- Chimera-users - RBVI Mailing Lists

measure a mean intensity of a segmented map
by 李智海 23 Jun '15

23 Jun '15

Hi, Here I want to evaluate the flexibility of variable domains of a density map. How can I quantify the mean intensity of segmented parts by Chimera? Thanks! Best wishes! Zhihai Li Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics. School of Life Sciences, Xiamen University. Xiang'an Road(South), Xiang'an District, Xiamen City, Fujian Province, China.

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Attribute Error: 'AtomType' object has no attribute 'amber_atom_type'
by Karl Sebby 22 Jun '15

22 Jun '15

Hi I am modifying several ligand/protein complexes; usually with the “Build Structures” tool. I modify ligands by changing and deleting atoms, or by using “Join Models” after building or importing a structure with “Start structure”. Sometimes, minimizing the ligand works fine, but other times I get the error: “Attribute Error: ‘AtomType’ object has no attribute ‘amber_atom_type’”. I cannot figure out what is causing this error or how to fix it. It seems to happen when I begin working from a saved session or a pdb that was written with the ‘write’ command and not when I go through a whole series of steps in one shot. Any ideas on what is going on? Thanks, All the best, Karl -- Dr Karl Sebby Left Side Research LLC 1661 K M Ranch Road Whitefish Montana 59937 Office: 406 623 4773

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Using the findHbond via Python Midas Module
by Ahir Pushpanath 22 Jun '15

22 Jun '15

Dear All, I am confused about what input I need to provide to the findHbond command in the FindHBond midas module. This is the help() on the command. findHBonds(models, intermodel=True, intramodel=True, donors=None, acceptors=None, distSlop=0.0, angleSlop=0.0, interSubmodel=False, cacheDA=False). For example if I want to find all H bonds between a pre-selected group of residues in loop, saved as: loop = chimera.selection.currentAtoms() and the rest of the protein molecule, what command would I have to run? I am assuming the output(such as the one given in the findHbonds runcommand) would be saved into a variable if I provide one? Ahir -- Dr. Ahir Pushpanath* PhD.* Senior Biologist, Johnson Matthey.

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help please
by Sezer Akgöl 22 Jun '15

22 Jun '15

how can I associate 2 protein with each other from their C and N terminals respectively

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Feature request - lock center of rotation to center of view ("pseudo-Coot mode")
by Oliver Clarke 22 Jun '15

22 Jun '15

Hi, I have a request for a future version of Chimera - would it be possible to add a command or menu item that (reversibly) locks the center of rotation to the center of view, such that when the view is translated, the cofr is updated automatically also? This is the way structure navigation works in Coot, and I find it is a much more intuitive and precise way to travel when examining the finer details of a structure (as one would expect given that the main purpose of Coot is model building while Chimera is exceptionally good for structural analysis and visualization). This would make navigation of large structures much easier, particularly when one is just browsing around the structure. In addition, it would be nice to have a dynamically updated pseudoatom to indicate the current center of rotation - this is implemented in Coot as the “pink pointer”, and I find it very helpful for getting my bearings. Cheers, Oliver.

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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 15 Jun '15

15 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 10 Jun '15

10 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 09 Jun '15

09 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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