperatures) then you would get a continuous fall-off. Again it is a >> pretty easy calculation in Python/numpy. But I'm not optimistic about the >> results. The trouble is we've created this horrible stair step surface and >> it will take pretty long range smoothing to get rid of the stair steps. I >> think a good smooth cut is going to require stepping back and not producing >> the stair steps in the first place -- you need a boundary definition that is >> smooth instead of discretized. For instance when we make a contour surface >> we trilinear interpolate the 8 nearest grid points and the surface comes out >> smooth. Not quite sure how to do the equivalent for watershed regions. >> >> Tom >> >>> Sounds good - thanks for all those insights, Tom. I agree that >>> solution is not ideal, but I'm glad it helps at least a bit. I just >>> got an idea that might be interesting to try - I mentioned that you >>> can Gaussian-filter the masked map, which would lessen that huge drop >>> in density values at the boundary, but this removes good detail from >>> the actual map as well. What I'm thinking to try is to do the filter, >>> but only apply it to voxels with 0 density values (the masked >>> portion); that way the original density map gets left alone, and the >>> boundary no longer has a drop from some density value to 0... what do >>> you think Tom, could there be an easy way to implement this using >>> current functions? Done voxel by voxel in python would probably be >>> exceedingly slow... >>> >>> Greg >>> >>> >>> >>> On Tue, May 24, 2011 at 7:04 PM, Ernesto Arias >>> wrote: >>>> Hi, >>>> >>>> I tried and is working. The problem is that I'm visualizing the volume >>>> close >>>> to the noise level, so the segmentation at lower thresholds could be >>>> trickier, but I think I'll can deal with it. >>>> >>>> I really appreciate your help. >>>> Ernesto. >>>> >>>> >>>> >>>> >>>> On Tue, May 24, 2011 at 4:20 PM, Tom Goddard wrote: >>>>> Hi Ernesto, >>>>> >>>>> Yes, now I understand. The Segger regions only include grid points >>>>> above the contour level that was displayed when you made the >>>>> segmentation. >>>>> So when you mask to one of those regions, then use a contour level that >>>>> is >>>>> the same or lower (or even a little higher) than the Segger contour >>>>> level >>>>> you get a horrible surface because the density has been set to zero >>>>> everywhere below the segmentation contour level. The solution is to use >>>>> a >>>>> low contour level when you do the segmentation -- a contour level >>>>> substantially lower than what you plan to use to actually view the >>>>> masked >>>>> regions, so that the zero density values are not near the eventual >>>>> contour >>>>> surface you will be displaying. The Color Zone approach is effectively >>>>> doing this, since it includes all the density out to a specified >>>>> distance. >>>>> >>>>> Tom >>>>> >>>>> Hi, >>>>> >>>>> I see what you mean, but I'm not sure why I get different results. Maybe >>>>> I'm not explaining well what I'm doing There are attached some images >>>>> and >>>>> volumes to illustrate it better. >>>>> >>>>> When I segment the map using segger, mask the original map using the >>>>> segger "Regions->mask map with selected" I get the segger.mrc map or the >>>>> segger_masked_region.png that I'm attaching. >>>>> However, when I place some markers around the same region of the >>>>> original >>>>> map, color the map using Color Zone, and do the Split map option I get >>>>> much >>>>> better results (color_zone.mrc and color_zone_masked_region.png). >>>>> >>>>> One thing I noticed is that the histograms of segger.mrc and >>>>> color_zone.mrc are completely different. The segger.mrc volume has a >>>>> sharp >>>>> cutoff at low threshold values whereas color_zone.mrc has a more >>>>> continuous >>>>> histogram. Could it be the problem? >>>>> >>>>> Thanks so much for your help. >>>>> Ernesto. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, May 24, 2011 at 10:10 AM, Tom Goddard wrote: >>>>>> Hi Ernesto, Greg, >>>>>> >>>>>> The Color Zone splitting tool uses the same method of setting density >>>>>> values to zero outside the region. So the jagged surface appearance >>>>>> should >>>>>> be every bit as bad looking as the Segger ones. If color zone really >>>>>> does >>>>>> look better you'd have to show me an example. It shouldn't look any >>>>>> better. >>>>>> >>>>>> The problem is fundamentally that Segger defined the boundary between >>>>>> regions by saying which grid point are in the region and which are >>>>>> outside >>>>>> the region. So the surface has stair steps matching the volume grid >>>>>> points. >>>>>> I don't have a good idea of how to smooth this jagged surface out. >>>>>> Ideally >>>>>> I'd want to see the jagged surface as smooth, but colored differently >>>>>> from >>>>>> the other parts of the surface. I'd like the different coloring >>>>>> because at >>>>>> this surface patch you have cut through high density -- it is an >>>>>> artificial >>>>>> boundary. When you hide that by masking it makes misleading images. I >>>>>> have >>>>>> an idea about how to achieve both these goals but it is not implemented >>>>>> yet. >>>>>> Basically I don't mask the volume. Instead I intersect the volume >>>>>> surface >>>>>> with the masking surface. By "intersect" I mean I show the mask >>>>>> surface >>>>>> wherever it lies inside the volume surface, and the volume surface >>>>>> wherever >>>>>> it lies inside the mask, and hide everything else. The mask surface >>>>>> and >>>>>> volume surface can have two different colors. Another way to think of >>>>>> this >>>>>> idea is that I clip the volume surface using the mask surface. We >>>>>> already >>>>>> allow you to clip a surface with a plane in Chimera. This is just a >>>>>> generalization where you can clip a surface with some arbitrary other >>>>>> surface. This isn't too hard to implement, but I want the boundary >>>>>> where >>>>>> the volume surface and the mask surface meet to be a smooth curve. >>>>>> That >>>>>> requires cutting up the the triangles of the original surfaces. I've >>>>>> been >>>>>> meaning to try this for years now. I think it would look great. >>>>>> >>>>>> One further comment. Segger makes its region surfaces using the list >>>>>> grid points in the regions, so how does it make the surface look >>>>>> smooth? >>>>>> The main trick it uses is "surface smoothing", 5 iterations with >>>>>> smoothing >>>>>> factor 0.25. You can enable this for the volume surfaces using the >>>>>> Surface >>>>>> and Mesh Options panel and see if it helps. Segger also rebins the >>>>>> grid >>>>>> points which may help the appearance and that is possible but not so >>>>>> easy to >>>>>> duplicate with a volume surface using standard Chimera features. >>>>>> >>>>>> Tom >>>>>> >>>>>>> Hi Ernesto, >>>>>>> >>>>>>> That is a good point, I'm not completely familiar with how the color >>>>>>> zone tool splits out a subsection of the map, so I am cc-ing Tom >>>>>>> Goddard, who I think wrote that tool, and is a developer of Chimera >>>>>>> and co-developer of Segger. Tom, could you look at the message Ernesto >>>>>>> sent and my reply, both below? Let us know if you have any further >>>>>>> insights into how we can make segmented-region-masked maps have nicer >>>>>>> boundaries... >>>>>>> >>>>>>> Greg >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Sun, May 22, 2011 at 8:26 PM, Ernesto >>>>>>> Arias >>>>>>> wrote: >>>>>>>> Hi Greg, >>>>>>>> >>>>>>>> Thanks so much for answering my question. Everything is crystal >>>>>>>> clear. >>>>>>>> For illustrating the segmentation results I can use the segmented >>>>>>>> regions, >>>>>>>> but I wanted to make a morphing and some movies using the segmented >>>>>>>> regions >>>>>>>> and I would be easier if I could save the maps without loosing >>>>>>>> details. >>>>>>>> I >>>>>>>> tried to use a lower threshold and also to filter the volume before >>>>>>>> segmenting it, but the results are not much better. >>>>>>>> >>>>>>>> I'm not a programmer so I'm sorry if I say nonsenses. Using Chimera >>>>>>>> "Color >>>>>>>> zone" tool you can color different regions in the volume using >>>>>>>> markers >>>>>>>> or >>>>>>>> atoms, and it has the option of splitting the colored regions into >>>>>>>> different >>>>>>>> maps and save them. In that case I don't notice a a coarser surface >>>>>>>> in >>>>>>>> the >>>>>>>> manually segmented maps. Could I use the segger information to color >>>>>>>> the >>>>>>>> volume with Color zone, and use the split map option to segment the >>>>>>>> map? >>>>>>>> >>>>>>>> Thanks again for your help, >>>>>>>> Ernesto. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Fri, May 20, 2011 at 7:50 AM, Greg Pintilie >>>>>>>> wrote: >>>>>>>>> Hi Ernesto, >>>>>>>>> >>>>>>>>> Sorry for the slow response - but thanks for the message and the >>>>>>>>> question. I believe the artefact you are noticing is that when you >>>>>>>>> mask the map with the segmented region, the map densities are set to >>>>>>>>> 0 >>>>>>>>> everywhere except inside the region. Hence instad of a gradual >>>>>>>>> decrease in density at the boundary, making the surface smooth, as >>>>>>>>> you >>>>>>>>> can see in your original map, now there is a sudden drop from some >>>>>>>>> density value to 0 in the segment-masked map. This manifests itself >>>>>>>>> as >>>>>>>>> a coarser surface (as you describe it, the triangles look bigger >>>>>>>>> because you can actually see them). I've sort of know about this >>>>>>>>> problem for a while, but I'm not sure I know yet a good way to >>>>>>>>> address >>>>>>>>> it. I've tried, for example, to extend the segmented regions by a >>>>>>>>> small number of voxels when masking the map, however this looks even >>>>>>>>> worse (it sometimes looks like little fragments coming out of the >>>>>>>>> surface). As long as you know why this happes (let me know if it's >>>>>>>>> still not clear, and I'll try to explain more), I hope at least it >>>>>>>>> seems reasonable. If you have any ideas on how to address it, please >>>>>>>>> let me know! Meanwhile, here are some things you might try to get >>>>>>>>> around this issue: >>>>>>>>> >>>>>>>>> 1) filter the masked map - use the Volume Data / Volume Filter tool >>>>>>>>> - >>>>>>>>> this will remove some signal from your map, but it will make the >>>>>>>>> boundaries smoother as well >>>>>>>>> >>>>>>>>> 2) if you're mainly concerned about illustrating the segmentation >>>>>>>>> results, re-segment the masked map, and use the segmented region for >>>>>>>>> illustration - the segmented region is always smooth as you might >>>>>>>>> have >>>>>>>>> noticed... >>>>>>>>> >>>>>>>>> I hope this helps, and again let me know if you have any ideas... >>>>>>>>> >>>>>>>>> Greg >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, May 17, 2011 at 6:51 PM, Ernesto >>>>>>>>> Arias >>>>>>>>> wrote: >>>>>>>>>> Dear Greg, >>>>>>>>>> >>>>>>>>>> My name is Ernesto and I'm a postdoc in James Berger's lab at UC >>>>>>>>>> Berkeley. >>>>>>>>>> I'm using segment 1.6 built in chimera 1.5.3 and is working >>>>>>>>>> remarkably >>>>>>>>>> well. >>>>>>>>>> I have a question and I'd be grateful if you could answer it. >>>>>>>>>> I want to save in individual mrc files the segmented regions of my >>>>>>>>>> map, >>>>>>>>>> but >>>>>>>>>> when I do it and open the volume of the subregion region it seems >>>>>>>>>> like >>>>>>>>>> the >>>>>>>>>> triangle size is bigger than in the segmentation and in the >>>>>>>>>> original >>>>>>>>>> volume. >>>>>>>>>> I tryed to save the segmented volumes using the "File->save" >>>>>>>>>> options >>>>>>>>>> of >>>>>>>>>> segger as well as "Regions->Mask map with selected", but I get the >>>>>>>>>> same >>>>>>>>>> results. >>>>>>>>>> I don't know if I'm explaining myself clear enough, so I attach two >>>>>>>>>> pictures >>>>>>>>>> to try to illustrate what is happening. >>>>>>>>>> Do you know how can I save segmented regions without this loss of >>>>>>>>>> quality? >>>>>>>>>> >>>>>>>>>> Thanks very much for you help, >>>>>>>>>> Sincerely, >>>>>>>>>> Ernesto. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>> >> >> > Thanks, Tom. That helped a lot. However, is there anyway to smooth out the masked edge? I end up with chopped voxels (looks like stair-steps), rather than getting an interpolated smooth surface at the edge. This is true whether I am masking directly, or the inverted view. > > Kelly > > On Mon, 16 May 2011 12:18:01 -0700 > Tom Goddard wrote: >> Hi Kelly, >> >> There is no command to position the volume eraser sphere using typed coordinates. >> >> If you want to erase a spherical region centered on the center of a virus map use the shape and mask commands: >> >> shape sphere radius 120 center 0,0,0 coord #0 color blue >> mask #0 #1 invert true >> >> The first command makes a spherical surface of radius 120 Angstroms at center 0,0,0 (Angstroms) in the map #0 coordinate frame colored blue. The second command copies the region of map #0 outside the sphere #1, making a new volume data set. >> >> The main trouble here is figuring out the coordinates of the center of virus map. The virus map origin is set in the Volume dialog Coordinates panel where you specify the grid index for position (0,0,0). In the above example I've got the map origin set to the center of the virus (EMDB 1058, grid index 87 for a size 175 map, base index is 0). You can use >> >> shape sphere radius 120 center #0 color blue >> >> which puts the center at the center of the bounding box of the displayed surface for map #0. But that doesn't in general give you the exact center of symmetry. So it is better to find the exact grid point that is the center of symmetry used when the map was calculated. >> >> Tom >> >>> Hi, >>> >>> I would like to place the origin of the eraser to correspond with the >>> center of my map but haven't found a way to define its position based on >>> coordinates, only by moving it with the mouse. Is there a line command >>> or other menu option that allows me to set the position more precisely? >>> >>> Thanks, >>> Kelly

1 0

Secondary Structures in MD data
by Simon Sham 01 Jun '11

01 Jun '11

Hi, I am interested in analysizing the secondary structures from a period of MD trajectories. Is it possible to do that in Chimera? Thanks for your insight. Best, Simon

2 2

Asymmetric partial charges on symmetric atoms
by Brian Fochtman 31 May '11

31 May '11

Hi, When adding partial charges (AM1-BCC) to small molecules in chimera, we observed that atoms in symmetrical groups are not assigned the same partial charge. Specifically, the two oxygens in a carboxyl group are not assigned the same partial charge. See excerpt from mol2 file below: carboxyl: 20 C20 23.4850 19.6920 64.8870 C.2 1 BCZ 0.9226 21 O21 22.2660 19.7760 65.0340 O.co2 1 BCZ -0.9253 22 O22 24.2040 20.8120 64.7970 O.co2 1 BCZ -0.7643 There is a significant difference in partial charge between the two carboxyl oxygens (0.161). This problem was observed in both older (with mopac) and newer (with sqm) versions of chimera. The molecule is peramivir from the pdb1L7F crystal structure. Similar problems were observed for other molecules that inhibit Neuraminidase for example those 1L__ pdb structures. This problem is also observed when assigning am1bcc charges to the mol2 file using antechamber/sqm directly. Best Regards, Brian Fochtman, Trent Balius, Sudipto Mukherjee

2 1

Chimera with 50000 pdb files
by mselvaraj＠mbu.iisc.ernet.in 31 May '11

31 May '11

Dear all, I have some 50000 pdbs obtained from a md simulation of my protein. I would like to calculate ellipsoid (with 'measure inertia' command) around the protein molecule in each pdb and get their axes. Is there a provision/script in chimera to run multiple pdbs and get the axes in a file separately? Any suggestions on this will be helpful. Thanks in advance. yours truly, M. Selvaraj, Graduate student, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

2 1

Molecular representation & FindHbond
by George Tzotzos 31 May '11

31 May '11

Hi everybody, I've successfully loaded my protein. It is represented in ribbon. I want to select three specific residues (e.g. HIS22, TYR53 and VAL124), show them in ball & stick and find Hbonds between them. I follow the procedure below: 1. select #0:22,53,124. Chimera returns: 55 atoms, 54 bonds 2. show sel 3. repr bs sel 4. FindHbond (see snapshot). Nothing is displayed. Instead, I see under the command window: 109 hydrogen bonds found. These are ALL the Hbonds found in the protein. I'd appreciate your guidance how to deal with this. Another related issue is the carboxy terminal residue. In this case VAL124. It is deprotonated. Is it possible to protonate it and then look for Hbons? Thanks in advance for your advice Regards George

2 2

Re: [Chimera-users] An ellipsoid around a protein
by Elaine Meng 30 May '11

30 May '11

Dear M, Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC'd here). In Chimera you can calculate and display the inertia ellispoid for any set of atoms with the command "measure inertia." For example, you could open the protein structure in Chimera, show the command line (from Favorites menu) and then enter the command: measure inertia protein The principal axis information is given in the Reply Log. There are other keywords, such as to control the color of the ellipsoid. See: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 29, 2011, at 9:45 PM, mselvaraj(a)mbu.iisc.ernet.in wrote: > Dear sir, > I would like to calcualte an ellipsoid with its principle axis for a > protein molecule,given its PDB. I came across your discussion on > chimera-users discussion.. Do you have a program that can calculate the > ellipsoid and its principle axes. It would be very help ful for my > analysis. Thanks in advance. > > yours sincerely, > M. Selvaraj, > Graduate student, > Molecular Biophysis Unit, > Indian Institute of Science, > Bangalore 560 012 >

1 0

system freeze completly with ubuntu 10.10
by Mario Dejung 27 May '11

27 May '11

Hello, I have some trouble with chimera on my old laptop. My complete system is freezing after a few seconds. I can not restart X server or switching to a console or anything, even the mouse pointer is not moving. I tried 32 bit chimera 1.5.2 and 1.5.3, both have the same problem. I have 64 MB graphical memory available, but the maps I am loading are very small, like less then 4MB and the system crashs also, even if I open just one map. Does anyone has a good suggestion? Since the whole system is freezing, I am not able to switch back to a terminal to look for error messages or similar. Kind regards Mario

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Import IMOD models into Chimera
by Thomas Heuser 27 May '11

27 May '11

Hi all, Is it possible to open IMOD model files in Chimera? I have used IMOD (with imodmesh) to generate a model of my structure and would now like to load this IMOD model file (.mod) as a volume into Chimera. Is that doable? Thanks a lot in advance and big cheers, Tom -- XXXXXXXXXXXXXXXXXXXXXXX Thomas Heuser Nicastro Lab Rosenstiel Center, MS029 Brandeis University 415 South Street Waltham, MA 02454-9110 Phone: (+ 1) 781 736 2608

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question about "measure rotation"
by Bobby Laird 25 May '11

25 May '11

I am using the measure rotation command in chimera to calculate the degree of rotation between two dimers, which make up a tetramer. I am using the following commands to accomplish this: mmaker #1:.A,.B #0:.A,.B pair ss write relative #0 #1 /tmp/ab-aligned.pdb close #1 open #1 /tmp/ab-aligned.pdb mmaker #1:.C,.D #0:.C,.D pair ss measure rotation #0 #1 I have noticed that when I use the "measure rotation" command that can get two different answers. I realize that the two answers are the result of an arbitrary decision made by the measure tool that result in a +/- of the same angle (i.e. 6 versus 174 degrees). Since I am looking at more several crystal structures, is there a way to force "measure rotation" to always make the same decision so that I know what relative direction the rotations are in to each other? Thanks _______________________________ Bobby W. Laird

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installation of headless chimera
by bharat gupta 24 May '11

24 May '11

Hi, I am new to chimera and I am trying to install it on fedora core 6 . After followng the instructions given in installation manual nothing happens in my system. Can anybody tell me how can I install the headless version of chimera .. Thanks in advance for help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46010(a)yahoo.com

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Re: [Chimera-users] Proline sidechain broken (with backbone as a ribbon)?
by Visvaldas K. 24 May '11

24 May '11

I'm very sorry, I take my question back. Actions->Atoms/bonds->Show will do the trick. Vis

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Proline sidechain broken (with backbone as a ribbon)?
by Visvaldas K. 23 May '11

23 May '11

Hi, I really like the default view of a loaded PDB file, where the whole protein is shown as a ribbon, but also the sidechains next to the heterogroups are shown. Proline shows up in this representation as a sort of rhomboid (or kite) shape, which is okay. However, I cannot achieve the same effect for proline when I select proline manually. If I do Actions->Atom/bonds->sidechain/base->show, the proline sidechain appears as a broken rhomboid, which looks more like a hook, i.e. a one of the bonds is missing to close the loop. How do I obtain a "closed" proline sidechain look? Thank you, Vis

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centering a volume to an atom's coordinate
by Roni Rayes 23 May '11

23 May '11

Hi, I am trying to center volumes (cylinders and spheres that I created using spider) to an atom from a pdb file. When I created the volumes I made sure that their center is in the middle of the box containing the volume. I tried to set the coordinate of the volume to the atom's coordinate (in the coordinate tab under volume viewer) but the position of the volume was not centered to the coordinates provided. Any idea on how to do that? Thank you Roni

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PipesAndPlanks
by George Tzotzos 23 May '11

23 May '11

Hi everybody, I'm dealing with a dimeric hexahelical bundle. I've been trying to name the individual helices (e.g. a1, a2, etc) and colour them differently to no avail. Obviously, I'm missing something. Your guidance will be greatly appreciated. Have a good weekend George PS. Sorry if you receive this message for a second time. It was sent from a different address earlier and I'm not sure if it reached the list.

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Pack molecules in Unit Cell
by Joe Osmundson 20 May '11

20 May '11

Hi everyone, I would like to transform a pdb so that it fits nicely in the unit cell, which seems to be described here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.… as "Pack molecules in unit cell". However, this is not an option when I bring up the options in the Unit Cell tool (although literally everything else that should be there IS indeed there). Is there a glitch in the most recent version? Is there an easy way to script this to essentially move the model (and its crystallographic mate) into the center of the unit cell? Thanks, Joe Osmundson Darst Lab Rockefeller University

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Completely reinstall chimera
by Daniel Hitchcock 20 May '11

20 May '11

Hi, I want to completely uninstall chimera and remove all the settings from the program. I notice though if I uninstall and reinstall though, it still has all the settings and history from before. How can I completely remove Chimera from the computer so I can return to default settings? Thank you -daniel

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solid-cylinder representation of helices
by Francesco Pietra 19 May '11

19 May '11

HI: Is any plan about a solid-cylinder representation of protein helices? It would be very useful to represent pathways of ligands inside a protein (in combination with centroid). Helices allow a less defined 3D perspective, especially when all is projected into a screen or paper. Thanks francesco pietra

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Visualising PDB files from AMBER
by George Tzotzos 18 May '11

18 May '11

Hi everybody, I've generated a average pdb structure from an AMBER trajectory. The structure contains one water molecule (named: WAT). I fail to visualise it in Chimera despite the fact that I can select it. I'm using Chimera 1.5.2 on OSX 10.6.7 Any ideas explaining this behaviour? I'm attaching the relevant file. Thank you in advance for your help Best regards George

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Re: [Chimera-users] Pseudobonds disappearing during morphing movie
by Elaine Meng 17 May '11

17 May '11

Hi Alan, Sorry, there isn't currently a command to apply residue class, only scaling (ribscale) and style (ribrepr): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon…> Some possibilities: - save session with morph already calculated and residue class applied. Your script would then restore the session, play the trajectory, and record the movie. I agree this is not as nice, since then you are saving two files instead of one, and the session file is large. You wouldn't have to wait for the morph to recalculate, however. - use a small python script to apply the residue class. Your Chimera script could open that python file, which automatically executes it. One of the other developers would have to supply the python (beyond my skill set, sorry), and that also requires having two files, albeit much smaller than a session file. In general when playing a morph with ribbons that show secondary structure, consider whether you need to recalculate the secondary structure assignments with "ksdssp" at each frame. To execute a set of commands at each frame, one would use the "perframe" command in combination with "alias": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> For example, your script could contain something like: alias ^redefine ksdssp #2 perframe redefine movie record coordset #2 1,21; wait 21; ~perframe I hadn't used ksdssp/perframe in my examples since (perhaps fortuitously) the secondary structure didn't change that much. If you are just displaying a tube or licorice which doesn't show secondary structure with different widths, it doesn't matter, however. You're right that the shape tube surface will not automatically morph along with the structures, but it might work to destroy/recreate it at each coordinate frame using "perframe". Interesting idea... I haven't tried it, though! I hope this helps, Elaine On May 13, 2011, at 6:10 AM, Alan Cheung wrote: > Thanks Elaine! Yes, the reported thickness was 3.333 (pixels?) and that seems to match the width of the pseudobond i see on the video. The width isn't too bad, and i can live with it. > > Thanks for the explanations and tip too. > > One last question : can I apply a saved residue class (from the ribbon style editor) via a command? I'm morphing a mixture of ribbon and side chain atoms and (for a leucine residue) the CA-CB bond is unrealistically long, but seems ok if i remove the orientation atom (O) from the residue class. I saw the "shape tube" feature in the documentation that draws a tube through CA atoms, but i guessed it's not morphable (and might also not include my precious pseudobond ;) ) > > Many thanks again for the quick replies! > > Alan > > On 12/05/2011 19:22, Elaine Meng wrote: >> Hi Alan, >> Never mind about the PDBs, I made up my own by deleting parts of the structures in my favorite morph test case. >> >> I think I answered all of your issues except for the pseudobonds completely disappearing with "morph movie nogui true" -- I did reproduce that problem, and it seems like a bug, albeit mysterious. I'll file a report about that one, but in the meanwhile I hope you will be able to manage without using that option. >> >> One minor thing is that I generally recommend adding a few more wait frames to the recording after the morph plays, to avoid any "motion blur" effect at the end you might get as a result of encoding. I didn't see much of that effect in my test case proteins using your script, however. It may be because the morph is spread out over 50 frames so there is less differences between adjacent frames, but I was also using different PDBs than you. >> Best, >> Elaine >> >> On May 12, 2011, at 9:25 AM, Elaine Meng wrote: >> >>> Hi Alan, >>> I haven't tried the whole script yet (can you send me the PDB files? I'll keep them private, i.e. only for the development group here if you send them just to me) but will try to address the low-hanging fruit in your set of questions: >>> >>> (A) lines thinner in saved movie. In general, lines such as silhouette edges and pseudobonds may turn out thinner in saved images and movies when you are doing "supersampling," which initially saves a larger image and samples it down to the final requested size. You can check if this is the issue by using File... Save Image to save a single image -- the dialog should report the maximum achievable linewidth given the requested size and amount of supersampling. The reason is that there is an upper limit to how fat your computer can draw the lines (at least via the method used by Chimera). If you have 2x2 supersampling, for example, Chimera will try to make the lines twice as fat in the initial larger image, but may run into this upper limit. Then when the image is sampled down to the final size, the lines may not be as thick as they appear in the interactive display. You could try using lower supersampling. Also make sure you are using a recent version (1.5.3 candida > te ! >>> or 1.6) because there was a lines-too-thin-in-images bug a couple of months ago. >>> >>> (B) setattr "p" vs. "g" -- this is because some attributes are for individual pseudobonds (p) and some attributes are defined for whole pseudobond groups (g). Individual pseudobonds don't have a linewidth attribute, it is set at the group level. All the pseudobonds in that group (for example, hydrogen bonds) would get the same linewidth and it is not possible to make different ones in the same group have different widths. If you are looking at the Selection Inspector or some other attributes inspector, it will show you which attributes are for individual pseudobonds and which are for groups. The balloon help will give the attribute name and allowed values. >>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelattrib.html> >>> >>> I will try to look at your other issues and get back to you, >>> 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 May 12, 2011, at 8:54 AM, Alan Cheung wrote: >>> >>>> Hi there - i'm scripting a complex movie and am having problems with >>>> pseudobonds during morphing. Script is pasted at the end. >>>> >>>> Part of the movie contains a morph between two structures, both of >>>> which are missing the same amino acid segment. Loading the two >>>> structures show the pseudobond for the missing residues and the >>>> resulting morph also contains the same pseudobond. >>>> >>>> I've been changing the thickness of the pseudobond with : >>>> >>>> setattr g lineWidth 8 >>>> >>>> and while the two static structures and the morph in the chimera >>>> window have a thicker pseudobond, the resulting movie (encoded to >>>> .mov) does not. Am i doing something wrong? >>>> >>>> Alan >>>> >>>> p.s. incidentally, when morphing by script, if one includes "nogui >>>> true" with the "morph movie" command, pseudobonds aren't kept in the >>>> morph at all. A bug? >>>> p.p.s. can someone explain to me the difference between "setattr g" >>>> and "setattr p"? I've read the manual but i don't understand why only >>>> the former seems to work for me. >>>> >>>> ## movie script >>>> >>>> open model1.pdb >>>> open model2.pdb >>>> morph start #0 frames 50 name morph1 method linear >>>> morph interpolate #1 name morph1 >>>> morph movie name morph1 >>>> coordset #2 1,1 >>>> setattr g lineWidth 8 >>>> ~modeldisplay # >>>> >>>> movie record supersample 3 directory ~/TEMP/ >>>> modeldisplay #2 >>>> coordset #2 1,51 ; wait 51 >>>> movie stop >>>> movie encode output morph1.mov >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > -- > Alan Cheung > Gene Center > Ludwig-Maximilians-University > Feodor-Lynen-Str. 25 > 81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76999 > E-mail: cheung(a)lmb.uni-muenchen.de

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labeling residues
by Daniel Gurnon 16 May '11

16 May '11

Hi all, A student of mine wants to make a wire sculpture of a protein, and I'm thinking of ways Chimera could make the task easier. Ideally, I would create a script that would display any protein in wire-form, with residue positions clearly and unobtrusively labeled. I'd like to use the command line to display a backbone as a licorice ribbon with residue numbers and 1-letter codes at the alpha carbon of each residue. so starting out, I would use: ribscale licorice; ribbackbone; rlabel @ca; But instead of "ALA 24.B", I want "A 24". Though I can get what I want using the Actions menu, I can't find a way to create custom rlabels via the command line. Is there a way to do this? If possible, I would also like to position each label near the spot on the ribbon closest to the alpha carbon (the "primary atom"). I can see how to do this with the molecule attributes panel, but I'm having difficulty setting the placement through the command line. And while I'm at it...is there a way to color a spot on the ribbon closest to the alpha carbon a different color than the rest of the ribbon? Thanks for the help! Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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