- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] UCSF Chimera
by Elaine Meng 22 Mar '09

22 Mar '09

On Mar 22, 2009, at 8:36 AM, Tarit Mitra wrote: > Dear Dr. Meng, > I am trying to learn to use the Windows version of Chimera. I would > like to contact a Chimera user in UK. Is it possible to do so? Can > you please help? > With kind regards > Yours sincerely > Tarit Dear Tarit, You could try the e-mail list chimera-users(a)cgl.ucsf.edu (actually I cc'ed it on this message). However, you don't need a live person to help you learn how to use the program. The Chimera download includes several tutorials, some for beginners: choose "Help... Tutorials" from the Chimera menu to see the list. Our Web site has additional tutorials (not just the ones in the Help menu): <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html> Besides the tutorials, there is a complete user's manual (choose Help... User's Guide from the Chimera menu). Just start Chimera and try one of the beginner tutorials, or just experiment, and you will gradually learn! Best, Elaine

1 0

Changing properties by command line
by Dipl.-Ing. Thomas Mitterfellner 19 Mar '09

19 Mar '09

Hello again! I could not find out how to change radii of selected atom via the command line. I had hoped this would work via '@/radius=', which I read in the quick reference, but I turns out that I obviously misunderstood the usage of the hints given there. Is it also possible to change the color and linestyle of coordinative bonds in the command line? Related to this: can the status and color of the molecule silhouette be changed from the command line? Thank you very much! P.S.: Chimera really produces great pictures and I especially like the silhouette effect, which I, up to now, always had to (partially) draw myself with some image editor.

2 1

Chimera does not always recognise atom name in PDB ATOM records
by Christian Schudoma 19 Mar '09

19 Mar '09

Hello Chimera-Users and -Devs, I encountered the following problem when trying to visualise the following purine molecule (Actually, I tried to do something more complex(*) but the same problem can be reproduced with this more simple example). For clarification, the first lines contain the column numbers. 1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012345678 HETATM 1 N1 CKN A 1 -0.003 1.586 -3.371 0.00 0.00 N HETATM 2 C2 CKN A 1 1.016 1.511 -4.278 0.00 0.00 C HETATM 3 N3 CKN A 1 2.313 1.566 -3.865 0.00 0.00 N HETATM 4 C4 CKN A 1 2.576 1.683 -2.541 0.00 0.00 C HETATM 5 C5 CKN A 1 1.559 1.758 -1.597 0.00 0.00 C HETATM 6 C6 CKN A 1 0.224 1.717 -2.032 0.00 0.00 C HETATM 7 N7 CKN A 1 2.100 1.858 -0.373 0.00 0.00 N HETATM 8 C8 CKN A 1 3.434 1.842 -0.568 0.00 0.00 C HETATM 9 N9 CKN A 1 3.731 1.742 -1.876 0.00 0.00 N When I load a pdb file containing these coordinates into Chimera, I get 9 non-connected dots (obviously representing the atoms) which can neither be coloured by hetero-atom, nor by element. Note that the atom names are located in the appropriate columns, i.e. between columns 13 and 16, more specifically in columns 15 and 16. I noticed that in other pdb structures 2-character atom names are located in columns 14 and 15 and when I put my atom names there, Chimera displays the purine ring system which then can be coloured by hetero-atom/element. Now it is nice that this workaround fixes my problem, however, according to the pdb file format specification (columns 13-16 are reserved for the atom name), atom names located in columns 15 and 16 are valid(*) and as such should be processible by visualisation tools etc. The behaviour occurs with the latest daily build as well as some older versions I found on my hard disk... (*) The purine is part of a larger cytokinin. I stumbled upon the described behaviour while using the AddHydrogen function on the whole molecule, which lead to the replacement of the purine with a hydrogen. (**) Unless there are some additional rules regarding the placement of atom names shorter than 4 characters, in which case I apologise for bugging you with this. Any comments on this? Best regards, Christian Schudoma -- Christian Schudoma, M.Sc. Bioinformatics Group System Integration Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 331 567-8624 email: schudoma(a)mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de

3 4

Re: [Chimera-users] Making movies
by Elaine Meng 19 Mar '09

19 Mar '09

> Hi Elaine, > BD simulations is brownian dynamics. Well my file is in a PDB > format, and basically consist of a single complex, with heteroatoms > living from one active site to the other. If you open the file as a > pdb file you will realized the heteroatoms HOH are static. But I > want them to be able to move from the active site of one enzyme to > the other in the complex. > > I was thinking that I can put the word Model, between the complex, > and each heteroatom HOH, so as to make the file seem to have many > pdb files. Hi Neville, Yeah, I eventually realized you meant Brownian dynamics! But what matters for Chimera is the format rather than how the trajectory was generated. To use "MD Movie" to play/record the trajectory, your PDB format options are: (a) put each frame in a separate PDB file The file names must include frame numbers, and files for all intermediate frames must also be present. The files must not contain END records. (b) put all the frames in one PDB file, but bracket each with MODEL and ENDMDL, as is done for NMR ensembles in the Protein Databank, e.g. 1g1p. The MODEL numbers are interpreted as frame numbers and should start with 1 or 0 and increment by 1. Either way, atom names, residue names/numbers need to be the same between frames. ** In general, each frame should have the same number of atoms. However, for "weird" cases where lots of atoms stay in the same position (which if I understand correctly is what you have), we have made a special provision: if the coordinates supplied for a frame represent only a subset of the atoms in the preceding frame, it will be inferred that the remaining atoms are present but have the same coordinates as in the preceding frame. Changes are cumulated in the forward direction and based on all frames, even when frames are skipped during playback. All of the atoms must be in the first frame, of course. In your case, I guess that would include the proteins plus the starting locations of the heteroatoms. You might need to renumber the HOHs to keep their identities across the frames... looks like what you sent gives each position a different residue number. This information as well as how to play the trajectory and record it as a movie are in the MD Movie manual page (choose Help... User's Guide, click Tools tab, click link "MD Movie"). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

Question about adding a sequence to a previous structural alignment...
by Sergio Garay 18 Mar '09

18 Mar '09

Hi all I've prepared an structural alignment of my 3 protein templates using MatchMaker/Match-Align tools. The question is: when I add my target sequence to the profile obtained in the step before, Does this procedure change my previous structural alignment?, or It just aligns the added sequence to my profile. The parameters that I used to add my target sequence are: Blosum-62, gap open, and gap extension penalties: 12 and 1 respectively. The second problem I have, its not related to chimera, but may be one of you can answer it. My target only has 29 % of identical residues with my templates, so Should I use a less stringent parameters to make my alignment? Any help would be appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

2 1

save image error in current daily build
by Ryan Pavlovicz 17 Mar '09

17 Mar '09

Hello, when trying to save an image with the current daily build of Chimera, i am finding that the program closes with the following error: X Error of failed request: BadAccess (attempt to access private resource denied) Major opcode of failed request: 129 (GLX) Minor opcode of failed request: 10 (X_GLXCopyContext) Serial number of failed request: 0 Current serial number in output stream: 15993 Just wanted to let you know. Thanks, ryan

2 1

Re: [Chimera-users] merge mrc volumes
by Anindito Sen 17 Mar '09

17 Mar '09

Hi Tom Carsten actually just took away my question. Thanks Carsten! It will be really helpful to have such feature ! Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 --- On Wed, 18/3/09, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: From: Tom Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] merge mrc volumes To: carsten.mim(a)yale.edu Cc: chimera-users(a)cgl.ucsf.edu Date: Wednesday, 18 March, 2009, 5:43 AM Hi Carsten, There's no facility in Chimera to combine (add) maps into a single map though it has been requested by many people and I am anxious to add such a command. Tom carsten.mim(a)yale.edu wrote: > Hi there, > I constructed a model with different .mrc files. Now I want to save the model as > a merged *.mrc file, containing all previous files. > > Thanks > > Carsten > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

merge mrc volumes
by carsten.mim＠yale.edu 17 Mar '09

17 Mar '09

Hi there, I constructed a model with different .mrc files. Now I want to save the model as a merged *.mrc file, containing all previous files. Thanks Carsten

2 1

Changing default element colors
by Dipl.-Ing. Thomas Mitterfellner 17 Mar '09

17 Mar '09

Hello! Can the default element colors be changed easily and if so, how? Thank you, Tom

2 2

Chimera
by taritkumar MITRA 17 Mar '09

17 Mar '09

Dear Sir, I have just installed windows version of Chimera. I am a retired Chemist taken up Molecular Modeling as a hobby. I have some experience of using Spartan and Hyperchem. I would very much like to use the Chimera specially for studies Docking. Are theire any publication or books which will help me in learning to use Chimera. I f so I would like to buy it. Can you please help? With regards Tarit taritmitra(a)hotmail.com

2 1

DICOM maps
by triffo＠rice.edu 17 Mar '09

17 Mar '09

anyone out there know the easiest way to get a DICOM map (typical format for medical CT/MRI data; volume density map; .dcm file extension) into chimera? Is there a translator out there that will reformat DICOM data into a chimera-friendly volume map? thanks, -Jeff

2 1

heme (fe) containing enzyme
by Agus Setiawan 17 Mar '09

17 Mar '09

Hi, I'm a student of Pharmacy and I just learn about chimera.Actually, I want to run a docking using Autodock so I have to minimze the structure of macromolecule first. I choose Chimera to minimize the structure of macromolecule. However, there is an error because the Fe atom doesn't have GAFF"Unable to find GAFF type for #0:500.A@FE"I also have a problem with hydrogen at Histidin residu"no MMTK name for H at standard HIS"How can Isolve this problem?I'll be very thankful for your answers.Best Regards, Agus Lee.

2 1

Re: [Chimera-users] Making movies
by Elaine Meng 17 Mar '09

17 Mar '09

On Mar 16, 2009, at 10:13 PM, yimnai forlemu wrote: > Hello Elaine, > I have a quick question and was wondering whether I can use chimera > to archieve my goals.I have ran a BD simulation and saved > trajectories of my particles. My question is whether it is possible > for me to use chimera to create a movie from the BD simulations > trajectory data.If yes please could you just direct me to the > tutorial that can help me accomplish that goal. > Thanks > Neville Hi Neville, I don't know what "BD simulation" is. Chimera's "MD Movie" tool can read trajectory output from several programs: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h… > If you have one of those formats, or can convert your output to one of those formats (for example, multiple PDB files), MD Movie can show the trajectory. You can control how the molecules look in Chimera as you normally do, then use "File... Record movie" from the MD Movie dialog to create a movie. This tutorial uses the MD Movie tool to do various things, including saving a movie: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#p… > There are other ways to save a movie (not necessarily using the MD Movie tool). This page has more general information including links to example scripts and other movie-making tutorials: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> I hope this helps, Elaine P.S. For a reliable response, please send mail to chimera-users(a)cgl.ucsf.edu rather than to me directly. If you send mail to only me and I'm run over by a bus, you will never get an answer!

1 0

Session management suggestions
by Thomas Goddard 16 Mar '09

16 Mar '09

Matt Dougherty sent 4 session file management suggestions. 1) Session description text, browsable. 2) Copying camera positions between sessions. 3) Session version numbers with matching filename extensions. 4) Automated checkpoint session saving. Details below. Tom Matthew Dougherty wrote: > 1) I frequently have to use a lot of session files in combination with a > lot of command files to generate animations. > > One session file might be used with multiple command files. > > I try to pack as much information into the filename as a way to keep it > all organized, but this is becoming cumbersome. > the filenames are becoming cryptic to keep them short; plus I multiple > drafts I need to maintain in case the researcher wants to go back to a > prior visualization. > > It would be good to have a item in the' File' pull-down-menu to handle > summaries or descriptions. > > By activating it, I could type in a paragraph as to what is going on > with the session. > > In a bigger picture, it would be good to be able to start chimera, and > somehow peruse through these descriptions, but not have to load the > session to read the description. > > 2) many times in an animation project I start with a common session file > containing all the data sets in sync, and create multiple derivative > session files to handle different aspects of the animation, usually with > the unused datasets deleted for a particular animation session for > reasons of improving computation speed and loading for a particular > animation clip. > > sometimes I would like to move a set of camera positions created in one > of the daughter session files to another daughter session file. > > Matthew Dougherty wrote: > 1) optional automated versioning. Sometimes I when I am working on an > animation I need to keep the intermediate versions, particularly when I > am less certain about what I am doing and the complexity of the session > goes up. > > check box somewhere that causes saving to automatically prepend "_V22" > before ".py", for version 22 in this example, and _V23 for the next > save, etc. > > 2) optional automated checkpoint saving such that the interval time can > be set. sometimes when working on a complex session it get a crash and > I have not saved it, so I have lost all my work from the previous save, > which could be 1-4 hours.

1 0

Octamer to dimer
by John Lowenstein 16 Mar '09

16 Mar '09

Dear Folks, In PDB 1ewj the structure comes up as an octamer. The physiological entity, in which I am interested, is a dimer. I can eliminate three of the for dimers, but I have not found a way to eliminate the six extra ligands (bleomycin) associated with the three eliminated dimers. (I want the dimer with two ligands.) Any suggestions? Thanks. Sincerely, John Lowenstein

2 1

confocal stack
by Benoit Zuber 16 Mar '09

16 Mar '09

Hello, Is it possible to browse through the planes of more than 1 volume at a time? I have some confocal data and I want to browse along the X axis of the dataset; each volume corresponds to a confocal channel. Cheers, Ben

2 1

adding CONECT records with nogui option
by shyamala 16 Mar '09

16 Mar '09

Hi Chimera users, I am sure there is a simple way to do this, but I need some help. I want to add CONECT records to a pdb file, given that the input file contains all necessary atom coordinate information. I need to do this within my shell script and I want to start chimera using the nongui option. Now, doing some google seach brought up this solution to add CONECT records (in the command line within CHIMERA gui) pdbrun nouser conect cat > filename.pdb where filename.pdb is the name of the output file with CONECT records added. the above mentioned command works when I pull up the file on GUI CHIMERA My question is then how would I use such a command when I want to use it in the nogui option. I have multiple files (>100) for which I need to add CONECT records and I want to do it with a script. Also, if someone could point me to a good resource for writing python scripts that can be then passed on to chimera, I would be grateful. Thanks, Shyamala Shyamala Iyer Graduate Student Department of Microbiology PO BOX 357242 University of Washington Seattle, WA, 98195

2 1

Problem adjusting sphere quality in script
by Marhoefer, R (Richard) 16 Mar '09

16 Mar '09

Dear Chimera Users, I want to adjust the quality of spheres, cylinders and ribbons in a script. From the moviemaking tutorial script I learned that I must use some lines of Python. Therefore, I used the code as found in the example: import chimera chimera.LODControl.quality = 20 When I open this script like in the tutorial, the value of "subdivision quality" in the "Effects" panel is indeed set to 20. However, the quality of spheres and cylinders remains untouched. From that point in time any further modifications of the value in the "Effects" panel do not have any effect. If I change the value of "subdivision quality" in the "Effects" panel before opening the Python code, anything works fine. Did anybody succeed with changing the sphere quality in a script? Kind regards, Richard Mit freundlichen Grüßen / With kind regards Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

2 1

command line
by Sirano Dhe-Paganon 16 Mar '09

16 Mar '09

After entering a command in the "command line" of UCSF-Chimera, I would like the command that I pasted to disappear. Currently, it does not disappear; how can I make it disappear after I press the enter button?

3 2

Chimera needs your vote.
by Nir London 16 Mar '09

16 Mar '09

There is a poll going on at the macromolecular modeling blog "What is your favorite molecular viewer?" http://rosettadesigngroup.com/blog/284/what-is-your-favorite-molecular-view… PyMOL is currently at the lead, but you might make the difference, go ahead and show your support for Chimera (or choose one of the other viewers if you like them more) but most importantly drop a comment as to why YOUR viewer is the best. Disclaimer: for fairness, similar messeges are sent to the other competitors mailing lists as well, but we like yours the most ;) Nir London. Rosetta Design Group. http://rosettadesigngroup.com/blog/

1 0

centering on an atom
by Sirano Dhe-Paganon 16 Mar '09

16 Mar '09

In UCSF-Chimera, I would like to center on an atom of a molecule without zooming-in towards the atom. I found the "focus" command, which centers the atom, but the command includes a zooming-in step; is there a "focus" or "center"-like option that does not zoom-in? Also, most visualization programs have a simple, one-click mouse-button to center on an atom; I cannot find this option in UCSF-Chimera. Sirano

2 1

Re: [Chimera-users] window size
by Elaine Meng 13 Mar '09

13 Mar '09

Hi Jean-Paul, For a more reliable response, please send questions to chimera- users(a)cgl.ucsf.edu rather than to me directly -- I might be out (sick or vacation), or others may know the answer when I don't! There is no preference for window sizes and locations. However, there is a startup option "--geometry" for the main window (but not other tools, sorry): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#geometry> How to specify startup options depends on your type of computer: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html> Some related things... After you start Chimera, you can use the "windowsize" command to specify the pixel dimensions of the main window. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/window.html> If you save a session, it should restore with the same main window size. I don't think the location is saved, however. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 13, 2009, at 11:16 AM, Jean-Paul Armache wrote: > hello, > i have a question. is there a way of saving the window sizes and > windows positions in chimera ? whenever i start chimera the default > all the windows have always the same position and sizes. i always > adjust it to the same position and size, but maybe there is a way to > save it as a preference ? i checked the preferences file, nothing > there. > thank you, > best regards, > jean-paul armache

1 1

chimera help
by Terrance Chiang 11 Mar '09

11 Mar '09

Hi, I've been trying to make an electrostatic potential map for the protein that I'm working on, but there seems to be some error with the file when I try to open it. I was wondering if you could help me with this. The error says: Missing "object 1 class gridpositions counts <l><m><n>" header line I also need help with using the pdb2pqr service that can convert files from pdb into apbs. Perhaps my error lies there. Thanks, Terrance Chiang

3 2

Atoms outside volume
by Tom Goddard 10 Mar '09

10 Mar '09

Hi Tsutomu, I guess you want the atoms outside a given contour level of the volume. There is a Chimera keyboard shortcut "oa" (outside atoms) to select those atoms. If you don't use shortcuts (Tools / General Controls / Keyboard Shortcuts) you can run them as ordinary Chimera commands using the "ac" command: volume #0 level 2.5 select #1 ac oa These 3 commands set the contour level for map #0, select all the atoms in PDB model #1, then run keyboard shortcut oa which changes the selection to just those outside the contour. If you have multiple maps open, the "oa" shortcut is using the highlighted one in the volume dialog. You can write the selected atoms to a file if desired with menu entry Actions / Write List.... If you really want atoms outside the volume bounding box, then just use a threshold less than the smallest data value (range shown in volume dialog). Tom Tsutomu Matsui wrote: > Dear Tom, > > My name is Tsutomu Matsui, a postdoc in Jack Johnson Lab at Scripps > Resaerch Institute. I love Chimera very much. I would like to select > all atoms inside or outside a volume file (density map). Is it possible? > > Thank you very much, > Tsutomu >

2 1

center of the molecule
by Bala subramanian 10 Mar '09

10 Mar '09

Dear Friends, How can i get the x,y,z of the center of the loaded molecule in chimera. While i do box generation generation for DOCK program, i want to tell the script to construct box by considering the x,y,z center of the molecule. Thanks, Bala

3 3