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Patch to center_of_points()
by Nader Morshed 10 Jul '12

10 Jul '12

It seems that the code in the Segger module for calculating the center of a region breaks when the region contain a large number of points. I don't have the error message on hand, but it complains about calling _contour.affine_transform_vertices with a double, rather than a float. It seems that in regions.py the summed coordinate is cast to a float32, then divided by the number of points, which can cause an implicit cast up to float64's when point_count is large! Here's a simple patch to share/Segger/regions.py that re-orders the calls to cast after division, rather than before: --- old/share/Segger/regions.py 2012-03-19 13:45:34.000000000 -0700 +++ new/share/Segger/regions.py 2012-07-09 14:55:26.241372503 -0700 @@ -873,7 +873,7 @@ plists = [r.points() for r in self.childless_regions()] s = numpy.sum([numpy.sum(plist, axis=0) for plist in plists], axis=0) - com = s.astype(numpy.float32) / self.point_count() + com = (s / self.point_count()).astype(numpy.float32) if transform: tf = self.segmentation.point_transform() import _contour -- Nader Morshed <morshed.nader(a)berkeley.edu>

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Motion of an atom
by Raju Purohit 10 Jul '12

10 Jul '12

Hello friends, I need some help here. I created a basic model having just an atom and set its coordinates as (0,0,0). Now I want to make it move along a certain path defined mathematically (say, along x axis) and I need to see it move. So I used a * for* loop. But I couldn't see and motion and soon realised that the loop is very quick in executing and thus I could see the atom at its last coordinates. So I tried to add delay of 0.5 seconds for each loop by importing *time* module and useing *time.sleep*. But still I couldn't see any motion and the coordinates of the atom is set only at the end of the *for* loop. I could not see the intermediate path. I am sure you people must have tried this earlier and this problem has a solution but I just couldn't figure it out. Can you please help me out? Thank you in advance. -- Raju R.N. Third Year, B.Tech Mechanical Engineering National Institute of Technology Karnataka, Surathkal

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Fwd: Question about coloring the points on a Ramachandran plot
by Eric Pettersen 20 Jun '12

20 Jun '12

Hi Trina, I'm forwarding this to the chimera-dev list to give the "Ramachandran plot guy" (Conrad Huang) a chance to answer. I think he's recently done many of the same things for a custom script so he's better suited for answering... --Eric Begin forwarded message: > From: Trina Manalo <trinamanalo_2014(a)depauw.edu> > Date: June 19, 2012 7:56:53 AM PDT > To: pett(a)cgl.ucsf.edu > Subject: Question about coloring the points on a Ramachandran plot > > Hi Eric, > > I had emailed you about the animated Ramachandran plots, which I have gotten to work. I have a new question to ask you concerning the points of the plot. > > I've tried coloring the plots by opening Chimera as an administrator and going to IDLE. Then I tried editing the file labeled "_init_" under the "Ramachandran" folder that comes with the program when it is installed. In the file, under "def _displayData(self)" I tried to do 2 things: > > 1. Change the non-selected residue points to be transparent, so that only the outlines of the non-selected residue points are visible. I want to do this so that the selected residue point is visible when it is behind a lot of points. I got it to be somewhat successful, however, only half of the points turn out this way. The other half turned out to be blacked out and I'm not sure why. > > 2. Get rid of the non-selected residue points all together so that the only point I see is the residue point that I am interested in following. I tried adding the phrase "marker='None' " in the "ax.scatter" line, but that didn't work. > > I'd greatly appreciate your help. > > Thanks, > Trina > > >

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Re: [chimera-dev] Chimera-dev Digest, Vol 98, Issue 1
by ladam 07 Jun '12

07 Jun '12

Le 04/06/12 21:00, chimera-dev-request(a)cgl.ucsf.edu a écrit : > Message: 2 Date: Mon, 04 Jun 2012 15:28:27 +0200 From: ladam > <ladam(a)smbh.univ-paris13.fr> To: chimera-dev(a)cgl.ucsf.edu Subject: > [chimera-dev] Rotating about an axis with mouse Message-ID: > <4FCCB7FB.5060709(a)smbh.univ-paris13.fr> Content-Type: text/plain; > charset=ISO-8859-1; format=flowed Hi all, I have a python script that > allows me to rotate a residue in a molecule of a desired angle around > a predefined vector. Now I'd like to be able to do this graphically > with the mouse on a selected residue. I have almost found what I want > if I use the 'Move selection' option in the 'Movement Mouse mode' but > this does rotate around the center of Mass or geometric center, not > around a vector. What I plan to do is derive the code from the > corresponding /share/MoveSelection/move.py module and try to insert a > vector instead of the center_of_rotation(self.movable_groups) but > there is maybe a better, simpler idea. Any suggestion? Thanks a lot > -- -------------------------------- Patrick Ladam Ma?tre de Conf?rence > Universit? Paris 13 - UFR SMBH CSPBAT - Service RMN 74, rue Marcel > Cachin 93017 Bobigny Cedex Tel: 01 48 38 73 25 Fax: 01 48 38 77 77 > mail: ladam(a)smbh.univ-paris13.fr ------------------------------- > ------------------------------ Message: 4 Date: Mon, 4 Jun 2012 > 09:04:03 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: ladam > <ladam(a)smbh.univ-paris13.fr> Cc: chimera-dev(a)cgl.ucsf.edu, > "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: > Re: [chimera-dev] Rotating about an axis with mouse Message-ID: > <1A06A067-7C81-49D0-B154-D1CC50737764(a)cgl.ucsf.edu> Content-Type: > text/plain; charset=iso-8859-1 Hi Patrick, If I understand correctly, > you can do what you want with "Constrained Move" (in menu under > Tools... Movement): > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/constrained/constr…> > (The purpose of "Movement Mouse Mode" is different, mainly to allow > moving subparts of a model. By default, mouse manipulation moves whole > models.) You can also specify center and axis of rotation if using > commands (turn, roll). > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html> I > hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer > Graphics Lab (Chimera team) and Babbitt Lab Department of > Pharmaceutical Chemistry University of California, San Francisco On > Jun 4, 2012, at 6:28 AM, ladam wrote: Thank you for the answer Elaine, Well the "constrained move" allows me to rotate the whole model, not a selected residue in the model (which is actually what i want to do). What I would need is to use the constrained mouse rotation on a subpart of the model (a previously selected residue or set of atoms for instance). So my guess is I should start from this Constrained Move module and modify it to apply the movements to the currently selected residue or atoms. At the moment I am going throught the code to see how to do it, I'll probably need some advice later on. Thanks again Patrick

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Re: [chimera-dev] [Chimera-users] undisplay label in distance monitor
by Eric Pettersen 07 Jun '12

07 Jun '12

On Jun 4, 2012, at 11:54 PM, Bala subramanian wrote: > Friends, > I have written a script to draw lines between atoms (using distance > monitor). I dnt want the distance label to be displayed with the > pseudo bond. Kindly write me the way to remove the label. My script > is below. > > model=chimera.openModels.open('myavg.pdb') > res=model[0].residues > MAT=loadtxt('mymatrix',dtype=float) > chimera.runCommand('focus') > for x in range(len(res)): > for y in range(len(res)): > if x <> y : > value=MAT[x,y] > > if 0.5 < value > 0.75: > b=distanceMonitor.newPseudoBond(res[x].atomsMap['CA'] > [0],res[y].atomsMap['CA'][0]) > b.drawMode=1 > b.radius=0.05 > #b.label=None I tried keeping this value as None and > empty string but it doesnt help. > b.color=getColorByName('red') > > else: pass > > else: continue > Hi Bala, distanceMonitor pseudobonds are designed to do exactly what you find them to be doing: showing an updated distance as the model is moved. What you need to do is make a normal pseudobond group for your own use that doesn't have all the special processing that distanceMonitor provides. Here is some example code: from chimera.misc import getPseudoBondGroup grp = getPseudoBondGroup("matrix bonds", associateWith=[model]) ...then later... b = grp.newPseudoBond(res[x].atomsMap['CA'][0], res[y].atomsMap['CA'] [0]) You will probably want to set some attributes of your group, like color and line type (dashed vs. solid). Here's some code for that: import chimera from chimera.colorTable import getColorByName grp.color = getColorByName("lime green") grp.lineType = chimera.Dash --Eric P.S. BTW, this question is probably better for chimera-dev than chimera-users...

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Rotating about an axis with mouse
by ladam 04 Jun '12

04 Jun '12

Hi all, I have a python script that allows me to rotate a residue in a molecule of a desired angle around a predefined vector. Now I'd like to be able to do this graphically with the mouse on a selected residue. I have almost found what I want if I use the 'Move selection' option in the 'Movement Mouse mode' but this does rotate around the center of Mass or geometric center, not around a vector. What I plan to do is derive the code from the corresponding /share/MoveSelection/move.py module and try to insert a vector instead of the center_of_rotation(self.movable_groups) but there is maybe a better, simpler idea. Any suggestion? Thanks a lot -- -------------------------------- Patrick Ladam Maître de Conférence Université Paris 13 - UFR SMBH CSPBAT - Service RMN 74, rue Marcel Cachin 93017 Bobigny Cedex Tel: 01 48 38 73 25 Fax: 01 48 38 77 77 mail: ladam(a)smbh.univ-paris13.fr -------------------------------

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Chimera-dev mailing list
by Raju Purohit 04 Jun '12

04 Jun '12

Dear sir/madam, I want to be added to Chimera mailing list. Thank you. -- Raju R.N. Third Year, B.Tech Mechanical Engineering National Institute of Technology Karnataka, Surathkal

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Iterating through chains
by Ryan Doherty 29 May '12

29 May '12

Hello, I'm trying to create a chimera script and am stumped. I'm trying to iterate through a series of PDB entries that contain a specific protein-protein interaction (some are NMR ensembles) to create a list of residues that within specific distances of the binding interface. I am able to successfully iterate through pdb files and residues, but am having difficulty iterating through chains of NMR ensembles. Is there a variable like m.chains or is the number of chains accessible through chimera.openModels.list? Also, do you have any example scripts that could help me? Sincerely, Ryan Doherty

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Fwd: Dividing a model into seperate models - one for each chain
by Mateusz Dobrychłop 09 May '12

09 May '12

---------- Forwarded message ---------- From: Mateusz Dobrychłop <dobry(a)g.pl> Date: 2012/5/9 Subject: Re: [chimera-dev] Dividing a model into seperate models - one for each chain To: Chimera BB <chimera-users(a)cgl.ucsf.edu> Hi Tom, Thank you very much for your response. My exact problem is that I'm trying to find a way to automatically save all the models (and submodels) that are opened in Chimera at a time. It's easy when models are numbered #0, #1, #2 etc - then, I use: opened=openModels.list() howmany=len(opened) while howmany>=0: command="write "+str(howmany)+" "+o_path+"/"+str(howmany)+".pdb" runCommand(command) howmany-=1 Unfortunately, when I split, let's say, #0 that contains 3 chains, and then use the above code, I get an error: MidasError: 3 model ids match "0" So maybe there's a different way to do it? I'd like to save #0.1, #0.2 and #0.3 to seperate files. I know it's possible from Chimera's interface, but I have no idea how to do it when my script doesn't have any info about the number of submodels etc. Thank you for your time once again, Mateusz 2012/5/9 Tom Goddard <goddard(a)sonic.net> > Hi Mateusz, > > The "split #0" command produces separate models for each chain. They are > numbered #0.1, #0.2, #0.3, ... with the same primary id number (0) and > different secondary id numbers. You can use these two-part id numbers in > any Chimera command (e.g. color blue #0.2), or you can refer to all the > models using #0. There is currently not a way to change the id numbers of > models. > > Tom > > > Hello, >> >> Is there a command / a way to split a model into seperate models (one for >> each chain)? I know there is the "split" command, but it divides the model >> into submodels. >> >> Mateusz >> >> >

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Dividing a model into seperate models - one for each chain
by Mateusz Dobrychłop 08 May '12

08 May '12

Hello, Is there a command / a way to split a model into seperate models (one for each chain)? I know there is the "split" command, but it divides the model into submodels. Mateusz

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