June 2015 - Chimera-users - RBVI Mailing Lists

Morph volumes after alignment
by Haselbach, David 28 Jun '15

28 Jun '15

Dear all, I have a few volumetric cryo EM Maps of the same protein in different conformations. And I would like to morph between those conformations. However, the volumes are not perfectly aligned in first place. So I align all of them on one of the maps using the "fit in map" functionality. This works great and when I look through the different structures with the volume viewer, they are perfectly aligned. However, if I morph through the maps using the following command: vop morph #0-19 playstep 0.003 constantVolume true frames 1000 the maps are morphed in their original position so the morph is quite jumpy. Is there a way to morph through them in the aligned coordinate system directly? Kind regards David ----------------------------------------------------------------------------------- Dr. David Haselbach Max-Planck-Institut für biophysikalische Chemie AG Stark Am Fassberg 11 D-37077 Goettingen dhaselb(a)gwdg.de<mailto:dhaselb@gwdg.de> +49-551-2011302

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ViewDock
by leila karami 27 Jun '15

27 Jun '15

Dear all Now, I want to save 1 pdb file containing target + one of poses of ligand for example, number 3. For this aim, what to do? I did following steps, but I did not succeed: file ---> save pdb ... In save models section, I selected both of target.pdb (#0) and (#1.3) In file name section, I wrote complex.pdb and then save. I encountered with error (see the below link): https://www.dropbox.com/s/bdkq1x1db96amhi/chimera%20error.png?dl=0 I tested other names such as $target.pdb and $1.3.pdb. Unfortunately, I encountered with the same error. Best regards,

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drawing shapes
by Bala subramanian 25 Jun '15

25 Jun '15

Friends, I have used HOLE program ( http://www.sciencedirect.com/science/article/pii/S026378559700009X) to find the pore radius of a channel as a function of z-axis. As output, the program gives the location of capsules (that were filled inside the channel), capsule length and radius etc, as a function of z-axis. Capsule graph option***** Data: cenxyz.cvec eff.rad area CAP.LEN cap.rad angle.X-axi cen.line.di integ.s/(ar point sourc *-14.00000* *2.23465* 15.68804 *1.72142* 1.39301 73.21487 0.00000 0.03187 (sampled) -14.50000 2.40709 18.20262 1.96609 1.46141 58.41143 -0.54015 0.05934 (sampled) -15.00000 2.51292 19.83844 1.37866 1.78410 73.19154 -1.11224 0.08454 (sampled) -15.50000 2.69525 22.82171 1.34834 1.97026 87.40431 -1.71545 0.10645 (sampled) I was wondering if i can use the shape command to draw the capsules in Chimera. I thought to create 'tube' with 'shape' command but i was not lucky. For instance, the following command didnt work (i opened channel as model #0) shape tube #0 radius *2.23* bandLength *1.72* center 0, 0, *-14.00 * Pls help to know some way to do this. Thanks, Bala -- C. Balasubramanian

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Windows 8.1 and nVidia Quadro drivers.. grrr
by Kenward Vaughan 24 Jun '15

24 Jun '15

Hello! I have Chimera working wonderfully with sequential stereo under Linux with our Quadro card (a K4200), but am getting terribly frustrated with trying to have it work at all under Win 8.1. The latest non-beta driver is installed. It took me a while to find where the nVidia control panel is located after finding that Chimera didn't recognize any stereo-capable hardware (including some references to togl and pixels). Blah. I started up the "wizard" of 3D, which gave me a nice slide show, but Chimera didn't see anything. Interestingly, rebooting directly into Linux gave the same problem, which had me fuming and frothing all over the place. A shutdown followed by fresh start into Linux reset the card. So the Windows driver touches something inside the card which has to be reset hard. There are multiple things installed when this driver is put on the system. Is it possible that there are things I don't want, which are slyly strengthening my thoughts about Windoze? Some searching of the archives was inconclusive for this system. I have played with the settings in the control panel but have found no combination that gets sequential stereo working. Does anyone know what settings should be changed from the defaults to get this working? Many thanks for any help! Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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savepos
by Dougherty, Matthew T 24 Jun '15

24 Jun '15

in defining the text string view_name, spaces are disallowed, eg "rotate 30". Although the position will be created, the reset command will not properly access the position key. What are the allowable characters? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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ViewDock
by leila karami 24 Jun '15

24 Jun '15

Dear Elaine, Thanks for your guidance. It was very good. Now, I want to know there is this possibility to have these separate 252 pdb files as 1 pdb file? Thanks for your time and consideration. Best

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How to crop a map
by Tom Goddard 24 Jun '15

24 Jun '15

You can crop a map using volume dialog menu Features / Region Bounds, then save it with volume dialog File / Save Map As…. Other Chimera map capabilities are described in the Guide to Volume Data Display in Chimera: http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html <http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html> Tom > On Jun 23, 2015, at 7:52 PM, 李智海 wrote: > > Adding to the previous one. > the map I want to convert has a same pixel size with the data set. So maybe the question could be that how can I cutting the boundaries of the map to fit the size of reconstruction images. > > Thanks! > > Zhihai Li > > >> On Jun 24, 2015, at 10:44 AM, 李智海 wrote: >> >> Hi, Tom >> An another question, >> I want to make a reference map for reconstruction, here I have a map but with different map size from my raw image, how can I scale the map dimensions into a specific value without changing the centre coordinates. >> Thanks! >> >> Zhihai Li >> >> >>> On Jun 24, 2015, at 2:00 AM, Tom Goddard wrote: >>> >>> If you used the Chimera Segment Map dialog (volume dialog menu Tools / Segment Map) then you select a segment (ctrl click on it) and use Segment Map menu entry Regions / Mean and SD. If you segmented the map by some other means and have the pieces as separate maps use volume dialog menu Tools / Measure Mean, SD, RMS. >>> >>> Tom >>> >>> >>>> On Jun 23, 2015, at 6:42 AM, 李智海 wrote: >>>> >>>> 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. >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >> >

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PDB not opening
by YAikhombA Mutum 24 Jun '15

24 Jun '15

Hi 1. I'm not able to fetch pdb's from Chimera by the command 'open 121p'. It just says 'opened 121p' in the reply log while it display a blank black screen. There are no active models displayed too (in the active models panel, there are no active tabs for models (0,1,2...)) despite the status in the reply log. The internet connections are ok (my browser is working fine). On checking the preferences (Favorites ---> preferences), everything seems fine (for instance in Category: Fetch (save fetched flie: True and use local files:True/False (I've tried both cases))). Even the category of web access seems ok. A day before I'd been able to fetch pdb's by just the command (open 1zik (say)). Now, the only way to retrieve it is to go to the rcsb website, download the pdb from a browser and then run it in chimera. Moreover, even if it (the pdb file) is already downloaded it doesn't run by entering the command (again the preferences are fine). How can I sort out this? 2. Is there a way to color the capped surface (the flat surface when you cut a protein virtually) based on sequence conservation color range. I tried the same way B factor surface capping is done as in the tutorials but the one for conservation doesn't work. It instead colors the 'whole' surface something else (Automatically uses default 'color by heteroatom' (red, tan and blue) not the colors I used for the sequence conservation). The same when I try to cap a surface based on hydrophobicity. Thanks in advance! Yaikhomba

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Issue with cytoscape plugin
by Juan Eiros Zamora 23 Jun '15

23 Jun '15

Hi Chimera users, I'm using cytoscape and structureviz to visualize interaction networks of my MD simulations. I've been using it for quite awhile now on the normal structure of my protein. Now I am simulating it with two adjacent phosphorylated serines (all is done with AMBER), and I think there are some issues with this because: 1) If I select a region of the protein that does not contain this "special" aminoacids, the RIN visualization works just fine 2) When I select the region that contains these two phosphorylated Serines (about +-10 aminoacids from them), when the RIN is set up on cytoscape I get the following error: RINLayout Fetching coordinates from Chimera... null Which is pretty generic. What is more confusing is that if I select all the system (which is not interesting for me, but I've done it anyway to try) it seems to work as well. My cytoscape version is 3.2.0 and all the apps in it are up to date: structureViz2 1.0.1 RINalyzer 2.0.0 I think the RIN is being calculated just fine, but it's having problems recognising the 3D shape in Chimera. Also, it fails to synchronize the colours, I don't know if this is related to what I'm reporting here, but I suspect it is. Does anyone know how can I proceed? It would be very useful for me to compare the RINS of the non-phosphorylated version of my system to the phosphorylated version. Thanks for any help, Juan Eiros

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ViewDock
by leila karami 23 Jun '15

23 Jun '15

Dear chimera users I have docking outputs from Swissdock (there is 252 binding modes for my ligand relative to the target protein). I used following to view my outputs: 1) File > Open , then load target.pdb 2) Tools > Surface/Binding Analysis > ViewDock, choose clusters.dock4.pdb (Dock 4, 5 or 6 format) Now, I want to have several pdb files in which there is target protein and each of binding modes, that is 252 pdb files. How to do this? Any help will highly appreciated.

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Chimera-users June 2015