- Chimera-users - RBVI Mailing Lists

Chimera on Linux
by Beale, John 30 Jul '07

30 Jul '07

I have been using Chimera on a Linux-equipped laptop for a long time. All that I had to do to get the software working was to download the appropriate version of Chimera and click on the executable. I am trying to install Chimera on a new Linux workstation. I downloaded the program for Linux, but when I try to run the executable I get a message that says that the software downloaded is for MS-DOS and not Linux, and I am unable to install Chimera. Has anyone run into this problem, and is there a fix for it? John Beale

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CSB 2007 Molecular Visualization tutorial
by Conrad Huang 30 Jul '07

30 Jul '07

Scooter Morris and Conrad Huang will be giving an introductory molecular visualization tutorial using Chimera on August 13 at CSB 2007 (the Conference on Computational Systems Bioinformatics) in San Diego. Interested folks can visit http://www.lifesciencessociety.org/CSB2007/index07.html for more information on CSB 2007. The tutorial abstract is attached below. An Introduction to Molecular Visualization Tutorial at the Computational Systems Bioinformatics (CSB) conference (AM2) University of California, San Diego August 13, 2007 Abstract Projects such as Structural Genomics are providing increasing numbers of experimental protein and protein-complex structures. Furthermore, increasing numbers of theoretical models are being predicted from primary sequence. Biologists have an increasing need to understand and communicate the structures, functions and relationships between these protein and protein-complex structures. As a result, molecular visualization is becoming an important tool for the presentation and communication of the results of biological experiments and research. This tutorial will provide a basic foundation for the understanding of molecular structures through use of visualization tools. Attendees will learn the basics of molecular visualization and will be provided an overview of available tools and techniques for visualization, analysis and modeling of protein structure. To make these concepts more concrete, attendees will be shown the academic program UCSF Chimera in more detail, and receive instruction in its features and use. The field of structural biology is still changing, and new techniques are continually being developed. Attendees will be shown how they can add new analysis techniques and their own data to the visualization. Outline: 1. Introduction to Molecular Visualization 2. Available Tools 3. Using UCSF Chimera 4. Scenarios of use 5. Extending Chimera

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Fwd: CCL: hydroxide for dock
by Elaine Meng 25 Jul '07

25 Jul '07

Begin forwarded message: > From: "Yubo Fan yubofan|-|mail.chem.tamu.edu" <owner- > chemistry(a)ccl.net> > Date: July 25, 2007 7:50:36 AM PDT > Subject: CCL: hydroxide for dock > Reply-To: "CCL Subscribers" <chemistry(a)ccl.net> > > Hi, everyone, > I'm preparing structures with Chimera for docking with Dock6. There > is a Zn-coordinating hydroxide that I want to keep in the > structure. When I prepare dock files, Chimera always treat it as a > water. Is there any way to define it as a hydroxide in Chimera? > Thanks, > Yubo > ============================================================ > Dr. Yubo Fan Email: yubofan_+_mail.chem.tamu.edu > Department of Chemistry Tel: 1-979-845-5237 > Texas A&M University > College Station, TX 77843 > ============================================================ Dear Yubo, I could answer more precisely if I could see the file, but without seeing it, I recommend: (a) looking at the residue name of the hydroxide in the text of the file. Is it WAT or HOH? If so, you could edit it to a different name, say XOH or HOM. (b) then, run Dock Prep in Chimera including hydrogen addition and all the steps before that (but don't assign charges or write the Mol2 file). (c) check the structure; if hydrogen is added where you didn't want it, simply delete it. For example, Ctrl-click to select an atom and use "Actions... Atoms/Bonds... delete" in the menu to delete it. The protonation states are intended to be reasonable at physiological pH, but if a group is expected to have a perturbed pKa (for example, in an active site or near an ion), it is a good idea to check it and manually add/delete hydrogens as needed. ( more details in http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html ) (d) run Dock Prep again with only the steps AFTER hydrogen addition (charge assignment and Mol2 file output) turned on. If it asks for the net charge of XOH (or whatever you named it), indicate -1. (e) that procedure will use Antechamber to calculate the partial charges on the hydroxide O and H. If, however, you already know the charges you want to use for these atoms, you can edit the charge values in the output Mol2 file. In that case you wouldn't even have to go through all these steps, but could simply also delete the extra hydrogen from the Mol2 file, if you can figure out which line it is! I just realized this last point, so it wasn't in my original reply. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Windows Vista
by Jason M Walraven 23 Jul '07

23 Jul '07

I just installed the latest version of Chimera on my Windows Vista operating system (home basic). Everything seems to work perfectly, except that the colors appear to be messed up. The colors appear darker than on my previous computer (with Windows XP). Has anyone else had this problem? All colors in all other programs are normal on my computer except for in Chimera. I assume it is a compatibility issue, but I don't know enough about it to say that for sure. jw

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Re: [Chimera-users] Reading a data set from a text file
by Thomas Goddard 17 Jul '07

17 Jul '07

Hi Kyaw, I see what you've done and see that you have a set of (x,y,z) coordinates. But I'm not sure what you want or what these coordinates represent. To make a surface out of a set of points you need to know which points are next to each other. In Chimera you need a set of points, and a set of triangles, each triangle defined by 3 integer indices into the set of points that give the triangle vertices. If you can define the set of triangles I can tell you how to make the surface. Tom Kyaw Zeyar Myint wrote: > Hello Tom, > I apologize for not being able to respond to you earlier. The > set of view vectors that I want to make surface out of it are in (x, y, > z) coordinates. > > So far, I've done a quick and 'rough' way of using these vectors for > display. What I did in chimera was that I wrote a mini plugin which > makes a .bild > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> file with a > set of cylinders, given a set of vectors. > Each cylinder is centered at origin (0,0,0) and drawn according > to the vector (which is from my set of view vectors). So if the V(x,y,z) > has (0.0523, 0.0000, 0.9986), then the cylinder is drawn by: > /.cylinder 0 0 0 0.0523 0.0000 0.9986 0.03 / in .bild file. > Then .bild file is fed into chimera and then a set of cylinders > is displayed. In a sense, each cylinder represents each view vector in > the set. But this is just a quick solution. > If you can share some ideas of how to better do this, please let > me know. I'd really appreciate your help. > > Thanks a lot! > Kyaw > (P.S: I've attached .bild file which you can display in chimera and see > what inside using a text editor.) > > ------------------------------------------------------------------------ > > > On Jun 29, 2007, at 1:03 PM, Tom Goddard wrote: > >> Hi Kyaw, >> >> I'm not sure I understand what type of data you want to display in >> Chimera. Is it a list of density values, or is it a list of x, y, and >> z coordinates? If it is density values in text rather than binary, >> you could reformat it into XPLOR format >> >> http://www.scripps.edu/rc/softwaredocs/msi/xplor981/formats.html >> >> which can be read into Chimera. >> >> Tom >

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presets criteria
by Roberta King 17 Jul '07

17 Jul '07

Hello, I have upgraded to Chimera 12417 with the new presets for visualization. What are the criteria within "Interactive 1:setup ribbons" preset for determining which residue side chains are depicted as sticks in the binding pocket? This is a useful shortcut, but I would like to understand the specific criteria. Thank you very much, Roberta ******************************** Roberta S. King, Ph.D. Associate Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island http://www.uri.edu/pharmacy/faculty/king

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 16 Jul '07

16 Jul '07

Hi Pasquale, You can definitely open multiple PDB files and move them independently. By default everything will move together, which might even be what you want. However, if you don't want them to move together, you can freeze any structure in place ("deactivate" it), move the other(s), and then "activate" the first structure again if you want it to be movable. There are several ways to control activation/deactivation; probably the easiest is to open the Model Panel (Favorites... Model Panel). Then just uncheck/check the box in the Active column to freeze/ unfreeze a model. We use the word model to mean the contents of a structure file (PDB, Mol2, etc.), so if you read in two separate PDB files, there would be two models listed in the Model Panel. Alternative ways of controlling activation/deactivation are with the little checkboxes under the Command Line and using the command "select". You would still be able to minimize multiple models as a single system by choosing all of them in the "Minimize Structure" dialog. Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 16, 2007, at 7:59 AM, Pasquale Iacono wrote: > well in order to make the dimer i used two separate pdb files and > imported them both into the same gaussian gjf file. then i imported > that file as a mol2 file into chimera, so unless i can manipulate > separate pdb files in chimera then that would be great but i cannot > figure out how to move separate pieces of my dimer. > > On 7/15/07, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Pasquale, > I had one long-shot possibility for getting the correct atom and > residue names - did you start with a PDB file before the guassian > calculations? If so, that file may have had the correct atom and > residue names. If that starting file had all the same atoms > (including hydrogens) and the order of the atoms is exactly the same > in that gaussian output, you could simply replace (probably with a > script) the coordinates in each line of the starting PDB file with > those from the gaussian output. That would only work if the order is > exactly the same, however. > > Otherwise it would be extremely tedious to figure out which > coordinates go with which atom/res/number. > Best, > Elaine

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ValueError: More than 2 coplanar positions specified!
by Mike Gretes 13 Jul '07

13 Jul '07

Hello, When trying to calculate hydrogen bonding between two molecules, I get the error: "ValueError: More than 2 coplanar positions specified!" I have successfully calculated h-bonding between two other similar molecules, so I'm not sure what the problem is (I have no alternate conformations or anything weird in the PDB files I don't think... is there anything that usually triggers this error?) thanks! mike ___________________ Michael Gretes PhD Candidate (Structural Biology) Senior Graduate Trainee, Michael Smith Foundation for Health Research NCJ Strynadka Laboratory Dept. of Biochemistry, University of British Columbia Life Sciences Center, 2350 Health Sciences Mall Vancouver, BC Canada V6T 1Z3 phone 604 822 7729 fax 604 822 5227 ____________________

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Forward of moderated message
by mailman-bounces＠cgl.ucsf.edu 13 Jul '07

13 Jul '07

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Re: [Chimera-users] Using mol2 files
by Elaine Meng 11 Jul '07

11 Jul '07

Hi Pasquale, As Eric figured out, your mol2 file does not contain substructure information. For the structure to be read by Chimera as a series of residues, there would need to be residue information in each line in the @<TRIPOS>ATOM section and then a corresponding @<TRIPOS>SUBSTRUCTURE section at the bottom. You would have to edit that information into your file. Otherwise, the structure appears as one big residue. Mol2 format description: http://www.tripos.com/mol2/mol2_format8.html ATOM section - need substructure ID and name (residue number and name) for each atom http://www.tripos.com/mol2/mol2_format33.html#1370 SUBSTRUCTURE section - more information on those substructures (residues) To get an example mol2 file, open a PDB file of a protein in Chimera, add hydrogens if you want those in your example, and then write it out as Mol2 (File... Save Mol2...) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 6, 2007, at 10:57 AM, Eric Pettersen wrote: > Hi Pasquale, > If your structure all got put into a single residue named UNK, > that typically means that your file was missing the @SUBSTRUCTURE > section (http://www.tripos.com/mol2/mol2_format33.html#1370) > There is an entry in our bug database (#3518) for better handling > of files with missing @SUBSTRUCTURE sections. I will add your name > to that report so you'll know when it gets fixed. For now, you > will have to edit your file and add an @SUBSTRUCTURE section "by > hand". > > --Eric >> >> On Jul 6, 2007, at 8:54 AM, Pasquale Iacono wrote: >> >>> Hey Elaine, >>> My structure is currently being labeled as one big residue >>> (UNK) and when I minimize it it says it does not recognize the >>> residue, so it seems like the calculation program is using >>> residue parameters and not those for specific atoms. Also, my >>> structure contains a Zn(II) metal center and I was wondering if >>> the parm files would detect it as such if it actually used the >>> atom types. I attached my mol2 file so you can check it out. Thanks >>> -Pasquale Iacono

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memory usage
by jean-francois menetret 11 Jul '07

11 Jul '07

It seems that Chimera is not releasing memory easily on our linux PC. Is this a know problem for Chimera ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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Chimera and Debian
by Arkadiusz Czader 11 Jul '07

11 Jul '07

Hi, I have a problem running 32 bit linux version of Chimera on Debian64. When I run it, it complains about some libraries. Below I pasted what I get when I type chimera in a terminal window arek@teton:~$ chimera Traceback (most recent call last): File "/home/arek/progs/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "/home/arek/progs/chimera/share/chimeraInit.py", line 231, in init import chimera File "/home/arek/progs/chimera/lib/python2.4/site-packages/PIL/__init__.py", l ine 15, in ? ImportError: libGL.so.1: cannot open shared object file: No such file or directory The library libGL.so.1 is only in /usr/lib. Should it be in a different place? Any help appreciated. cheers, Arek ____________________________________________________ | | __ __ | | Arkadiusz Czader | | | _| | __ | | Department of Chemistry | | | | | | | | | | University of Houston | | | | | | | | | | Houston, TX 77204-5003 | | | | |_|_| | | | Phone: (713)-743-5101 | \ \_| ___ | | | E-mail: aczader(a)uh.edu | \___| |/ | | | | | | | | | | | | |__| |__| | |____________________________|_______________________| ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/

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Re: [Chimera-users] pdb-l: Selecting phytols in Chimera?
by Eric Pettersen 09 Jul '07

09 Jul '07

On Jul 9, 2007, at 6:39 AM, Morgan Ryan wrote: > Is it possible to write a selection string that will select all the > phytol substituents in a model? I'm looking at photosystem II. I > would like to select all the phytol side chains of the many > chlorophyll molecules and hide them, so that only the porphyrin-like > chlorin ring structures are visible. Can that be done? Thanks! Morgan Hi Morgan, I think the only direct way is to use the command line (Favorites- >Command Line). This command should do it: ~disp :cla@c=; disp :cla@c?a,c?b,c?c,c?d It undisplays all the carbons in the chlorophyll (:cla@c=) and then redisplays the carbons involved in the porphyrin ring (all of which have 3-letter names that end in A-D). You might want to consider posing Chimera-specific questions to the Chimera users mailing list (chimera-users(a)cgl.ucsf.edu) since there will be more people able to answer there. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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clobbered chimera, can't start from fresh install (help)
by William Jeffrey Triffo 09 Jul '07

09 Jul '07

hello, I changed some of the preferences for the IDLE shell, which produced errors that would not allow IDLE to run (tried to remap a couple of keys). This problem persisted when restarting Chimera. so, I deleted that install (Mac OS X) and re-installed the most recent release, but still produced the errors, and cannot launch IDLE. I went ahead and deleted the files in ~/.chimera, but the errors still occur. Are there any other user-specific files that I can delete that might be causing the problem? I am assuming this is the case, because even a fresh install has the same problem. I submitted a bug report about the IDLE preferences issue I experienced, but am hoping a simple fix might allow me to launch IDLE again. thanks, -Jeff

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occupancy calculation
by bala 09 Jul '07

09 Jul '07

Hello, 1) I want to calculate the occupancy of water around few base pairs in a RNA duplex. I had one query while i was going through the "calculate atomic occupancy" documentation. "For example, cations or water hydrogens may tend to occupy space around a negatively charged solute group" In the options give for this particular calculation, nowhere there is an option to select whether i am interested in WATER or ION occupany. How then chimera calculates the occupancy. 2)I presume that chimera calculates the occupany of say water as follows, if i select a residue, it puts the residue in a grid and calculated the density of water molecule in the grid points in frame. Is this the way it calculates the occupancy. I am not getting how i should differentiate occupancy and density. thanks, Bala

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chimera question
by 明明 08 Jul '07

08 Jul '07

Dear sir: I download the software UCSF chimera(version: chimera-0.2422-win32.exe). the I setup it in my computer(Windows XP). I want to use it to open my pdb file and the VIPERdb file. But I always could not open them. It always says that: Error reading C:\Documents and Settings\ft\1K3V.pdb: typeerror: argument 1 should be a str( see reply log for python traceback info). Then I want to ask for you help. How can I open the pdb file and VIPERdb file correctly? please read the appendix Thank you. Qiting Harbin veterinary research institute --------------------------------- Mp3疯狂搜-新歌热歌高速下

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chimera question
by 明明 08 Jul '07

08 Jul '07

Dear sir: I download the software UCSF chimera(version: chimera-0.2422-win32.exe). the I setup it in my computer(Windows XP). I want to use it to open my pdb file and the VIPERdb file. But I always could not open them. It always says that: Error reading C:\Documents and Settings\ft\1K3V.pdb: typeerror: argument 1 should be a str( see reply log for python traceback info). Then I want to ask for you help. How can I open the pdb file and VIPERdb file correctly? please read the appendix Thank you. Qiting Harbin veterinary research institute --------------------------------- Mp3疯狂搜-新歌热歌高速下

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Custom presets
by Eric Ganz 06 Jul '07

06 Jul '07

Is there a way to create new presets for molecule views? We want to apply the attributes of one molecule to subsequent molecules. Is there an easy way to do this? Our second question is how to set half-bond mode off for our views.

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Re: [Chimera-users] Using mol2 files
by Eric Pettersen 06 Jul '07

06 Jul '07

Hi Pasquale, If your structure all got put into a single residue named UNK, that typically means that your file was missing the @SUBSTRUCTURE section (http://www.tripos.com/mol2/mol2_format33.html#1370) There is an entry in our bug database (#3518) for better handling of files with missing @SUBSTRUCTURE sections. I will add your name to that report so you'll know when it gets fixed. For now, you will have to edit your file and add an @SUBSTRUCTURE section "by hand". --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Using mol2 files
by Pasquale Iacono 03 Jul '07

03 Jul '07

Hi I imported a .mol2 file from Gaussian to Chimera because I want to run an amber minimization with a better parameter set. However, the mol2 files are not like pdb files and do not come with atom types for amber calculations. Is there anyway to (auto?)assign amber atom types to the atoms in my file so your program can run a calculation? Thank you. -Pasquale Iacono, B.S. Ithaca.College

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POVray shininess
by Tom Goddard 03 Jul '07

03 Jul '07

Edward Egelman wrote: > Hi, > The new POV rendering is very nice, but suffers from one problem > that I do not see how to fix. Is there any way to control the surface > properties (reflectivity, "shininess", etc.)? I only see the standard > brightness and transparency for the "save as" feature. > Regards, > Ed Hi Ed, You can control the shininess of surfaces in Chimera using menu entry Tools / Viewing Controls / Shininess. The shininess you set is exported to POVray when you save a raytraced image. The POVray appearance doesn't exactly match the Chimera graphics window appearance so you may need some trial-and-error experimentation to get the desired shininess in the POVray output. Tom

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seg faults
by Tom Goddard 03 Jul '07

03 Jul '07

Edward Egelman wrote: > Hi, > I have a question about very complicated chimera sessions (20 or so > large PDB files, 10 or so large brix volumes). We will sometimes get a > segmentation fault and the session will close. This is on a 32-bit > linux machine with 2GB memory (our only system with stereo display). > If we move to a 64-bit machine with more memory, will we be less > likely to crash? Or is this due to some internal memory limitations in > chimera itself? A second question is whether you have any experience > (or know of others who have) using fast nvidia stereo boards (such as > the Quadro FX3500) to accelerate display operations in chimera. > Regards, > Ed > -- Hi Ed, There are only two Chimera crash situations that I understand and are frequently reported. Computing molecular surfaces of PDB models (menu entry Actions / Surface / show) crashes for many large PDB models. If the surface calculation gives an error but does not crash it has usually corrupted memory and Chimera will crash later. The solvent excluded surface code comes from Michel Sanner and is very complex (~20000 lines of C code). We have been working on a replacement for it for over a year but it is not yet ready. The second type of crash is caused by graphics driver bugs. These are common, more so on higher-end graphics cards where Chimera takes advantage of OpenGL features that are used by few applications, also more common on laptops. Here are some of the graphics driver problems observed in Chimera. http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html#cards I have never had Chimera crash when I am working with large PDB models and maps (using Mac systems with 1-2 Gb memory), but that is probably because I only work with a few models and maps at a time, and for short sessions. It could be that memory allocation failures cause crashes in these situations. I am doubtful that using the 64-bit Linux Chimera will help. Using the 32-bit Linux Chimera on a 64-bit machine almost certainly will not help because the 32-bit address space can only access 4 Gb of memory and segments of that address space are already used by shared libraries and program stack -- so you probably only have 2 Gb of usable space. With 2 Gbytes of physical memory you probably have at least 4 Gb of virtual memory, so the 32-bit address space is the main limitation. Chimera catches memory allocation failures for large allocations (e.g. opening a new map) and those do not cause a crash. It is only when a small allocation that is not checked fails that a crash might happen. The difference in speed rendering surfaces between say a Quadro FX 3400 and an ATI Radeon Pro 9800 (in my 3 year old desktop computer) is about a factor of 4. That is about the speed up to expect between a card that is a couple years old and the latest graphics card. Benchmark scores using Chimera for different cards are on the web http://www.cgl.ucsf.edu/chimera/benchmarks.html although there are few numbers for the latest cards. For volume surfaces look at the Surface column of the table. The score is the grid size of a triangulated cube that can be rendered at 10 frames per second. Since the number of triangles increases as the square of the size you should look at the *square* of the ratio of scores between cards to gauge the increase in speed expected for a fixed size volume. Tom

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Fixing MSMS crash
by Thomas Goddard 02 Jul '07

02 Jul '07

P. Qian sent me a PDB model that caused Chimera to crash when calculating an MSMS surface (menu Actions / Surface / show). He got it not to crash by shifting the coordinates of all atoms (by moving and saving the PDB with "use untransformed coordinates" turned off, and reloading that file). This is a little nicer than changing atom radii as we've advised in the past. Not sure how often a simple shift (or rotation) avoids the crash though. Tom

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Origin question with maps
by Eduardo Sanz-Garcia 29 Jun '07

29 Jun '07

I found that the origin of /mrc/ maps is read correctly and can be used to place one map in respect of another. For example: 1.mrc (origin: 10,0,0) is going to be shifted 10 pixels with respect of map 0.mrc (origin: 0,0,0). I can not reproduce the same behavior with CCP4 format (.map) . The origin is not read correctly. Thank you.

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conjoined unit cells
by Bartosz Siemiński 29 Jun '07

29 Jun '07

Hi all, I was working with Chimera for some time, beeing convinced I don't need no help, until I'd got to this. Is there a possibility of conjoining several (let's say four, nine or sixteen) unit cells? I use the el. density map (converted to cpp4, so it could be loaded by Chimera) for structural alignment and such an operation would be very usefull. Thanks in advance, Bartek ____________________________________________________________________________ Czy już jesteś w Yahoo!? Masz dosyć spamu? Poczta Yahoo! dysponuje najlepszą ochroną przed spamem http://pl.mail.yahoo.com

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