- Chimera-users - RBVI Mailing Lists

Chimera in Virtual machine
by Milo Westler 18 Jun '15

18 Jun '15

Well I thought I had this figured out, but then my VM broke and I can't get chimera to run in my VM again. I am running Vritualbox with a guest system of ubuntu-mate 15.04. I want to be able to use chimera in the VM for a workshop that we are presenting. I have installed the 64 bit version for linux. I get: ~> chimera pci id for fd 4: 80ee:beef, driver (null) libGL error: core dri or dri2 extension not found libGL error: failed to load driver: vboxvideo libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 751 Current serial number in output stream: 752 ~> And when I run: /opt/UCSF/Chimera64-1.10.1/share> python __main__.py Chimera is misconfigured. Please reinstall chimera. Thanks, -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

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Query on GPI-anchor proteins
by Aditya Padhi 17 Jun '15

17 Jun '15

Dear Chimera Users, I am working on a protein, which is known to cleave few GPI-anchor proteins (Glycosylphosphatidylinisotol). Also, I know that there are several other candidate GPI-anchor proteins which may or may not be cleaved by my protein of interest. I was wondering, if there is any tool/method in Chimera using which I can atleast get some preliminary information on which of the proteins that could be probably cleaved by my protein of interest. The 3D structure of my protein of interest and most of the GPI-anchor proteins is not available. I was therefore wondering if there is any such tools/methods available that I am missing using which I can find out which of the GPI-anchor proteins are being cleaved. Any suggestion/guidance would be highly appreciated. Thank you so much, Aditya

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What happened to my model?
by Sara Cuellar 17 Jun '15

17 Jun '15

So, in my line of work we are focusing on the protein Dihydrofolate Reductase. Using Jmol, I was able to remove all chains except for chain A, and also increased the diameter of the backbone so that it may be printed. When I opened it in Chimera to export it from VRML file to an STL file, it still looked fine. However, when it was opened in my 3d printing program, parts of the protein were missing. All I see is floating fragments. Is there any way I can fix this using chimera? I have included images of the protein.

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Scripted registration of a perframe python script
by Kersey Black 17 Jun '15

17 Jun '15

Hi, I have been 'opening' a python script file from within Chimera to start a session and in that script I open the MovieDialog manager (mdm) and read in a pdb with a series of models to be viewed as a trajectory. That part is working thanks to help from other responses in chimera-users. To modify the molecule (color, etc) it seems like the mdm.ensemble.molecule is giving me the access, though that may not be the right approach for my needs, because it seems to act on all frames. What I would like to do, from within this same initial python script, is to apply/register a perframe (also in python) script to control things like color on a frame by frame basis. I would like to do this as a way of keeping all of the setup in a single script file such that then I just need to record the movie manually, or perhaps there is a way to do this also from the script. Thanks much for any help and/or direction to documentation on the python api to the MovieDialog that allows control of these functions. Kersey

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ImportError: no module named chimera
by 陈雷 16 Jun '15

16 Jun '15

Hello, I got a problem when calling chimera in a python script. ImportError: no module named chimera Here is the line in my script: from chimera import runCommand. Python version is 2.6.6 and chimera is 1.8 in Linux. Would you please help me out with this? Thanks. Best regards, Ryan

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ImportError: no module named chimera
by ryanch＠mail.ecust.edu.cn 16 Jun '15

16 Jun '15

Hello, I got a problem when calling chimera in a python script. ImportError: no module named chimera Here is the line in my script: from chimera import runCommand. Python version is 2.6.6 and chimera is 1.8 in Linux. Would you please help me out with this? Thanks. Best regards, Ryan

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restoring sessions with python & triggers
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

Normally a save session by a python extension is invoked by a trigger SAVE_SESSION. For restoring a session, several related chimera APIs are available that are typically not used. 1) post model restore: SimpleSession.registerAfterModelsCB(afterModelsRestoredCB, arg) 2) BEGIN_RESTORE_SESSION and END_RESTORE_SESSION triggers. I need to reset extension gui values based on midas positions. I presume a normal restore in the session file does not guarantee that these midas positions will be loaded at that time, so I need to delay the gui updates until the restore process has ended or possibly when the models are loaded loaded. What is the distinction between END_RESTORE_SESSION and registerAfterModelsCB? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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setting viewing pref using python
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

the viewing dialog sets the Camera:Stereo parameters:units to inches, and Side View:Side to right. using python how can I reset them to mm & top? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [Chimera-users] Request for axes measurements
by Elaine Meng 14 Jun '15

14 Jun '15

Hi, You’re welcome, but I don’t have any further details than what is already given in the manual: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> It’s recommended you send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of me directly, in case others may be able to provide better answers! 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 Mar 31, 2015, at 6:26 PM, Jayaraman T <jram(a)pusan.ac.kr> wrote: > > Hi Elaine Meng, > Yes i could figure now the axes as well as angle measurements between them and thanks for your timely help. > > I would be happy if you could tell me the principle on which these axes are calculated. I have noticed that it's from Eigen vector values that are calculated for the coordinates of the set of atoms. > > I'm really interested on the backend for this calculation particularly, might help a bit progressing more for my research. > > Thanks again.

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on MD movie and morph conformation by chimera
by Smith Liu 12 Jun '15

12 Jun '15

Dear All, Will you please introduce to me on how to combine chimera MD movie function and morph conformation function to make conformation change movie files to insert into PPT files? Smith

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mol2 for NH3
by MPI 11 Jun '15

11 Jun '15

Dear Users, I try to prepare a mol2 from pdb for ammonia (NH3) and ammonium (NH4+), respectively. I used two commands: addh and addcharge with am1 method. eg, addh addcharge all method am1 It turns out that Chimera gave two similar mol2 files for NH4+ but NOT for NH3. I wonder what command and parameters are needed to produce a correct mol2 for NH3. Here are the input pdb files for NH3 and NH4, respectively. # NH3 HETATM 2860 N NH3 A 402 53.512 -12.964 -36.364 0.88 45.66 N # NH4 HETATM 2858 N NH4 A 404 56.362 -12.467 -27.097 1.00 30.80 N Thanks, Dewey

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Problems detecting a left-handed helix
by Felipe Vasquez 11 Jun '15

11 Jun '15

Hi, I am trying to visualize several of the secondary structure details on a protein of interest, and I recently had notice (by several research papers) about the existence of a left-handed helix on it. However, I could not detect the helix using UCSF Chimera (it is simply considered as a loop). Why could this happen and how could be resolved? I have tried to modify the ksdssp cut-off parameter, but it was unsuccessful, so I think now that maybe the specific nature of the helix (left-handed polyproline-like type II) could be a bit tricky for the program. What would you suggest? Thanks in advance for your help an patience. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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Determination of angles formed by distances and ring axes
by Felipe Vasquez 11 Jun '15

11 Jun '15

Hi, I have problems trying to calculate the angle between two lines: one is really built as the distance between a residue atom from a protein and the centroid of a benzene ring (from a ligand), and the other is the line corresponding to the axis of the benzene ring. How could I accomplish this objective? I have read similar issues by chimera-users on the web, but I could not find enough information to complete the calculation (I could only estimate the first distance). In case of problems to clearly comprehend this particular task, please refer to the page 3, Fig 1, panel C in the attached research paper (phi angle). PD: Is it normal that the centroid of a benzene ring is above the ring itself? Because in the process of build the first distance, I don't know whether I have to calculate the distance between the centroid and the residue atom (which I found to be shorter), or instead calculate the distance between the center itself of the plane and the residue atom (which would be a bit longer). Thanks in advance for your time and assistance in this matter. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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file size of a trajectory
by MPI 10 Jun '15

10 Jun '15

Dear Users, I use the lastest version of Chimera to read trajectory (.xtc) files output from Gromacs ver 4.6.5. When a .xtc file size larger than 2GB in most cases and 1GB in some cases, Chimera gets choked and crashed. When a .xtc file size < 1GB, Chimera works very well. I wonder if this is a limitation for reading Gromacs trajectory files. Is there a solution ? Thank you. Dewey

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tetrahedral symmetry
by Morris, Kyle 10 Jun '15

10 Jun '15

Dear Chimera Developers, I have a volume reconstructed from Relion 1.3 imposing tetrahedral symmetry. Curiously, I am not able to find the symmetry group using: $ measure symmetry #0 Chimera returns C3, even with adjusting the parameters it uses to identify the symmetry group. The model is aligned as following the Xmipp convention for T symmetry (http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry#T) which is the same as what Chimera calls T,z3? Any advice on getting the measure command to work in this convention would be greatly appreciated. Thanks! Best wishes, Kyle Morris University of Warwick, UK

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Save Cluster Figure as Phython Object
by Beuerle, Matthias 10 Jun '15

10 Jun '15

Dear all, I have been using the Clustering tool in the MD Movie/Analysis/Cluster to examine my trajectories and I found it very useful. Now I would somehow like to save the box-chart matplotlib object in order to adjust the figure, so that I can use it for a publication, since the dialog buttons do not allow a lot of modifications. Is this possible somehow? Alternatively I would be very happy as well if one could use the output obtained from the 'Save' button to recreate a similar figure (in which I have failed so far). Help is very much appreciated. Kind regards, Matthias

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joining two proteins
by López de Heredia Alonso, Miguel 08 Jun '15

08 Jun '15

Hi, I am new to Chimera, so perhaps someone could give me a hand. I have used Robetta for predicting the structure of a protein I am interested in and it gave back models for different parts of the protein. I would like to join them, so I am trying to join two models by a C-N peptide bond. I have selected the corresponding atoms in the last amino acid in one of the proteins and in the first amino acid of the other protein I want to join. With both atoms selected I took the "Join Models" option in "Build Structure" with the "C-N peptide bond" selected. And the "Apply" button does not activate. (See the screen shot attached) I have gone through the manual and I do not see what I am missing or what I am doing wrong. Any help is welcome. Thank you very much in advance. Kind regards, Miguel

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APBS electrostatic potential
by Felipe Vasquez 06 Jun '15

06 Jun '15

Hi, I am interested on calculating the electrostatic potential of a molecular surface on a protein (specifically visualizing that potential on a previously cavity determined by CASTp). However, althought I did get reasonable results using Coulombic potential, I could not obtain similar results using APBS potential (I obtained a surface too electrostatic, charged negatively and the values have a huge range, not only from -10 to 10 as in the case of Coulombic potential). Should I modify some default values out of the calculation parameters in order to get a similar result to that obtain by Coulombic potential? And it is absolutely indispensable add hydrogens in an APBS estimation? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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surfaces and
by A G Szabo 03 Jun '15

03 Jun '15

I have been working with a very large structure of many subunits, the E.Coli Ribosome particle with the Signal Recognition Particle attached (PDB 2J28) I was able to create an image of the SRP part of the complex. I selected that subunit. And was able to hide all the other subunits. So with the subunit selected I tried to visualize only that image as a surface. Wouldn't let me, getting an error message that it was too large and I should somehow split it. Don't know how to do that. I know the whole dataset is very large, but the SRP portion is only 400 amino acids. A work around would be if I could somehow select the SRP subunit and have it as a dataset to reload as that subunit alone. Then not so big. Don't know how to do that either. Your suggestions. I couldn't find anything in the tutorials that might help. I was able to show the surface of another PDB file that was much smaller. Arthur G. Szabo Professor Emeritus Chemistry Wilfrid Laurier University Waterloo Ontario Canada.

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Re: [Chimera-users] FW: Python code problem
by Mahendra B Thapa 03 Jun '15

03 Jun '15

Dear Eric I had not realized that not every amino acid consisted of CB atom. Thank you for the code which worked; just want to add a very minor addition ( """ ) to the left of the code, i.e. *sel = OSLSelection("""#0.1:%d.B@CB""" %i)* instead of *sel = OSLSelection(#0.1:%d.B@CB""" %i)* I tried another code as import string rc("open " + 'test.pdb') # 60 models, each model has chains A,B,C for i in [2196,2197]: for j in range(3429,3450): for *k* in ['A','B','C']: sel = OSLSelection("""#0.3:%d.%s@CA""" %(j,k)) sol = OSLSelection("""#0.2:%d.B@CA""" %i) if ((len(sel.residues()) != 1) or (len(sel.residues()) != 1)): continue if ((len(sol.residues()) != 1) and (len(sol.residues()) != 1)): continue rc("""distance #0.2:%d.B@CA #0.3:%d.%s@CA""" %(i,j,k)) I got the output as (without any error message) Distance between #0.2:2196.B@CA and #0.3:3450*.C*@CA: 104.315 The 'for' loop did not work for *k* (above) and only gave results for C only but not for A and B. Thank you for help, Mahendra Thapa University of Cincinnati,OH On Fri, May 29, 2015 at 1:55 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* Eric Pettersen > *Sent:* Friday, May 29, 2015 11:55:18 AM (UTC-06:00) Central America > *To:* Thapa, Mahendra (thapamb) > *Cc:* chimera-users(a)cgl.ucsf.edu > *Subject:* Re: [Chimera-users] Python code problem > > Hi Mahendra, > In the first case, as you saw, it tries exactly two distances; the first > involving :2011.B and the second involving :2420.B. In the second case it > will try every distance from :2011.B through :2419.B (note that the range > command does not include the ending number in the range). This means if > the structure is missing *any* of those residues then the distance > command will fail with the error you got, since the atom spec will only > select one atom. > So you either need to explicitly use just the residue numbers that exist, > or you need to test if the residue you are about to try to use exists. So > code to do that might be: > > from chimera.selection import OSLSelection > sel = OSLSelection(#0.1:%d.B@CB""" %i) > if len(sel.residues()) != 1: > continue > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On May 29, 2015, at 6:37 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> > wrote: > > Dear Chimera users, > > The command I used was > chimera --nogui test.py > I tried two codes (following previous posts and tutorials in chimera) in > 'test.py' as follows > > (i) > import os > from chimera import runCommand as rc > from chimera import replyobj > rc("open " + 'test.pdb') > for i in [2011,2420]: > rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) > > *This code gave the result as expected*: > Executing test.py... > Opening test.pdb... > 60 models opened > Distance between #0.2:2010.B@CB and #0.1:2011.B@CB: 72.346 > Distance between #0.2:2010.B@CB and #0.1:2420.B@CB: 92.979 > Executed test.py > > (ii) > import os > from chimera import runCommand as rc > from chimera import replyobj > rc("open " + 'test.pdb') > for i in range(2011,2420): > rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) > > * This code gave the result as* > ' You selected %d.' % numSelected) > MidasError: Exactly two atoms/axes/planes must be selected. You selected > 1. > Error while processing test.py: > MidasError: Exactly two atoms/axes/planes must be selected. You selected > 1. > > File "/opt/UCSF/Chimera64-1.5.3/share/Midas/__init__.py", line 1266, in > distance > ' You selected %d.' % numSelected) > > What could be the error this code? Only difference between two codes is: > "for > * i in [2011,2420]:" & "for i in range(2011,2420):" * > That is, I am interested to use range operator in 2nd case instead of two > values as in the 1st case. > > Thank you for help, > Mahendra Thapa > University of Cincinnati,OH > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > >

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savepos
by Dougherty, Matthew T 03 Jun '15

03 Jun '15

Hi, I have been automating the creation of positions using python scripts. Something relatively simple like p001, p002, etc. When I examine the positions using the python commands from Midas import positions pnames = positions.keys() at first things appear as I would expect, but later the sequence changes relative to the index, why is that? for example, using this to print the positions pnames = positions.keys() i=0 for pname in pnames: print i,pnames[i] i=i+1 I get these results: savepos p000 savepos p001 0 p000 1 p001 (as expected) savepos p002 0 p000 1 p001 2 p002 (as expected) savepos p003 0 p000 1 p001 2 p002 3 p003 (as expected) savepos p004 0 p004 1 p000 2 p001 3 p002 4 p003 (not as expected) savepos p005 0 p004 1 p005 2 p000 3 p001 4 p002 5 p003 (not as expected) I would expect pnames[0] to correspond to the first position created, pnames[1] to the second posiiton created, etc., assuming no ~savepos used. Want to create a situation where the default names would be pxxx, but could later be altered to more meaningful names but maintain the order of creation, or getting a session file from someone I would use their position names and tack on my default names to the end of the position list. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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to color EM map
by Smith Liu 03 Jun '15

03 Jun '15

Dear All, Suppose I have an EM map for a protein complex of 4 subunits. I have fitted them in chimera. Will you please tell me how to give each part of the map a different color based on the subunits? For example, for subunit A, B,C, D part of the EM map, how to color the map accordingly in blue, red, yellow and purple? Smith

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volume viewer/Data menu
by Dougherty, Matthew T 03 Jun '15

03 Jun '15

Hi, What is the pattern for the sequence of the Data list? Is there a way to sequence it the same as the Model Panel? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Unable to Change Lighting of Side Chains / Atoms
by David Nelson Bunck 02 Jun '15

02 Jun '15

Hello, Recently, for some reason, the settings changed on Chimera such that the atoms and side chains do not change color when I try to change the lighting settings. Thus when I get the protein (in ribbon format) to look appealing and shiny, the metal atoms in the protein remain black. Changing colors or lighting do not make any difference. The same is true for the side chains as well. This also occurs on several different sequences, so it is not just the one file. Sorry for the seemingly trivial question, but I have poked around for a while at the different settings and can't seem to find how to undo this change. Thanks for your help! david -- david bunck bunck(a)caltech.edu (626) 395-8919 Postdoctoral Scholar Heath Research Group Division of Chemistry and Chemical Engineering California Institute of Technology

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Cage maker
by Anindito Sen 02 Jun '15

02 Jun '15

Dear All, Is it possible to generate a synthetic 3d density map of hexagons and/ pentagons using the Cage building option with file extension like mrc or spi or pif ( the usuals). If so, how to save it in such a format ? Thanks Andy Sent from my iPad

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H-bond angle criteria (cut-off)
by Felipe Vasquez 02 Jun '15

02 Jun '15

Hi, I am using the H-bond function in UCSF Chimera and I noted that the relaxed parameter for angle criteria is 20 by default. However, since that I have no hydrogen atoms in the pdb structure, I assume that the angle theta (donor-hydrogen-acceptor) cannot be used by Chimera as an angle criteria, and so the psi or phi angles might be used instead. Which angle is actually used in the relaxed parameters? And most important, what is the default value of that angle (angle minus relaxing value)? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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Re: [Chimera-users] Mouse control
by Elaine Meng 02 Jun '15

02 Jun '15

Dear Prof. Szabo, I can’t see your image, but the following might help: menu: Actions… Focus - OR - command: focus … if you don’t have anything selected, either of the above should center and resize to frame all of the displayed stuff in the main window. By “selected” I mean when you Ctrl-click on something in the main window, it is highlighted with green outline. If you have something selected, you can use that same menu action to focus only on the selected part (the corresponding command would then be “focus sel”). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuactions> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/focus.html> Then, if needed, you can enlarge by zooming with the mouse or in the Side View, or with the “scale” command. I hope this helps! For future questions, we recommend you send to chimera-users(a)cgl.ucsf.edu instead of only to me, so that others can see the answers, or give better answers than mine. Regards, Elaine —— Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 2, 2015, at 1:27 PM, A G Szabo <agszabo(a)bell.net> wrote: > Elaine > You were helpful in early April I thought I would ask another question. > > I have been working with a PDB file, 2J28, that is the structure of a > full ribosome with a Signal Recognition Protein and piece of RNA bound to > the ribosome. I figured out how to get rid of all the various parts of the > Ribosome, and visualize only the SRP and piece of RNA attached to it. > > The problem is that I can't figure out how to centre that part of the > overall structure. If I move the SRP/RNA with the wheel on the mouse it > does move to the center of the screen but in the process it becomes very > small. > > I need to be able to transpose the SRP/RNA and then enlarge it. > > Can't figure it out and while there is some stuff in the tutorials and > user info, I couldn't find anything that pertained to what I needed to > do. > > This is the SRP - RNA structure from Protein Workshop after all the > ribosomal particles were hidden. > > > > The image in Chimera is even smaller. > > Thank you again for your help. > > Arthur G. Szabo > Professor Emeritus > Chemistry > Wilfrid Laurier University > Waterloo Canada. > > <winmail.dat>

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Aligning on crystal axis
by Mohamed Noor 02 Jun '15

02 Jun '15

Hello. Is there any easy way to align the view along the crystal axes, such as the ab, ac and bc faces separately? Thanks.

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Python code problem
by Mahendra B Thapa 29 May '15

29 May '15

Dear Chimera users, The command I used was chimera --nogui test.py I tried two codes (following previous posts and tutorials in chimera) in 'test.py' as follows (i) import os from chimera import runCommand as rc from chimera import replyobj rc("open " + 'test.pdb') for i in [2011,2420]: rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) *This code gave the result as expected*: Executing test.py... Opening test.pdb... 60 models opened Distance between #0.2:2010.B@CB and #0.1:2011.B@CB: 72.346 Distance between #0.2:2010.B@CB and #0.1:2420.B@CB: 92.979 Executed test.py (ii) import os from chimera import runCommand as rc from chimera import replyobj rc("open " + 'test.pdb') for i in range(2011,2420): rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) *This code gave the result as* ' You selected %d.' % numSelected) MidasError: Exactly two atoms/axes/planes must be selected. You selected 1. Error while processing test.py: MidasError: Exactly two atoms/axes/planes must be selected. You selected 1. File "/opt/UCSF/Chimera64-1.5.3/share/Midas/__init__.py", line 1266, in distance ' You selected %d.' % numSelected) What could be the error this code? Only difference between two codes is: "for * i in [2011,2420]:" & "for i in range(2011,2420):"* That is, I am interested to use range operator in 2nd case instead of two values as in the 1st case. Thank you for help, Mahendra Thapa University of Cincinnati,OH

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Ramachandran plot for a selection
by Elena Lilkova 28 May '15

28 May '15

Dear Chimera community, First I would like to just say that I am new to Chimera. I made a MD simulation of a protein using NAMD. Now I am interested in generating a Ramachandran plot for the whole trajectory, but only for a specific selection of my protein, namely three specific residues. I fail to succeed. Could anyone probably suggest a solution? Elena Lilkova elilkova(a)phys.uni-sofia.bg PhD student, Atomic Physics Department, Faculty of Physics, University of Sofia "St. Kliment Ohridski" 5 James Bourchier Blvd. 1164 Sofia, Bulgaria Elena Lilkova elilkova(a)phys.uni-sofia.bg PhD student, Atomic Physics Department, Faculty of Physics, University of Sofia "St. Kliment Ohridski" 5 James Bourchier Blvd. 1164 Sofia, Bulgaria

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Distances in biological assembly
by Mahendra B Thapa 27 May '15

27 May '15

Dear Chimera users The biological assembly of a virus in pdb format consists of 60 models; each model with 3 chains :A, B and C. I am interested to find atoms within 4 angstroms of the atom, say CA atom of residue 2059 of chain B of model 2. The chimera crashed in graphical interface (it could be due to size of the pdb file.), so I used the following command [ http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-November/002069.html ]: chimera --nogui file_test.cmd > data_rest.log where 'file_test.cmd' consists of open test.pdb findclash #2:2059.B@CA overlap -4 hbond 0 The output file 'data_rest.log' consisted of Opening test.pdb... 60 models opened Opened test.pdb containing 60 models, 677040 atoms, and 89700 residues No contacts No contacts *I want to know whether I have used right chimera command /code. *Any suggestion might help me. Thank you, Mahendra Thapa University of Cincinnati,OH

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scale bar
by Dmitry 27 May '15

27 May '15

Dear developers, How are you? I have a question about scale bar. I am not completely sure that the scale bar I drew is correct. What are the scale settings for drawing the scale bar? By the default the scale bar is in Angstroms isn’t it? In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc) Is there the same possibility in Chimera? Thank you Sincerely, Dmitry

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Starting multiple copies of Chimera on Mac
by Tom Goddard 26 May '15

26 May '15

It is possible to run multiple copies of the same Chimera on a Mac. Here’s how. From a Terminal (/Applications/Utilities/Terminal) type the command open -n -a Chimera The -n option tells the Mac to start another copy of the application. If you prefer to start the second copy by clicking an icon then you can make that icon using /Applications/Automator, choose to make an Application, select Run Shell Script, enter the command open -n -a Chimera as the script to run, then File / Save… to save this application as “Chimera+” or whatever you want to call it. This icon always starts a new copy of Chimera so you can have as many running as you like. Tom

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Re: [Chimera-users] On the seeking of the orthologs
by James Starlight 25 May '15

25 May '15

Elaine, George, thank you very much for the suggestions and ideas!! One question- do you know some DB where is possible to seek for the orthologs (e,g based on HMM) agains *several* target sequences with flexible options like to detect minimal percent of the homology for orthologs which to be found or alternatively to make such search based on some *shared* features between those targets (e.g common structural motifs responsible for ligand binding etc) which might be specified by user initially? George, the idea to focus on particular specie seems interesting- initially I've thought in the same way but to focus on the human OR (because here I'm more comfortable with dynamical range patterns of those receptors based on the in vivo Matsunami data for instance). BTW briefly have a look on those DB I didn't find there engine to seek for the orthologs agains given target. Doest this option really exist within it? All the best, James 2015-05-22 21:10 GMT+02:00 George Tzotzos <gtzotzos(a)me.com>: > I would start from BioMart. I’m also working on OR (albeit insect ones). Try also MGI (Mouse Genome Informatics). Starting from mouse Ors you can scoop orthologs in other mammalian species. > > Cheers > > George > >> On 22 May 2015, at 18:44, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi James, >> Your questions are more about bioinformatics project design rather than Chimera use. >> >> Chimera provides basic BLAST searching of NCBI’s “nr” and “pdb” sequence databases, but these are the same databases generally used by BLAST whether you use it from Chimera or from another program, or stand-alone. Also, Chimera can fetch specific individual sequences from UniProt based on UniProt identifier, but that isn’t searching, it is just getting data you already knew you wanted. >> >> I believe NCBI’s “nr” and UniProtKB are both meant to be comprehensive (cover “all” sequences) but in their own ways, and you would have to go to those resources or their publications to learn the details. There are probably also specialized GPCR and/or olfactory receptor sequence databases. Then there are multiple ways of searching, with individual sequences or with derived patterns such as hidden Markov Models (HMMs). This is a really broad topic and in my opinion, beyond the scope of this forum. You’ve probably done some of this already, but I would recommend reading similar studies in quality journals by authors you respect, to see how they have designed their projects. >> >> Chimera doesn’t have HMM-related tools or evolutionary trace, it just allows conservation analysis on your whole alignment, or subsets of that alignment opened in separate windows. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On May 22, 2015, at 9:22 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >> >>> Dear Chimera users! >>> >>> I'd like to ask some suggestion regarding my bioinformatician task and >>> possible ways of its realisation using some bioinformatics methods >>> implemented in Chimera. >>> >>> 1)I need to seek for some sequence database (here I don't know >>> absolutely how to do it) of the olfactory receptors and to select 10 >>> sequences of the Ors corresponded to 10 different mammalian species -> >>> according to my idea it should be very different species associated >>> with different ecological niches so its olfactory spectrum should vary >>> dramatically. >>> Here the question: in what DB such search should be better with the >>> inclusion of flexible search criteria's like what I've listened above? >>> >>> 2)After allocating of those 10 sequences I should to find *all* >>> possible orthologs against them-> to find all OR in another species >>> which have conservation degree agains target above chosen threshold . >>> Eventually I'll need to make some analysis regarding overall >>> conservation of the OR within different species and to point out what >>> OR are most important (conservative) in different organisms in >>> accordance to some pre-defined criteria's (i.e ecological niche of the >>> species because it's associated with the odor spectrum). Here the >>> question: would the methods like blast-search be enough for such task >>> or I should to use also methods like evolutional tracing (to find all >>> important residues in different OR which tend to co-evaluate) based on >>> its alignment data? >>> >>> I would be very thankful for any suggestion! >>> >>> James >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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On the seeking of the orthologs
by James Starlight 22 May '15

22 May '15

Dear Chimera users! I'd like to ask some suggestion regarding my bioinformatician task and possible ways of its realisation using some bioinformatics methods implemented in Chimera. 1)I need to seek for some sequence database (here I don't know absolutely how to do it) of the olfactory receptors and to select 10 sequences of the Ors corresponded to 10 different mammalian species -> according to my idea it should be very different species associated with different ecological niches so its olfactory spectrum should vary dramatically. Here the question: in what DB such search should be better with the inclusion of flexible search criteria's like what I've listened above? 2)After allocating of those 10 sequences I should to find *all* possible orthologs against them-> to find all OR in another species which have conservation degree agains target above chosen threshold . Eventually I'll need to make some analysis regarding overall conservation of the OR within different species and to point out what OR are most important (conservative) in different organisms in accordance to some pre-defined criteria's (i.e ecological niche of the species because it's associated with the odor spectrum). Here the question: would the methods like blast-search be enough for such task or I should to use also methods like evolutional tracing (to find all important residues in different OR which tend to co-evaluate) based on its alignment data? I would be very thankful for any suggestion! James

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clustering
by Rafael Rocha 22 May '15

22 May '15

hello, I have a set of ligands that share Some atoms in common. How I can clustering only those atoms? Also, how I can change the variation of RMSD for this cluster analysis in the "ensemble cluster" tool of chimera? Thanks, Rafael.

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chimera improvment suggestion
by Michał Kadlof 21 May '15

21 May '15

I have small improvement suggestion: Is it possible to display directories in Open File dialog with different font than files, for example bold? I'm loosing a lot of time on scrolling my directories tree to find particular file to open. Highlighting of directories would be very handy. -- best Michał

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Re: [Chimera-users] How can I calculate RMSD with chimera script
by Eric Pettersen 19 May '15

19 May '15

Since runCommand() doesn't return any value, you need to call the underlying Python rmsd() function, which isn't hard to do. Somewhere at the top of your script put: from Midas import rmsd and then replace: rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k)) with: val = rmsd("#0:{0}-{1}".format(s,k), "#1:{0}-{1}".format(s,k)) --Eric On May 19, 2015, at 12:45 PM, Michał Kadlof <ramidas(a)gmail.com> wrote: > Yes it work, but then I have to write and run another script to parse output from chimera which cost HDD access time. I was wonder, if it possible to do it in single script without dumping output to separate file. > > -- > Michał > > 2015-05-19 18:53 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: > Hi Michał, > Redirecting output from a program into a file is pretty easy in any Unix/Linux shell. This would redirect Chimera's non-error output into a file named "chimera-output.txt": > > chimera chimera-arguments-you-normally-use > chimera-output.txt > > You can also redirect the error output, but the syntax for that depends on the shell you are using. You should be able to easily Google it if you need to do that. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On May 19, 2015, at 1:16 AM, Michał Kadlof <ramidas(a)gmail.com> wrote: > >> Hello, >> >> I have a need of calculating about 1000 of RMSDs between two particular regions of reference model and testing model. I would like to do this with chimera script. I'm using chimera-1.10.1-Headless Linux 64-bit and have no access to any GUI. >> >> Currently my script looks like this: >> >> import sys, os, re >> from chimera import runCommand as rc >> >> << not important stuff >> >> >> rc("open %s" % (native)) >> for i in models: >> rc("open " + i) >> rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k)) >> rc("close #1") >> rc("close all") >> rc("stop now") >> >> This allow me to see output on the screen, but I don't know how to capture it for further processing. I found somewhere something like this: >> >> from chimera.tkgui import saveReplyLog >> << do something >> >> saveReplyLog('replyLog.txt') >> >> But it seem to work only in versions with GUI. >> >> Please help. >> >> -- >> best whishes >> Michał Kadlof >> >> University of Warsaw >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Load AMBER parm/traj from command line.
by ros 19 May '15

19 May '15

Hello! Is it possible to start up chimera and have it load an AMBER topology and trajectory file? For example, in Linux, you can start VMD with: vmd -parm7 name.prmtop -netcdf traj.nc And will load the topology with the corresponding trajectory frames. In chimera we do that using the 'Get Ensemble info' window in the MD movie tools. Is it possible to do it in a single line? Thank you! Rodrigo.

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How can I calculate RMSD with chimera script
by Michał Kadlof 19 May '15

19 May '15

Hello, I have a need of calculating about 1000 of RMSDs between two particular regions of reference model and testing model. I would like to do this with chimera script. I'm using chimera-1.10.1-Headless Linux 64-bit and have no access to any GUI. Currently my script looks like this: import sys, os, re from chimera import runCommand as rc << not important stuff >> rc("open %s" % (native)) for i in models: rc("open " + i) rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k)) rc("close #1") rc("close all") rc("stop now") This allow me to see output on the screen, but I don't know how to capture it for further processing. I found somewhere something like this: from chimera.tkgui import saveReplyLog << do something >> saveReplyLog('replyLog.txt') But it seem to work only in versions with GUI. Please help. -- best whishes Michał Kadlof University of Warsaw

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depth cue by color for tomogram
by Michael Elbaum 18 May '15

18 May '15

Hello all, I noticed a new sort of 3D color glasses (http://chromatek.com/) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses. I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient. thanks for any help, Michael Prof Michael Elbaum Dept of Materials and Interfaces Weizmann Institute of Science Rehovot 76100, ISRAEL tel +972 (0)8-9343537 fax +972 (0)8-9344138

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Select multiscale model surface pieces with command lines
by TUBIANA Thibault CNRS 18 May '15

18 May '15

Hi everyone! I Want to script a movie, but to do so, I need to select some surface pieces of a virus multiscale model with command line. I didn't find any way to do that. I try to select them with the mouse (ctrl+click) and then rename the selection with "namesel", it works but when I save the session and reload it, theses selections are cleared.... I can't do that each times I load my session because I have plenty of them and it's to generate the movie on SSH on another computer more powerfull... I can't split them to create a new model (for exemple with coordinates) because I will have to update all my "savepos" position... Did someone know how to do that ? Thank you a lot for your help, Regards, -- Tubiana Thibault PhD Student Institut de Biologie Intégrative de la Cellule CNRS UMR 9198 CEA-Saclay, Bâtiment 532 - Pce 12A 91191 Gif-sur-Yvette 06.79.90.95.85 http://www.tubiana.me

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Problem running Chimera remotely on CentOS7 system
by "Kestilä, Veli-Pekka" 12 May '15

12 May '15

Hi, I have following error when trying to run Chimera remotely on CentOS7 system from OSX this seems to affect also Windows with Xming libGL error: dlopen /usr/lib64/dri/swrast_dri.so failed (/opt/sci/UCSF-Chimera64-1.10.1/lib/libgcc_s.so.1: version `GCC_4.7.0' not found (required by /usr/lib64/dri/swrast_dri.so)) libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1359 Current serial number in output stream: 1359 On windows the error is: ibGL error: dlopen /usr/lib64/dri/swrast_dri.so failed (/opt/sci/UCSF-Chimera64-1.10.1/lib/libgcc_s.so.1: version `GCC_4.7.0' not found (required by /usr/lib64/dri/swrast_dri.so)) libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 145 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1350 Current serial number in output stream: 1350 How I can get this to work? Intended use would be in classroom where we don't have permissions to run or install Chimera. Greetings, Veli-Pekka Kestilä -- Veli-Pekka Kestilä / Huone 4318 / Biokeskus 3 (Viikinkaari 1) / 050-3000014

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Acylation of peptide
by Remmer Salas 08 May '15

08 May '15

Hi! I am new to Chimera and I am trying to modify the PDB file of a peptide by acylation. I have also a PDB file for the fatty acid which I got by removing the bound protein. I used the join models to form a peptide bond but prompted with this error: The following problems occurred while reading PDB file for anomt1.pdbStart residue of secondary structure not found: HELIX 1 1 LEU 2 LEU 10 1 8Model 1 (anomt1.pdb) appears to be a protein without secondary structure assignments.Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3Use command 'help ksdssp' for more information.TypeError Exception in Tk callback Function: <bound method BuildStructureDialog._addParamBond of <BuildStructure.gui.BuildStructureDialog object at 0x04F9FBF0>> (type: <type 'instancemethod'>) Args: ()Traceback (innermost last): File "C:\Program Files\Chimera 1.10.1\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.10.1\share\BuildStructure\gui.py", line 313, in _addParamBond self._appbDihedral.get(), phi=self._appbPhi.get()) File "C:\Program Files\Chimera 1.10.1\share\BuildStructure\__init__.py", line 869, in cnPeptideBond cn[1].residue.phi = phi File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 91, in setPhi _setAngle(bond, phi, getPhi(res), "phi") File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 134, in _setAngle br.angle = (newAngle - curAngle, br.biggerSide())TypeError: unsupported operand type(s) for -: 'float' and 'NoneType' TypeError: unsupported operand type(s) for -: 'float' and 'NoneType' File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 134, in _setAngle br.angle = (newAngle - curAngle, br.biggerSide()) My first question is how to solve this error. Second, how can I optimize the generated PDB file using Chimera? I want also to convert this optimize PDB file to PQR. Any advice is greatly appreciated.

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clip planes
by Bharat Lakhani 08 May '15

08 May '15

Dear All I want to visualize the core of my protein, Is it possible to slice the protein right into two half in order to visualize the core of the protein. I tried using chimera pre-capping model but it has not been work out well. Any suggestion on this would be great. Thanks

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Coloring selected residues based on B-factor
by Mahendra B Thapa 07 May '15

07 May '15

Dear Chimera users, While using Chimera to study a protein with 511 residues, I colored residues 1- 274 'dark grey', residues 274-417 'tan' and residues 418-511 'dark khaki'. I want to color residues, say, 313,350,412,415,485,503, from blue to red with an increasing order of B-factors, say respective B-factors are 40,13,2,21,33,6 without altering the color of other residues. I manually put these B-factors values for the corresponding residues; rest residues have no b-factor values as the structure is obtained from a simulation. I tried some unsuccessful attempts visiting some previous posts (sorry if I missed such posts close to my query). Any comments and suggestions might help me. Thank you, Mahendra Thapa University of Cincinnati,OH

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aborting a volume command
by Dougherty, Matthew T 07 May '15

07 May '15

I issued this command, which works correctly. volume #2 planes z,1,100,1,10 I try to abort it around slice 50 using freeze, which does not terminate. Is there a way to abort it? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Displaying and calculating protein surface enclosed pockets
by Matthias Fellner 07 May '15

07 May '15

Good day I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software. Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question. I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket. How can I display the "negative" (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details. If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed. Thank you Matthias Fellner

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listen selection command
by Mungo Carstairs (Staff) 07 May '15

07 May '15

Hi, I am trying out a REST listener for selections in Chimera and need help. I can talk to Chimera over REST. I can start an Http listener in Jalview - and verify it in my browser. I have sent this command to Chimera: listen start selection rest http://134.36.162.131:64745/ Then silence. I haven't managed to provoke Chimera into sending me a SelectionChanged notification. I am making selections in the Chimera window - as I can see by the 'Inspect Selection' panel. I have also started Chimera standalone (no REST service) and tried the listen command in the command line, but yet to see any output on a selection. What have I missed or how can I diagnose what I am doing wrong here? Thanks, Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096

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Re: [Chimera-users] [chimera-dev] VolumeEraser
by Tom Goddard 06 May '15

06 May '15

Hi Alex, Surfnet in Chimera does not produce a volume, only surfaces. It calculates the volume but then computes surfaces and deletes the volume. If you would to measure the enclosed volume of the disconnected pieces produced by surfnet, first make those pieces independently selectable with command sop split #0 where #0 is the id for the surfnet model (use Favorites / Model Panel to find the correct id number). Then select the piece of interest (ctrl click on it), then get its enclosed volume with command measure volume sel To type commands to Chimera use menu Favorites / Command Line. This question belongs on the chimera-users mailing list, not the chimera-dev list which is for programming issues. Tom > On May 6, 2015, at 8:18 AM, Alex wrote: > > Dear Sirs, > I recently started using chimera, please apologise my lack of knowledge. > In order to erase a surfnet volume I am trying to use the Erase volume module, but it doesn't work. Are the surfnet objects available to be used in VolumeEraser functions? Is there another way to study volume intersections? > If you know, please point out the article which describes the procedure for this kind of volume calculation. > > Best regards, > Alex > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>

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