- Chimera-users - RBVI Mailing Lists

chimera help - calmodulin
by roach a.p.l. (aplr1g08) 07 Dec '09

07 Dec '09

Hi, I am a student trying to do a project on the protein calmodulin. I have just started using chimera and have gone though your tutorials and understood everything as it is very clear but i don't know how i would select the protein calmodulin and put it in the chimera display to make my images. I realise this is probably a simple step but this is all new to me and i would much appreciate your help. Thank you Annabel Roach

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Maximizing performance with large volume data maps
by Ryan Rochat 07 Dec '09

07 Dec '09

Hello, I was wondering how much video memory Chimera is capable of accessing. I currently have a 898Mb videocard that begins to slow down with a 550x550x550 map (at step size 1). This map is actually a downsample of the true 1100x1100x1100 map coming in at 5GB. I was contemplating going for a much larger video card at 4GB, however I was curious to what extent I could expect to see acceleration using Chimera with such a massive dataset (600+MB) and video card. Thank you, Ryan H. Rochat MS MD/PhD Candidate (Baylor College of Medicine) Graduate Student SCBMB (Baylor College of Medicine) Chiu Lab One Baylor Plaza N420 Alkek Houston Texas 77030

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Re: [Chimera-users] To consult the Morph conformation
by Elaine Meng 07 Dec '09

07 Dec '09

Dear Jiraporn, Sorry, Morph Conformations only includes parts that are in both structures in the morphing trajectory. In your situation, I suggest text-editing one of the input PDB files (more details below). Morph Conformations maps residues in the starting structure to residues in the ending structure by creating a sequence alignment. Where the residue in the starting structure is aligned with the same type of residue in the ending structure, the whole residue will be included. Where the residue in the starting structure is aligned with a different type of residue, only the parts that are the same will be included, which will include the backbone and sometimes part of the sidechain. Where there are backbone atoms, you can show a ribbon. If the residue is aligned with a gap, it will not be included. Here is the explanation in the manual: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#p… > Currently Morph Conformations will only use the sequence alignment it figures out itself. A future improvement will be to allow the user to provide the sequence alignment (perhaps avoiding some of the gaps), but that is not available yet. I took a look at your proteins, 3DRR and 3DRS. They are the same protein, and the only difference is that the 3DRR crystal structure has more residues at the C-terminal end, forming a helix. 3DRR ends at 557 and 3DRS ends at 548. I guess you want that end part shown in the morphing trajectory. The structures look nearly the same in the residues before the difference, so to do this I would just use a text- editor and add the end residues from 3DRR onto the 3DRS structure. For example, make a copy of the 3DRR PDB file, then edit it to replace 543-end with 543-end from the 3DRS PDB file. Then you would just open the new edited 3DRR with the longer tail and then morph from that to 3DRS. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 5, 2009, at 1:29 AM, Nok :p wrote: > Dear Chimera teme, > > First of all, I would like to introduce myself. My name is Jiraporn > Yongpisanphop. Now, I am a master student of KMUTT university in > Bioinformatics field. > > My thesis topic involve in drug design. A part of my work is > concerning about overaly binding pocket of single mutant enzymes > (PDB file: 3DRR and 3DRS). And, I > > use Morph Conformation method. It is good but it not complete for my > work. Because the intermedate structure was generate from compare of > same amino acid > > of both structures. However, the difference amino acid was kept only > reference model. Therefore, I would like to consult you how I will > keep amino acid that > > differece of both structures into intermediate structure. > > Thank you very much for your kind. > > Best regards, > > Jiraporn

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Movie spinning and slicing a density map
by Thomas Goddard 06 Dec '09

06 Dec '09

Hi Andy, I've added an example movie spinning and slicing a virus EM density map to the Chimera Animations page. See the bacteriophage phi6 entry. There is also a link to the movie script. http://www.cgl.ucsf.edu/chimera/animations/animations.html Tom -------- Original Message -------- Subject: making a movie From: Anindito Sen To: Thomas Goddard Date: 12/2/09 5:50 PM > Hi Tom > > I am not sure if this email can be out on the general Chimera wiki. THe > following movie is from a published work of mine. Can you help me > getting the script for generating such a movie. There is a Chimera session in the > webpage but I think its a bit too much for me to understand. > > Please feel free to reframe the question and put it in the Chimera wiki > email list which may prove helpful to others. > > Thanks for your help. > > Best > > Andy > > > > http://emnavi.protein.osaka-u.ac.jp/emnavi_detail.php?id=1500 > > Dr. Anindito Sen (Ph.D) > >

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drawing elipsolids
by Keren Lasker 03 Dec '09

03 Dec '09

Dear Chimera team, Is there a way to draw ellipsoids in Chimera. The ellipsoid is defined by its center and 3 radii. Thanks for your help. Best, Keren.

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How to clip surface using mclip
by Marhoefer, R (Richard) 03 Dec '09

03 Dec '09

Dear Chimera Team and Users, I like to clip the surface of a model (but not the model itself) using the command mclip. Unfortunately, this command apparently is waiting for a model number and therefore works on the surface as well as the model itself. On the other hand, the interactive tool "Per Model Clipping" allows to clip the surface only. Because I like to use clipping in a movie, using the interactive interface is not an option. Does anybody know how this could be acomplished using the command line? Kind regards, Richard 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. --------------------------------------

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Re: [Chimera-users] missing ribbon loop
by klumpler＠sci.muni.cz 03 Dec '09

03 Dec '09

Dear Elaine, I think PDB is alright, I send it as a attachment. Could you help me with the editing? Thank you very much Tomas > Hello, > My guess is there is something strange about the structure or the format of the input file -- for example, maybe the residues don't all have the same chain ID, or the backbone atoms do not have the expected names (N,CA,C,O). If Chimera does not show a ribbon at that position even though you told it to show ribbons for everything, it is probably necessary to edit the input file to fix the problem. I couldn't be more specific without seeing the file. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Nov 27, 2009, at 2:16 AM, klumpler(a)sci.muni.cz wrote: > >> Hallo, >> please, can you tell me how to create missing part of ribbon >> representation of loop? >> >> Using "ball and stick" representation is peptide chain complete without >> gap, but in "ribbon" representation is one residue missing and forms the >> gap. >> >> Thank you very much >

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keyboard input gone
by Zhou, Wei 02 Dec '09

02 Dec '09

Hi, Yesterday I installed the latest 1.4 32bit linux version of chimera into my opensuse 11.1. Soon after I fetched some pdb files and started to use it, at some point, I can no longer input any text into the program, such as typing another pdb id, or typing a command line, or type a file name to save it. I can still use mouse. Please help. I'm here at mission bay, rock hall. My extension is 60421. Thanks, Wei Zhou

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phenix map not reading in chimera
by Geoffrey Feld 02 Dec '09

02 Dec '09

Greetings, I'm trying to make a figure showing off my best density from a 2Fo-Fc map I generated using phenix.refine. The output file has a .map suffix. However, Chimera gives an error about the header, which I've included: MRC header value nsymbt (538976288) is invalid. How do I give Chimera a map with a header it can read? Thanks, -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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Chimera question with Mac
by Durga Velukumar 30 Nov '09

30 Nov '09

Hello, I'm an undergraduate student at the University of Georgia and I'm using your system, UCSF Chimera, for my powerpoint presentation. I'm having some problems with trying to create a movie. I have a MacBook Pro, which I just got this recent August, and downloaded the latest Chimera version for the Mac. I'm trying to save the commands in a separate file, like TextEdit, but I don't know what type of file to save it as. I'm hoping to be able to open the file through Chimera to play the movie. I tried saving the commands as "movie.cmd" but TextEdit is not allowing me to save that type of file. Any help would be greatly appreciated. Thank you, Durga

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Bond change
by Bruno Cramer 30 Nov '09

30 Nov '09

Hi After getting the conformations as *.sdf (or *.pdb) files with Macromodel (from Shroedinger) and/or Vconf(VeraChem) I use Chimera to add missing H's and add charges with amber 99. After these steps are completed, I split the sdf conformations-file into single *.mol2 files. All works fine except for the last step, that changes a single bond into a double bond in each molecule. I am correcting this manualy opening the *.mol2 file with Texd editors and changing the double bond into single bond the the benzene rings. Opening a chosen conformation from the *.sdf file it looks correct.So, the problem happens during conversion/splitting process. Question: How can this arbitrary bond change be avoided? Attached zip file with *.mol2 examples of one compound after splitting process. Thank you Regards Bruno

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missing ribbon loop
by klumpler＠sci.muni.cz 30 Nov '09

30 Nov '09

Hallo, please, can you tell me how to create missing part of ribbon representation of loop? Using "ball and stick" representation is peptide chain complete without gap, but in "ribbon" representation is one residue missing and forms the gap. Thank you very much

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structure manupulation
by Haixin Sui 24 Nov '09

24 Nov '09

Tom and Elaine, Is there a simple way to manipulate part of a protein structure in Chimera? What I would like to do is the following. Let's say I have a molecular compose 8 helixes. 7 of them fit in the cryo-EM map perfectly but one short helix is off probably owing to conformational change. I would like to move the short helix into the density map manually. The difficult part is how to make a smooth transition for loop regions at both ends of the helix. Would you please give me some advice on this? Thanks! Haixin -- Haixin Sui, Ph.D. Wadsworth Center NYS Dept. of Health Empire State Plaza P.O. Box 509 Albany, NY 12201-0509 (518)474-4235 (office) (518)473-0309 (lab) IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

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Display of double-bond in Chimera
by J H 24 Nov '09

24 Nov '09

Dear Chimera, Is there a way to display a molecule's double bond as double-bond (i.e., two lines between the atoms instead of one) in chimera? Thanks a lot. Best, Jules.

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Moving PDB between 3 orientations
by Thomas Goddard 23 Nov '09

23 Nov '09

Hi Chris, To show a molecular model moving between three orientations you would use Chimera commands savepos and reset and matrixcopy. Here's how I'd go about it. First put copies of the molecular model at all 3 positions. If you have saved these in 3 Chimera session files I would open all 3 sessions telling Chimera not to close the previous session when I open each new session. Now open a 4th copy of the molecule. Suppose the original 3 copies are model numbers #0, #1, #2 and the 4th copy is model #5. To align the 4th copy with #0 use matrixcopy #0 #5 (The matrix being copied is the positioning matrix, the rotation and shift that places the molecule in the scene.) Record the positions of all the models now with savepos p0 The name p0 could be anything. We'll use it later with the reset command. Also save positions with the 4th model in the other 2 states: matrixcopy #1 #5 savepos p1 matrixcopy #2 #5 savepos p2 Now to move the 4th model pack to position 0: reset p0 and to move it from position 0 to 1 over 50 frames reset p1 50 and then from 1 to 2 reset p2 50 In a movie recording command script remember to put a "wait 50" between these two commands so they don't both try to run simultaneously. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html There is a movie making tutorial that explains some of this: http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html Tom -------- Original Message -------- Subject: Re: [Chimera-users] how to link three EM confirmations in morph map From: Chris Arthur To: Thomas Goddard Date: 11/23/09 1:40 PM > Hi Tom, > I have one other question. I have a pdb (the same pdb loaded into > chimera 3 times), that I have docked into three distinct EM maps. I > would like to make a movie showing the rotation of the pdb as it goes > from one docked state to the next, to the next. I guess this would be > similar to the morph command but for pdb's instead of EM maps. Any > suggestions? > Thanks, > Chris > > > The Scripps Research Institute

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Make volume have mean 0, standard deviation 1
by Thomas Goddard 23 Nov '09

23 Nov '09

Hi Terry, Chimera does not automatically scale density maps. You can use a command like vop scale #0 shift -8.0 factor 0.2 to shift map #0 values by -8.0 and then scale by 0.2. If the mean were 8.0 and standard deviation were 5.0 then this would normalize to mean 0 and SD 1.0. This creates a new volume data set. There is no capability to shift and scale an existing map without making a new volume data set. The Volume Filter dialog (menu Tools / Volume Data) can do the same thing. Python code to do the shift/scale is in chimera/share/VolumeFilter/scale.py There is a menu entry Tools / Volume Data / Volume mean, SD, RMS that reports the mean and SD and RMS about zero of the highlighted map in the volume dialog. There is no command equivalent (I should make the measure command do this). The Python code that does this is in chimera/share/VolumeStatistics/__init__.py Tom -------- Original Message -------- Subject: question about ccp4 formatted map density From: Terry Lang To: Tom Goddard Date: 11/23/09 11:39 AM > Hey Tom, > > I am looking into some new schemes for scaling electron map > density. I know you said that the scaling to a mean of zero and > standard deviation of 1.0 is implemented in the current release. > However, I can't seem to find where the code is located. I am really > interested in figuring out where exactly scaling happens and if it's > automatic or needs to be requested. Any input you can provide would be > greatly appreciated! > > Sincerely, > Terry >

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Re: [Chimera-users] [chimera-dev] Rotation about the axis of symmetry
by Elaine Meng 23 Nov '09

23 Nov '09

On Nov 23, 2009, at 2:06 AM, Liam Browne wrote: > I want to rotate a model by 90 degrees about the axis of symmetry, > but I seem to be having problems setting the axis correctly. > After two identical models are superimposed I use measure rotation > and get the following: > > Matrix rotation and translation > -0.04092271 -0.36724445 0.92922379 -82.20183653 > -0.91203666 0.39354649 0.11537022 -54.21831923 > -0.40806183 -0.84276490 -0.35104539 11.47082481 > Axis -0.55288898 0.77167664 -0.31437070 > Axis point -56.22800779 0.00000000 25.47389901 > Rotation angle (degrees) 119.94780111 > Shift along axis 0.00338820 > > What should I do to rotate the model at the same axis but by 90 > degrees? > > Many thanks, > Liam Hi Liam, You can just use the reported values -- the tricky part is remembering to indicate that they are in the coordinate system of the first model in the "measure rotation" command, and also using the reported axis point as the center of rotation. Let's say you used the command "measure rotation #0 #1". Then the values in the Reply Log are for the transformation of #1 relative to #0 expressed in the coordinate system of #0. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation > Now you can use the values in the Reply Log to rotate #1 further. Keep in mind that this transformation will be applied on top of any existing transformations. If you want only the new rotation and not prior transformations, you would need to "reset default" first. To rotate model #1 90 degrees about the reported axis and use the reported axis point as the center, the command would be: turn -.55288898,.77167664,-.31437070 90 center -56.22800779,0,25.47389901 mod #1 coord #0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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question
by Laura Packer 20 Nov '09

20 Nov '09

To whom it may concern: I am not sure if I am sending this inquiry to the correct e-mail address. If not, I apologize for any inconvenience. I am looking to acquire a list of atoms that are within a certain distance of a set other atoms. I have googled this question and have learned how to select these atoms: bfsdjf select <description of atoms/residues> z<5.0 # or zr<5.0 or select <description of atoms/residues> za<5.0 What I would like to know is how to get a list of these results. It is not appearing in my reply log as I thought it might. Thank you for your time. Sincerely, Laura Packer packer(a)bu.edu

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how to link three EM confirmations in morph map
by Chris Arthur 19 Nov '09

19 Nov '09

I am wondering what would be the best way to link three EM maps using Morph Map? I have three sequential conformations of a protein and I would like to show a movie morphing from 1 to 2 to 3 if possible. Thanks in advance for any tips. Regards, Chris Christopher Arthur Ph.D. Staff Scientist Milligan/Unwin Lab The Scripps Research Institute carthur(a)scripps.edu 858-784-7073

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<< Versions to download >>
by Hatuey Hack 18 Nov '09

18 Nov '09

Hello, I would like to know if it is possible to put the version number of Chimera in the download or to add it to the file name. Regards and keep the good work!, Hatuey ___ Mike Ditka <http://www.brainyquote.com/quotes/authors/m/mike_ditka.html> - "If God had wanted man to play soccer, he wouldn't have given us arms."

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control of scale in STL output files
by Jonathan Schaefer 18 Nov '09

18 Nov '09

Hi- I've got a question about controlling the scale of protein models in .stl files generated by Chimera under File/Export Scene in the GUI. I'm trying to print a 3D model of two interacting proteins with a rapid prototyping machine that takes .stl files as input. The two proteins are co-crystalized and contained in one .pdb file (1nbf). I want the two proteins to be printed at the same scale so that I could fit them together like legos. Can I achieve this by getting a scale set, then showing just the first chain and exporting the data to a .stl file, followed by showing just the other chain and exporting the data to a second .stl file? I'm a novice to Chimera, so I might be missing something obvious. Any help you offer will be appreciated. Jonathan Schaefer Morgan Lab UCSF

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making a movie in Chimera
by Victor Padilla-Sanchez 18 Nov '09

18 Nov '09

Hi, my name is Victor and I would have a question about a problem that I have making movies. I record the movie in MPEG 4 format and everything seems fine but when I want to play the movie in Quicktime I obtain just a black screen playing just that. Could you help me with this problem. Thank you very much Victor

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capping surface with a VRML model
by Damien Larivière 18 Nov '09

18 Nov '09

Dear all, It is possible in Chimera to cap the clipped surface of an isosurface made with the Multiscale Model tool. However, if the isosurface is exported in VRML and then reopened in Chimera, it is no more possible to cap the clipped surface. This function (surface capping) is very interesting in particular when the scene is crowded by many proteins. Is it a way to cap VRML model? Many thanks for your help! Damien

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down arrow goes all the way to empty selection
by Eric Pettersen 17 Nov '09

17 Nov '09

> On Oct 2, 2009, at 1:27 PM, Cathy Lawson wrote: > > > (4) It is great to have the down and up arrow to narrow and broaden > > selection, would be great if a final down arrow would lead to > > clearing the selection. > > After some discussion we have decided to do this, though it won't make > it into the next release since we are already in a feature freeze / > debugging mode for that. > > --Eric This is implemented now and will be in tomorrow's daily build and the eventual 1.5 release. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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residue label
by Bala subramanian 17 Nov '09

17 Nov '09

Friends, I would like to know how to use our own strings with 3D label. suppose if i give 'rlabel :3', residue 3 is labelled as LEU 3. But i want to pass a string that should replace LEU 3. Hope i am clear. I know 2D label can use a string but i wish to use string especially with 3D label. Thanks, Bala

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suggestion/stereo
by Dougherty, Matthew T. 16 Nov '09

16 Nov '09

I am finding that getting the optimal stereo view requires ongoing adjustment of the stereo parameters, particularly when multiple people are observing the structure simultaneously (e.g., depthQ stereo projector). Currently these numbers have to be typed in, requiring me to break my gaze, move a mouse, and type a number. Ideally it would good to have controls similar to binoculars, such that you maintain constant view and adjust by turning knobs. Getting hardware knobs may be impractical, but these improvements could help. 1) two small buttons (+/-) next to each stereo parameter. 2) commands that would do the same (small incremental changes). Then I could have my nostromo n52 USB game box dedicate the dual axis thumb button for stereo adjustment by issuing keyboard commands. Thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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help with raytrace
by Corey Fugate 16 Nov '09

16 Nov '09

I am trying to improve image quality using the raytrace option. The script is below - reset view_1 movie record directory /Users/fugate/Desktop pattern partA_* fformat png raytrace true wait 15 delete :.B move x 1.25 15;wait wait 15 movie stop Everything works fine without "raytrace true". I should note that I do not have the movie encode command because I want to have the individual images ( for a larger Flash project). When I compare the raytrace true images produced from the script to an image generated using the "save image" option under the File menu setting "raytrace with POV" to true. Am I missing something? Corey

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Apply rotation with precision
by Damien Larivière 15 Nov '09

15 Nov '09

Dear Chimera team, Once two pdb structures are opened, the command measure rot #1 #0 give the orientation of one structure with respect to the other one under the form of: Position of 1Wxx_chB1.pdb (#0) relative to 1Wxx_chB1.pdb (#1) coordinates: Matrix rotation and translation 0.99727151 0.01713873 0.07180395 46.50921950 -0.01715871 0.99985272 -0.00033862 3.66357812 -0.07179918 -0.00089436 0.99741871 15.01300748 Axis -0.00376406 0.97263698 -0.23229967 Axis point 231.74603365 0.00000000 -638.91369622 Rotation angle (degrees) 4.23351417 Shift along axis -0.09924878 Let's suppose that I want to decrease the rotation angle from 4.233° to 0.5°: I can use "Movement" and select the model to be rotated in order to do that with the mouse but I will not be accurate. Is there way to do such rotation with precision? Thank for your help Damien

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Re: [Chimera-users] help with raytrace
by Corey Fugate 13 Nov '09

13 Nov '09

Doh! Sorry lack of sleep results in incomplete sentences. The raytrace option in the script looks exactly like the chimera window quality and nothing like an image made using raytrace. Corey On Nov 13, 2009, at 4:12 PM, Thomas Goddard wrote: > You didn't say what was wrong with the raytraced image. So we are > missing something. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] help with raytrace > From: Corey Fugate <fugate(a)hawaii.edu> > To: chimera-users(a)cgl.ucsf.edu > Date: 11/13/09 1:12 PM > >> I am trying to improve image quality using the raytrace option. >> The script is below - >> reset view_1 >> movie record directory /Users/fugate/Desktop pattern partA_* >> fformat png raytrace true >> wait 15 >> delete :.B >> move x 1.25 15;wait >> wait 15 >> movie stop >> Everything works fine without "raytrace true". I should note that >> I do not have the movie encode command because I want to have the >> individual images ( for a larger Flash project). When I compare >> the raytrace true images produced from the script to an image >> generated using the "save image" option under the File menu setting >> "raytrace with POV" to true. >> Am I missing something? >> Corey >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [Chimera-users] Fields in dms format
by Elaine Meng 12 Nov '09

12 Nov '09

No -- that would overcount the area, because it would overlap for neighboring dots. The area is an *estimate* for the piece of surface around the dot that is not assigned to any other dot. If you added up the areas for all the dots for one atom, it would *approximately* equal the surface area for that atom. However, to get the total area for an atom, residue, etc., don't do that -- just use the already existing areaSES (and areaSAS) attributes of atoms and residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces > Elaine On Nov 12, 2009, at 10:34 AM, Yasser Almeida Hernández wrote: > Thanks for your help... > About the estimated surface area in the 8th field, i view this > number as the area enclosed by the neighboring dots, where the > guessing dot is the center of a square formed by this dots. What do > you think about that? > > *-----* > | | > | * | > | <-|-- Area > *-----* >

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Fields in dms format
by Yasser Almeida Hernández 12 Nov '09

12 Nov '09

Hi all... In the .dms format: 1 - What's the meaning of the digit (allways 0) after the SR (or SC, SC)? 2 - What's the meaning of the number in the 8th field? I've read the help of this format, but i don't understand the meaning of these numbers Thanks... -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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nmrclust: linux terminal
by Austin B. Yongye 12 Nov '09

12 Nov '09

Hi everyone, I am trying to use nmrclust to cluster a set of about 5K conformers with the chimera gui. It is been ~5hrs now, and still running. I was wondering whether the algorithm can be run via the linux terminal. I found this posting: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003195.html Could some one please let me know how to use this python code to run the clustering in the linux terminal invoking the python environment? Thanks, Austin-

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Select / Structure / secondary structure / turn broken
by Tom Goddard 12 Nov '09

12 Nov '09

Hi Haixin, I suspect "turn" doesn't just mean not helix and not sheet but I don't know. Others in my lab will know so I've forwarded your question to the Chimera mailing list so they can answer. If you want to select all residues that are neither helix nor sheet you can use the command: select ~ :/isHelix :/isSheet Tom -------- Original Message -------- From: Haixin Sui To: 'Thomas Goddard' Date: 11/6/09 2:27 PM > Tom, > > How have you been? > > This email is to report a small bug I experienced. The "select"-> > "structure"->"secondary structure" -> "turn" function is not working. It > worked for selection of "helix" and "strand". Selection of "turn" is the > only one does not work. I am using chimera alpha version 1.3( build 2577) > 2008/12/09 00:54:36 on a laptop PC running Windows XP. > > While I have a lot of different molecules aligned in a map, this selection > function is very useful for me. Any suggestion? > > Best regards from > > Haixin > > -- > Haixin Sui > Research Scientist IV > Wadsworth Center > Empire State Plaza > P.O. Box 509 > Albany, NY 12201-0509 > > Assistant Professor > SUNY-Albany > School of Public Health > Department of Biomedical Sciences >

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coarse-grained MD
by Francesco Pietra 11 Nov '09

11 Nov '09

I know that questions about coarse-grained MD wit amber have already been raised. However, I wonder whether any plan is going on - if feasible at all - to implement in the ambertools something like the cg builder of vmd. Or ask chimera software if a conjoint effort may allow us amber users to approach cd md "at home", benefitting of the amber's secure code. thanks francesco pietra

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Re: [Chimera-users] Coloring range for residues
by Eric Pettersen 10 Nov '09

10 Nov '09

Hi Ibrahim, I'm glad it helped. I've opened a Trac ticket for your request for restricted rainbow coloring, so you'll get a notification when it gets implemented. It could be quite some time before I get to it, though if others request it also it could happen sooner. --Eric On Nov 9, 2009, at 8:28 PM, Ibrahim Moustafa wrote: > Hi Eric, > > Thank you very much, as usual, I got the help I expected from > chimera team. > > Actually, the conformational change for the structure I have is > dramatic and involves wide range of residues. It is really painful > for the eye to follow the structural change for a certain element. > Coloring the residues in few colors did the job; however, the > rainbow coloring using the script you sent did a much better job. > It would be useful if this command can be added to the chimera!. > > Many thanks, > Ibrahim > > -------------------------------------------------------------------------------------------------------------------------- > Ibrahim M. Moustafa, Ph.D. > Biochemistry and Molecular Biology Dept. > 201 Althouse Lab., University Park > Pennsylvania State University > PA 16802 > > Tel. (814) 863-8703 > Fax (814) 865-7927 > > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Monday, November 09, 2009 7:29 PM > To: Ibrahim Moustafa > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Coloring range for residues > > Hi Ibrahim, > I'm not 100% sure why you want to rainbow the > highlighted part of your structure, rather than use a single color, > or color the rest of the structure dark gray, or make the rest of > the structure semi-transparent, or many other possible highlighting > schemes. > Anyway, there's no way to do it without resorting to > (simple) Python. Put the following in a file that ends in ".py": > > import chimera > residues = chimera.selection.currentResidues() > residues.sort() > for i, r in enumerate(residues): > r.highlightNum = i+1 > > Then select the residues you want highlighted in > Chimera. Run the Python script by opening it with the "open" > command or with the File->Open dialog. Then run this Chimera command: > > rangecolor highlightNum,r min blue mid white max red sel > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Nov 9, 2009, at 11:14 AM, Ibrahim Moustafa wrote: > > > Dear Chimera team, > > I wonder if there is a way to color a certain range of residues > using rainbow. > I tried to use the rainbow command with atom_spec but it applied for > the whole chain. > > What I want to do is to color part of the structure as a rainbow > (from blue-white-red) with an increasing order of residues number. > I just wanted to highlight a region of conformational change so the > eye can follow which part of the structure has changed dramatically. > > > Thanks in advance for your help. > > Ibrahim > > -- > Ibrahim M. Moustafa, Ph.D. > Biochemistry and Molecular Biology Dept. > 201 Althouse Lab., University Park, > Pennsylvania State University > PA 16802 > > Tel. (814) 863-8703 > Fax (814) 865-7927 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Re: [Chimera-users] Coloring range for residues
by Elaine Meng 10 Nov '09

10 Nov '09

Hi Ibrahim, Just thought I would mention that there are some other interesting ways to show conformational changes or conformational variability in a single picture. Some images are attached at the bottom. You can assign attributes to residues, and then show those attribute values on one or more structures with color and/or "worms". If two or more structures are associated with an alignment and you show the alignment "RMSD" header, that automatically creates the residue attribute named mavRMSD, where the values are the alpha-carbon RMSDs for residues in the same column of the alignment. If you only have two structures it boils down to the CA-CA distance between the two residues in each column of the alignment. You are probably thinking "but I don't have an alignment!" -- however, in Chimera it is easy to make one. If you have > 2 structures already superimposed, you can use Match->Align (under Tools... Structure Comparison) to create and display the sequence alignment. If you have 2 structures, you can use MatchMaker to both create the pairwise sequence alignment and superimpose the structures. Here is an example with a G protein in the "on" and "off" conformations, using the command version of MatchMaker: open 1tad open 1tnd del ~ :.a mm #0 #1 show true That will create the pairwise sequence alignment with RMSD header shown. Then in the alignment window, choosing "Structure... Render by Conservation" brings up the dialog for mapping colors and/or worm fatness onto the structures. In that dialog, change the attribute from "mavConservation" to "mavRMSD" to see the histogram of values. Then use the Colors or Worms section in the dialog to map the values. You can do it for either or both structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html… > I attached images for the example above, where mavRMSD is shown with: (a) worms for both structures (b) color on one structure (c) both color and worms on one structure You could also do the coloring with command "rangecolor" instead of with the dialog <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> The example uses two conformations of the same protein, but it will also work with different proteins along as they are similar enough for Matchmaker to create a good alignment. Or instead of using an alignment, you can create your own attribute in a text file and then use "rangecolor" or the "Render by Attribute" tool (under Tools... Depiction), actually the same dialog used above for showing mavRMSD, to show your custom attribute on the structure. There is a description of the file format <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > and example files <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Probably more information than you wanted 8-) Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] External SAS calculation
by Yasser Almeida Hernández 10 Nov '09

10 Nov '09

It would be nice that Chimera also compute and save the SAS (like a grid), since there're a few softwares to do this task spacifically. I hope this will avaible in the future... Anywere, thanks a lot for your helps -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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Re: [Chimera-users] problem with surface representation
by Miriam Gochin 10 Nov '09

10 Nov '09

Outstanding! That worked perfectly! Thank you so much, Tom. Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463 ________________________________________ From: Tom Goddard [goddard(a)cgl.ucsf.edu] Sent: Monday, November 09, 2009 10:07 PM To: Miriam Gochin Subject: Re: [Chimera-users] problem with surface representation Hi Miriam, I think the cusps (two points) are just parts of the surface. The surface is obtained by rolling a sphere of a 1.4A radius over the molecule and the surface is all points reached by that rolling sphere. The cusps happen because that sphere does not fit between the residue 36 and 104 HE2 atoms. If you reduce the probe radius to 1.2 A then you get rid of the cusp but the surface is slightly different. You would change probe radius in the same dialog where you changed vertex density. Tom -------- Original Message -------- Subject: Re: [Chimera-users] problem with surface representation From: Miriam Gochin <miriam.gochin(a)tu.edu> To: Tom Goddard <goddard(a)cgl.ucsf.edu> Date: 11/9/09 9:31 PM > Hi Tom, > > Thanks for the suggestions. That does improve things a bit, but not completely. Maybe I just have bad geometry at that position? I attach the pdb file. The residues involved are #36 and #104, if you have time to take a look at it. > > Best, > > Miriam > Touro University - CA > miriam.gochin(a)tu.edu > 707-638-5463 > ________________________________________ > From: Tom Goddard [goddard(a)cgl.ucsf.edu] > Sent: Monday, November 09, 2009 8:50 PM > To: Miriam Gochin > Cc: Chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] problem with surface representation > > Hi Miriam, > > I guess the surface is being divided into two few triangles. You can > increase the number of triangles by increasing the "vertex density" > parameter. To do this, select the surface (ctrl-click it), use > inspection selector (menu Actions / Inspect), set the "Inspect" menu in > the inspector dialog to MSMS Surface, increase the "vertex density" > parameter, say from 2 to 5, and press the Enter key after typing in the > new number. That should give a smoother surface. > > Another step that can improve the lighting of the surface is to enable > glossy lighting in the Lighting panel. Menu Tools / Viewing Controls / > Lighting, quality -> glossy. Some old graphics cards don't support this. > > Tom > > -------- Original Message -------- > Subject: [Chimera-users] problem with surface representation > From: Miriam Gochin > To: Chimera-users > Date: 11/9/09 8:07 PM > >> I am having trouble with some pointed edges to my surface (attached). It only happens in one location - everywhere else the surface is smooth. I appreciate any suggestions. >> >> Thanks, >> Miriam Gochin >> Touro University - CA >> miriam.gochin(a)tu.edu >> >> > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Re: [Chimera-users] External SAS calculation
by Yasser Almeida Hernández 10 Nov '09

10 Nov '09

Hi Tom... I'm actually interested in compute and save the accesible surface as a grid (like DMS). If Chimera doesn't compute the SAS surface (with MSMS code), why it ask for the probe radius in Favorites > Preferences > New Surfaces? Thanks -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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problem with surface representation
by Miriam Gochin 09 Nov '09

09 Nov '09

I am having trouble with some pointed edges to my surface (attached). It only happens in one location - everywhere else the surface is smooth. I appreciate any suggestions. Thanks, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Coloring range for residues
by Ibrahim Moustafa 09 Nov '09

09 Nov '09

Dear Chimera team, I wonder if there is a way to color a certain range of residues using rainbow. I tried to use the rainbow command with atom_spec but it applied for the whole chain. What I want to do is to color part of the structure as a rainbow (from blue-white-red) with an increasing order of residues number. I just wanted to highlight a region of conformational change so the eye can follow which part of the structure has changed dramatically. Thanks in advance for your help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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External SAS calculation
by Yasser Almeida Hernández 09 Nov '09

09 Nov '09

Hi all.. In the Chimera source where is located the sources files for the calculation of SAS. I'm writing a python script for calculate the SAS and i want to call the Chimera's routines to do this task... Best regards -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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access rotation and translation matrices
by Lori Nyland 05 Nov '09

05 Nov '09

Hello, I have been trying to rotate a large volume relative to a reference volume using the vop resample command. The problem is that both volumes are nearly 2GB. However, If I were to bin the volumes (by n) and had access to the rotation R(alpha, beta, gamma) and translation T(x,y,z) matrices I could perform the rotation in an alternate program via R and nT. Thanks! Lori

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How to increase h bond width
by Kshatresh Dutta Dubey 01 Nov '09

01 Nov '09

Dear Users, I want to increase the hydrogen bond width and change bond color. How can i do this ? Any help is heartily appreciated. Regards Kshatresh

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classifying contact interactions
by M. Shahid 31 Oct '09

31 Oct '09

Dear All, I have a question regarding the contact interactions between a protein-ligand complex. I can retrieve the contacts by the findclash command in --nogui mode as below: chimera --nogui protligcomplex.pdb clash.com and similarly I can find the hbonds. The output I am getting is as below: -------------------------------------------------------------------------------- 32 contacts atom1 atom2 overlap distance LIG 1 H ALA 265.A O 1.045 1.435 LIG 1 O ALA 265.A O 0.550 2.430 LIG 1 N GLU 169.A OE2 0.439 2.666 LIG 1 H GLU 169.A CD 0.116 2.584 LIG 1 O ASN 253.A 1HD2 0.094 2.386 LIG 1 H ALA 265.A C 0.090 2.610 LIG 1 C ALA 265.A O 0.059 3.121 LIG 1 N ASN 253.A OD1 -0.037 3.142 LIG 1 C ALA 265.A O -0.039 3.219 LIG 1 N GLU 169.A HG3 -0.072 2.697 LIG 1 C PHE 168.A HB2 -0.081 2.781 LIG 1 N GLU 169.A CG -0.113 3.438 LIG 1 N GLU 169.A CD -0.125 3.450 LIG 1 N GLU 169.A CD -0.128 3.453 LIG 1 C MET 270.A HG2 -0.140 2.840 LIG 1 N PHE 168.A CD2 -0.163 3.488 .......... .... ... .. . -------------------------------------------------------------------------------- Now I want to further classify these contact interactions into more other types: Aromatic and Ionic (anion < - > cation). Is there any way in Chimera to achieve this? Or if I want to do it with some scripting, which atoms I would say are involved in ionic and aromatic interactions considering the distance value as well? I would be very much grateful if someone suggest me a way to do this. Thanks, Best regards, -- Shahid.

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Help Installing Chimera
by Muhammad Ahmad Chaudary 30 Oct '09

30 Oct '09

Hi, I am trying to install chimera on Fedora 11 and i am running into problems. After config i tried running make and got the following error. #first i got the error evp.h not found Even though yum said openssl was installed. Anyway i downloaded openssl and tried to install it manually. But i still got the same error. So then i copied the openssl header files folder to /usr/include This got me past this error. #Next i got this error gcc -g -O2 -o sha1_keygen sha1_keygen.o -L/home/ahmad/chimera/src -lchimera -lpthread -lcrypto /usr/bin/ld: cannot find -lcrypto collect2: ld returned 1 exit status make[1]: *** [sha1_keygen] Error 1 I just installed openssl with the default options. Any ideas what i am doing wrong here! Ahmad

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binning large volumes
by Lori Nyland 28 Oct '09

28 Oct '09

Hello, I have two volumes with the same dimensions and each are nearly 2GB. I can use the vop resample command in a 64 bit Chimera for Linux and reassign one volumes coordinates relative to the other. However, it is slow to execute, but it does work. In order to speed things up is there a way to bin the volumes (to use less space), place it through the vop resample command, and then un-bin the volume without losing information? Thanks! Lori

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script for
by lorenzo 28 Oct '09

28 Oct '09

Dear all, I'm trying to write a script to interpolate between two structures and save the intermediate conformations as pdb files. I need a script since I have to repeat this procedure several times. As far as importing the structures and interpolating is concerned I have no problem: open A.pdb open B.pdb morph start #0 morph interpolate #1 frames 6 (I need 5 intermediates) What I don't manage to figure out is how to save the intermediate configurations. Figuring out that morph interpolate was generating a trajectory stored as the model #2 I tried write format pdb trajectory #2 out.pdb but it didn't write anything I also unsuccessfully tried with perframe write format pdb out.pdb but I still got no output. Does anybody have any suggestion? Regards Lorenzo Bongini

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problems display a mrc or ccp4 file
by maillist＠dejung.net 27 Oct '09

27 Oct '09

Hi all, I have problems diplaying a 3D map in chimera. I recognized this problems with .mrc and .ccp4 maps. And only at my system. When I load a map, I get an image like this: http://download.dejung.net/chimera.png My version of chimera is: $ chimera --version chimera snapshot version 1.4 (build 28596) 2009-08-20 19:46:50 GMT I tried also other versions (chimera alpha version 1.3 (build 2577)) but they will not start at all. Tell me there is a segmentation fault at the beginning without any molecule, map or other things. Just exits directly at start up. Friends of mine told me, it will be maybe the wrong graphic driver, but I all ready tried different ones. At the Moment I use nvidia drivers 185.18.14 on a Linux 64 bit system. I have no idea now, so hope someone can help me at this point... Best regards! Mario

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