June 2015 - Chimera-users - RBVI Mailing Lists

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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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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Chimera-users June 2015