- Chimera-users - RBVI Mailing Lists

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 02 Jun '15

02 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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