- Chimera-users - RBVI Mailing Lists

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 12 Jul '07

12 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 30 Jun '07

30 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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mrc maps
by Gorelik, Tatiana 29 Jun '07

29 Jun '07

Hi, I image an .mrc map in Chimera. The surface map is displayed using a selected range. As a result I see blobs. I want to be able to select such a blob and get back its 3d information - coordinates, etc... Would it be possible to implement this feature? Greetings, Tatiana ************************************ Tatiana Gorelik, PhD, Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Welderweg 11 55099 Mainz Germany Tel.: 0049 6131 39 22347 Fax: 0049 6131 39 23768 e-mail:gorelik@uni-mainz.de ************************************

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Reading a data set from a text file
by Kyaw Zeyar Myint 29 Jun '07

29 Jun '07

Hi, I am Kyaw Myint, a summer intern at NIAMS branch of NIH. I am working under the supervision of Dr. Bernard Heymann from the Lab of Structural Biology research. The project I am working on currently is to improve the 3D reconstruction of viruses' structures from 2D electron micrographs. The programs I am using include Chimera and Bsoft. For the project, I want to read in a data set from a text file and display the 3D surfaces based on that data set. I'd like to use Chimera for that purpose and I'd really appreciate any suggestion or comment on how I should do that. Thank you very much for your help in advance. Looking forward to hearing from you soon, Kyaw

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rotating items in chimera
by William Jeffrey Triffo 29 Jun '07

29 Jun '07

hello, is there a way to return to a rotational position, without using 'savepos' and 'reset'? For instance, if I don't want to reset translation(s) (which using savepos/reset might do), but just want to return to a 'top down' view, or a specific rotation with respect to the viewer's global axes? I realize that with multiple objects in potentially different rotational orientations, this would require which object to use to calculate the rotation. thanks, -Jeff

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Transformation matrices
by Eduardo Sanz-Garcia 29 Jun '07

29 Jun '07

I am getting the rotation matrices (I am not interested in the translation column) using matrixget command. My naive question: Should I use in this way: x' x y' = [3x3 matrix] y z' z or in this other way? z' z y' = [3x3 matrix'] y x' x Thank you very much.

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IMOD mesh/surface colors
by William Jeffrey Triffo 28 Jun '07

28 Jun '07

hi, is there a way to control the color of surfaces generated from IMOD meshes in Chimera? when I select a surface, and pick a new color in the color editor, I notice that the color of the 'IMOD contours' in the Model Panel changes, but that there is no change in the color of the actual rendered surface. thanks, -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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Use of a copyrighted figure for software review note
by Anselm.Horn＠chemie.uni-erlangen.de 27 Jun '07

27 Jun '07

Dear all, sorry, if this is a bit off-topic, but I did not find any e-mail address more suitable on the Chimera website. As I learned from the CCL there is a new Chimera version out. I think this would be a nice opportunity to write a short software review note (approx. 1 column) in the "Nachrichten aus der Chemie", the members journal of the German Chemical Society GDCh, in order to inform a broad public of Chimera. For this I'd like to use the graphic "DNA and Netropsin" from the Chimera Image Gallery, in case there is space enough to have a figure printed as well. The image, however, is marked copyrighted, and thus I'd like to know, whether I may use it for my purpose and what statement/copyright notice should be included in the figure caption. Thanks in advance. Best regards, Anselm

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how to "connect" two proteins
by Damir Perisa 26 Jun '07

26 Jun '07

hi all, maybe this is a little bit too far over the capabilities of chimera, but i hope somebody can help me or give input. i would like to connect two PDB structures into one chain of aminoacids. one PDB is from one globular domain, the other is from another globular domain including linker. i would like to try to put them together and see how (what possible conformations) they fit together. what orientations are possible and how it would look like (visualisation, making movies, convincing non-scientists, ...). i could edit the PDB files in a text editor, but i would not want to calculate the cordinates by hand first - are there no tools to glue together chains? thanx for any input how to do this with chimera or any other programme, best regards, Damir -- Damir Perisa Master Student Biozentrum, University of Basel Department Biochemistry / Focal Area Infection Biology Klingelbergstrasse 50-70 CH-4056 Basel, Switzerland phone: +41 61 267 1492

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Question on Chimera
by Ki Kim 25 Jun '07

25 Jun '07

Hello, I would like to know what is the best way to draw the surface of the binding site of a protein. I would like to add some water molecules to the protein and treat these water as part of the protein. Thank you for your help. Sincerely, Ki Kim

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Re: [Chimera-users] error running Antechamber
by Eric Pettersen 23 Jun '07

23 Jun '07

On Jun 23, 2007, at 11:12 AM, S Datta wrote: > Thanks a lot Eric. You suggest that I modify the input > files by putting the cobalt with residues of their > own. Do you mean as a separate file or in the > methylcobalamin file that i downloaded from the PDB > database ? Also one of the ligands to the > methylcobalamin is a histidine from the protein. Change it in the same file. Change the residue name and number, being careful to keep the rest of the columns in the same place. Also make sure that the new residue number isn't the same as some other residue. The fact that protein histidines are coordinating the metal shouldn't be an issue. Let me know if you run into problems. --Eric

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error running Antechamber
by S Datta 22 Jun '07

22 Jun '07

Hi I am trying to prep a ligand using chimera for docking. When I try to add charges, one error which is always present is "Atom whose IDATM type has no Sybyl type: #-99.-99:1@CO(type: Co). At the end the reply log asks to check the total charge and spin multiplicity. When I manually change the total charge, after the Atom error briefly appears, Chimera either freezes (windows) or runs the program /../antechamber/exe/mopac.sh (in linux) infinitely. Could someone help me decipher what is going wrong ? I tried to change the input format of the ligand file from .pdb to .sy2 but that didnt help. thanks a lot SD ____________________________________________________________________________________ Got a little couch potato? Check out fun summer activities for kids. http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&…

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discontinuous ribbon for nuc. structure
by bala 20 Jun '07

20 Jun '07

Hello, While i make the ribbon representation for an RNA duplex, sometimes ribbon is discontinuous in between, what could be the reason for it ? I hve two conformation sof the same duplex taken at 1ns interval from MD trajectory. For one conformation, ribbon is continuous but for the other there is a discontinuity at the middle.. I analysed the structure, it seems ok. thanks in advance, Bala

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Delphi calculation for electrostatic surface potential
by Shunsuke Meshitsuka 18 Jun '07

18 Jun '07

Dear Doctors, I want to calculate surface potential by Delphi type calculation. I have tried from Menu bar, tool --- DelPhi ,but have not obtained the results. Please let me know the way to use them for the calculation of surface potentials from a PDB fie in linux version of chimera-1.2417. Shunsuke Meshitsuka D.Sci., D.Med. Tottori University Graduate School of Medical Science Institute of Regenerative Medicine and Biofunction, Division of Integrative Bioscience 86　Nishimachi Yonago Tottori　683-8503　Japan tel +81-859-38-6422 fax +81-859-38-6423 Email: mesh(a)grape.med.tottori-u.ac.jp

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Help me please with this error
by David Gil Carton 15 Jun '07

15 Jun '07

Hi, I have a HP9400 (AMD Opteronx64bits-Red Hat Linux64bits) with a NVIDIA Quadro FX3500 256MB and I have installed the "chimera-1.2417-linux_x86_64.exe". My problem is that when I run chimera I have this message, %chimera X Error of failed request: GLXUnsupportedPrivateRequest Major opcode of failed request: 129 (GLX) Minor opcode of failed request: 16 (X_GLXVendorPrivate) Serial number of failed request: 1313 Current serial number in output stream: 1314 %glxinfo name of display: :0.0 display: :0 screen: 0 direct rendering: No server glx vendor string: NVIDIA Corporation server glx version string: 1.4 server glx extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGI_video_sync, GLX_SGI_swap_control, GLX_ARB_multisample, GLX_NV_float_buffer, GLX_ARB_fbconfig_float, GLX_NV_swap_group client glx vendor string: SGI client glx version string: 1.4 client glx extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_allocate_memory, GLX_MESA_swap_control, GLX_MESA_swap_frame_usage, GLX_OML_swap_method, GLX_OML_sync_control, GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group GLX extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro FX 3500/PCI/SSE2 OpenGL version string: 1.2 (2.0.2 NVIDIA 87.62) OpenGL extensions: GL_ARB_depth_texture, GL_ARB_imaging, GL_ARB_multitexture, GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_shadow, GL_ARB_texture_border_clamp, GL_ARB_texture_cube_map, GL_ARB_texture_env_add, GL_ARB_texture_env_combine, GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat, GL_ARB_texture_non_power_of_two, GL_ARB_transpose_matrix, GL_ARB_window_pos, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_func_separate, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_multi_draw_arrays, GL_EXT_packed_pixels, GL_EXT_point_parameters, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shadow_funcs, GL_EXT_stencil_wrap, GL_EXT_texture3D, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add, GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod, GL_EXT_texture_lod_bias, GL_EXT_texture_mirror_clamp, GL_EXT_texture_object, GL_EXT_texture_rectangle, GL_EXT_vertex_array, GL_ATI_texture_float, GL_ATI_texture_mirror_once, GL_IBM_rasterpos_clip, GL_IBM_texture_mirrored_repeat, GL_INGR_blend_func_separate, GL_NV_blend_square, GL_NV_copy_depth_to_color, GL_NV_depth_clamp, GL_NV_fog_distance, GL_NV_light_max_exponent, GL_NV_multisample_filter_hint, GL_NV_texgen_reflection, GL_NV_texture_env_combine4, GL_NV_texture_rectangle, GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp, GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod, GL_SGIX_depth_texture, GL_SGIX_shadow, GL_SUN_multi_draw_arrays, GL_SUN_slice_accum glu version: 1.3 glu extensions: GLU_EXT_nurbs_tessellator, GLU_EXT_object_space_tess What I have to do to resolve my problem? Thanks, David Gil Electron Microscopy Structural Biology Platform CIC bioGUNE Bizkaia Technology Park, Bld 800 48160 Derio-Bizkaia Tel Platf. +34 946 572 516 Fax +34 946 572 502 http://www.cicbiogune.es Este correo electrónico se ha enviado desde CIC bioGUNE. Su contenido, y el de cualquier fichero que le acompañe, son confidenciales y de uso exclusivo de la persona física o jurídica a la que va destinado. Está estrictamente prohibida, y puede ser ilegal, la copia o difusión no autorizada de este correo, o de sus documentos adjuntos, o revelar cualquier información que pudieran contener. Si ha recibido este correo electrónico por error, por favor notifíquelo al remitente o contacte con el teléfono + 34 944 06 13 00 y bórrelo de su sistema informático. Posta elektroniko bidezko mezu hau CIC bioGUNEtik bidali da. Bertako edukia, eta erantsita egon daitekeen edozein fitxategirena, konfidentziala da, mezuaren hartzaile den pertsona fisikoak edo juridikoak bakarrik erabiltzekoa. Erabat debekatuta dago, eta legez kanpokoa ere izan daiteke, mezu hau edo erantsitako fitxategiak baimenik gabe kopiatzea edo zabaltzea, bai eta bertako informazioa besteri jakinaraztea ere. Mezu hau zuretzat ez bada, adieraz iezaiozu bidaltzaileari, edo deitu + 34 944 06 13 00 telefono-zenbakira eta ezabatu zure ordenagailutik. This e-mail is from CIC bioGUNE. The e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised dissemination or copying of this e-mail or its attachments, and any use or disclosure of any information contained in them, is strictly prohibited and may be illegal. If you have received this e-mail in error, please notify or telephone + 34 944 06 13 00 and delete it from your system.

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cavities
by Pablo Emiliano Tomatis 15 Jun '07

15 Jun '07

hello It is possible to find cavities of a protein using chimera? Any hepl??? thanks in advance -- Lic. Pablo E. Tomatis Instituto de Biología Molecular y Celular de Rosario (IBR) Área Biofísica - Departamento de Química Biológica Fac. Cs. Bioq. y Farm. - U.N.Rosario Suipacha 531 - S2002LRK- Rosario- Argentina Phone:+54-341-4350661/4350596 (ext.110) Fax:+54-341-4390465

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to view nmr pdb structures
by Shunsuke Meshitsuka 15 Jun '07

15 Jun '07

Dear researchers, I have used chimera as a viewer of proteins. I have a question how to overlay the 20 structures of NMR pdb data by chimera. When there are 20 structures of structurename01.pdb, structurename02.pdb,,,structurename20.pdb, > chimera structurename**.pdb makes a random location and random orientation of each protein. Please let me know the method. Shunsuke Meshitsuka D.Sci., D.Med. Tottori University Graduate School of Medical Science Institute of Regenerative Medicine and Biofunction, Division of Integrative Bioscience 86　Nishimachi Yonago Tottori　683-8503　Japan tel +81-859-38-6422 fax +81-859-38-6423 Email: mesh(a)grape.med.tottori-u.ac.jp

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release next week
by Elaine Meng 14 Jun '07

14 Jun '07

Dear Chimera users, As you may know, we made a production release earlier this month. Since then, a few bugs have come to our attention that were not revealed by our test suite or by users during the "release candidate" phase. We plan to make another production release late next week with the following fixes: - ensure POV-Ray image view always matches that in Chimera, instead of most of the time 8-) - make Minimize Structure work with metal ions (those in Amber parm94: calcium, magnesium, iron, etc.) - fix saving of sessions when sequences have been added to an alignment in Multalign Viewer (current workaround is to save the modified alignment to an alignment file) There may be additional updates and minor fixes not mentioned here. Best, 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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Re: [Chimera-users] rotating items in chimera
by William Jeffrey Triffo 14 Jun '07

14 Jun '07

hi Elaine, I just loaded a pdb, selected an off-center atom, typed 'cofr' at commandline, and the cofr does not appear to change (rotation looks the same in the chimera window). I submitted a bug report, -Jeff Elaine Meng wrote: > > > On Jun 14, 2007, at 11:56 AM, William Jeffrey Triffo wrote: > >> thanks, >> >> I have actually had some weird instances where 'cofr' didn't seem to >> reset the center, if I can reproduce I'll let you know. >> >> -Jeff > > Yes, do (and send to the chimera-bugs address)! > E > -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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Re: [Chimera-users] export scene to maya, obj, iges, stl, dwg-dxp?
by Greg Couch 14 Jun '07

14 Jun '07

Just to follow up, the Maya VRML2 importer is actually a conversion program in Maya's bin directory. On Windows the program is called wrl2ma.exe and on Linux and Mac OS X it is called wrl2ma. See the Maya documentation for details. - Greg

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export scene to maya, obj, iges, stl, dwg-dxp?
by Damir Perisa 14 Jun '07

14 Jun '07

dear all, is it possible, to export a scene from chimera to mayaBinary, obj, iges, stl or dwg-dxp formats? i have checked and chimera can export to a X3D format (vrml) as well as PovRay. i didn't find any info about transforming one of these to some other format. has anybody successfully exported chimera scenes (ribbon+surface+single_residue_atoms mix structures, not just a pdb file as atoms alone) to a file-format used by designers? thanx in advance for any help, damir -- .·´¯`·.¸.·´¯`·.¸¸.·´¯`·.¸.·´¯`·.¸.·´¯`·.¸.·´¯`·.¸¸.·´ ° ° ° ° ° ° ><((((º> ° ° ° ° ° <º)))>< <º)))><

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Reading a data set from a text file
by Elaine Meng 14 Jun '07

14 Jun '07

Hi Kyaw, The only ways I can think of are: - create a VRML file describing a surface with those points, read into Chimera - write a Python script to be opened in Chimera that reads in the numbers and generates a Chimera surface model However, I do not know the details about how to do either of these things. Others, feel free to chime in! 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 Begin forwarded message: > Hi Dr. Meng, > > I am sorry for my vague question. > > I have a table of numbers in a text file and I'd like to read in > those numbers and convert them into cartesian coordinates so that > they can be displayed as a surface in Chimera. > > If you could give me some suggestions on how to do it, I'd really > appreciate it. > > Thank you, > Kyaw _______________________________________________ Chimera-dev mailing list Chimera-dev(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Chimera: Reading a data set from a text file
by Kyaw Zeyar Myint 14 Jun '07

14 Jun '07

Hi, I am Kyaw Myint, a summer intern at NIAMS branch of NIH. I am working under the supervision of Dr. Bernard Heymann from the Lab of Structural Biology research. The project I am working on currently is to improve the 3D reconstruction of viruses' structures from 2D electron micrographs. The programs I am using include Chimera and Bsoft. For the project, I want to read in a data set from a text file and display the 3D surfaces based on that data set. I'd like to use Chimera for that purpose and I'd really appreciate any suggestion or comment on how I should do that. Thank you very much for your help in advance. Looking forward to hearing from you soon, Kyaw

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Problems with DMS installation
by 63668＠unimo.it 14 Jun '07

14 Jun '07

DMS is the only program requested to generate DOCK input files I was not able to install. I read something similar in this same mailing list. The first problem I encountered was an error message referred to "radii" directory. Thus I created the radii directory and I put radii.proto file into it. Now the error message is "Unknown atom type N", and by eliminating N atoms from my input file the new error message is "Unknown atom type CA", and so on. It seems that the program is not able to recognize atoms with their atomic radii, thus I think that the problem is still in this file. Any suggestion? Thank you, Valeria ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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toolbar
by Eric Pettersen 13 Jun '07

13 Jun '07

On Jun 13, 2007, at 12:21 AM, Graham Palmer wrote: > Eric: Another thing. In Favorites/Preferences/ Category Tools I > checked putting the Command Line on the Toolbar. But it never > appears there by default. I must always select the Command Line > in Favorites. I would prefer having it on the Toolbar by default. Hi Graham, You need to click the "Save" button on the preferences panel to make your changes permanent. --Eric

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new feature: conversion of atomic coordinates to electron density map
by Thomas C Marlovits 13 Jun '07

13 Jun '07

Hi, I am not quite sure, whether this is possible with Chimera ... but it would be great if there is a feature that would allow to convert a .pdb structure (atomic coordinates) into a map usually obtained by electron microscopy (sections) - for example into mrc/ccp4 format. Even filtering this map then to different resolutions (including storing entire maps) would be an interesting feature. Thanks, -Thomas __________________________________________ Thomas C Marlovits, PhD, M.A.S IMP - Institute of Molecular Pathology IMBA - Institute of Molecular Biotechnology, Austrian Academy of Sciences Dr. Bohr-Gasse 3 A-1030 Vienna AUSTRIA marlovits(a)imp.univie.ac.at Tel (+ 43) 1 79044 4630

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Looking for a Ramachandran plot display
by Oren Shalev 12 Jun '07

12 Jun '07

Hi all, I'm looking for a tool or an extension that displays the Ramachandran plot of a protein model, similar to the DeepView (SPDBViewer) tool. I'm not interested in the interactive features, just the display of residues as dots on the phi/psi plane, with dots colored, for example, by their C-Alphas' color. Do you know if such a tool was written for Chimera? With regards, Oren

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atoms/residues within a certain distance of another structure
by Terry Nelson 12 Jun '07

12 Jun '07

Hi, 1. I was wondering if Chimera has the option of finding for instance : "residues within 5 Angstrom of a bound protein inhibitor" or "residues within 3Ang. of solvent molecules", etc. I use a similar command in VMD that specifies the residues. 2. Does Chimera archive mails have a search engine that I missed? Cheers, Terry

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atoms/residues within a certain distance of protein
by Terry Nelson 12 Jun '07

12 Jun '07

Hi, 1. I was wondering if Chimera has the option of finding for instance : "residues within 5 Angstrom of a bound protein inhibitor" or "residues within 3Ang. of solvent molecules", etc. I use a similar command in VMD that specifies the residues. 2. Does Chimera archive mails have a search engine that I missed? Cheers, Terry

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Re: [Chimera-users] dock prep in batch mode?
by Eric Pettersen 11 Jun '07

11 Jun '07

On Jun 9, 2007, at 7:52 AM, figo wrote: > I have seen your solution to the dock > prep in batch mode (http://blur.compbio.ucsf.edu/pipermail/dock- > fans/2007-May/001043.html ) , but when I run the command : > chimera --nogui pdb:1gcn dockprep.py , the chimera want to Fetch > protein 1gcn from web site www.rcsb.org, I have download the > entire PDB, so how can I specify the PDB path to the chimera? Thanks. If you have the PDB files laid out the same way that the RCSB distributes them (e.g. entry 1GCN is in gc/pdb1gcn.ent) then Chimera will automatically look in /mol/pdb and /usr/mol/pdb for them. To have it look elsewhere you need to edit the file <your Chimera installation>/share/chimera/pdbDir and follow the reasonably simple instructions contained in that file. The drawback is that you will need to do that edit every time you install a new Chimera. Putting a better mechanism in place is on our to-do list. Other alternatives include putting the full path to the PDB file in your command, or putting all the files you need into one directory and using the PDB preferences (Favorites...Preferences...[change to PDB category]) to get Chimera to look in that directory. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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