- Chimera-users - RBVI Mailing Lists

Virus Capsid Reconstruction--Slow Performance
by Carlos Lopez 28 May '10

28 May '10

Hello, I am currently trying to make a pseudo-atomic resolution model of a virus capsid, but I've run into memory problems whenever I try to combine all the asymmetric units together into one large PDB file composed of 60 copies of the asymmetric unit arranged using icosahedral symmetry. My problem is that I keep running out of memory, and I was wondering whether this is normal for the dataset I'm working on. The method I use has worked fine for smaller models, so I'm sure I'm running into the memory problems because this model is particularly large, but I still wanted to check with you guys to see what else I could try. I first start out with an asymmetric unit composed of 52 copies of protein gp24 (PDB ID: 1YUE [monomer] and 1Z1U [hexamer]). That is, I use 8 hexamers and 4 monomers. The individual chains in the unit are stripped to their alpha-carbon backbone by removing all their residues (including the solvent) to minimize how much memory they take up. The monomer weights 47.274 kDa (with residues), so that gives about 22,347 total residues for the asymmetric unit. After stripping off everything except the backbone, I ended up with a 6.4 MB PDB file. After positioning the model, I then run the command sym #1 group i,222r. This creates the 59 other copies in the expected locations. The problem arises when I try to combine all the units together into one model. Having all the models open takes up about 10 GB (out of my machines 16 GB) worth of memory, though there is still some inactive and free memory left. When I then use the copy/combine command, the memory required rises steadily until it starts to page out to the swap space and bring the machine to a grinding halt. I tried leaving it to run overnight (+18 hours), but even then it still wasn't finished. To recap: I'm trying to do a memory intensive reconstruction. I've already: 1) closed all the other models I'm not working on 2) closed all other programs on the machine 3) removed all the side chains so I'm only working with the alpha-carbon backbone 4) tried the chimera --nogui option to send the commands without having to render the graphics It's still having issues, so I was wondering if you had any additional ways I can cut down on the memory usage enough to combine the units into one map. Here are some of the things I'm still thinking of checking on: 1) Running the job on a computer with no graphics card but more RAM than my desktop station. I am able to SSH to the machine and send instructions through the console and the chimera --nogui option. Is it a problem that it doesn't have a graphics card? 2) Checking for a memory leak in Chimera--I've noticed that sometimes not all the memory is given back when I manually close models in the model panel. How can I check for sure/fix it from within a session? I've been able to deal with this by closing my session and opening it again, but it'd be best to be able to do it from within a session. 3) My system keeps saying I still have 4 GB of inactive RAM, though it's never used. I don't know if this is an issue with Chimera or with my machine, but I'll try to find out. If you need any more info, please let me know. Thank you for your help! ~Carlos Lopez My system specs: Mac Pro 4,1 Mac OS X 10.6.3 Quad-Core Intel Xeon, 2.66 GHz 1 proc, 4 cores 16 GB memory Graphics Card NVIDIA GeForce GTX 285, VRAM total: 1024 MB Chimera: Alpha version 1.5 build 30286 2010-03-23 platform: darwin 64bit, windowing system: aqua

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a simple question
by Amitoj Chopra 27 May '10

27 May '10

Is there any way to use the R script and bio3d package to open a pdb with Chimera using R? Thank you. Amitoj

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locking docking
by Alex Perálvarez Marín 27 May '10

27 May '10

Dear all, after running a Docking, I want to build a covalent bond between the receptor and the ligand and then run MD simulations. Is it done with the "build structure" menu? There is another way of doing it? Probably this has been discussed earlier, can you direct me to that topic? Thanks a lot! Alex

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creating virus capsid
by Elaine Meng 27 May '10

27 May '10

On May 25, 2010, at 10:39 PM, 江一波 wrote: > hello meng! > how can i construct a virus by chimera? > i have get a nucleocapsid protein about a virus from > http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtosh… > such as ,i get ID :2I9F structure...one of a nucleocapsid for a virus ...this is symmetrical structure! > i want construct a virus ...how can i do? is there somethings paper about how to construct ? > thank you!!! Sometimes the PDB file will include matrix information needed to build the capsid. If it does, you can use the Chimera tool "Multiscale Models" to show the whole thing. However, the authors of this structure (2I9F) did not include the necessary information in the PDB file. Next I tried to see if that structure is in VIPERdb, which would also allow showing the whole thing in Chimera. However, when I tried "File... Fetch by ID" and entered 2i9f for the VIPERdb database, it was not found. Sorry, I don't have any ideas about how to make a whole capsid from this structure. A different structure that does include the information is 1POV. If you open that one, then start Multiscale Models (under Tools... Higher-Order Structure) and click the "Make models" button near the bottom, it will show the whole capsid. Please send Chimera questions to the chimera-users(a)cgl.ucsf.edu address. Thanks, Elaine ------------------------------ Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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translation of proteins with added pseudobonds
by Joern Lenz 26 May '10

26 May '10

Dear all, here is my problem: I have a protein and added pseudobonds that make up a triangle in order to highlight a pharmacophore. However, as soon as I loaded in the pseudobonds and translate my protein afterwards, the triangle made of pseudobonds does not do the same translation but kept being at its original position. Is this a bug or am I doing something wrong ? Any answer is much appreaciated. Cheers, Joern

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problems reading .rec file
by Shawkey,Matthew D 25 May '10

25 May '10

Hi, I have a .rec density map 2000x2000x1000 (xyz) but when i open it in Chimera it only shows the first image of the series (i.e. the dimensions are 2000x2000x1). do i need to convert it to a different format? thanks Matt ***************************** Matthew D. Shawkey, Ph.D. Assistant Professor Department of Biology Integrated Bioscience Program University of Akron Akron, OH 44325-3908 (office) +1 330-972-8192 (lab) +1 330-526-3225 http://gozips.uakron.edu/~shawkey

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measure rotation rod
by le monk 25 May '10

25 May '10

Hi all, I have used measure rotation to draw a rod down an axis of symmetry. Does anyone know a way of altering the diameter, length and color of the rod? Many thanks _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now

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prmtop
by richardbonnet 24 May '10

24 May '10

Dear, Is there a way to use writeprmtop with the command line? Is it a way to use chimera to write prmtop amd inpcrd files for a ligand (gaff type + am1-bcc charge) + the corresponding protein (Gasteiger charges + ff99sb) with the command line? I have lot of problems with input format for antechmaber. It can intersting to use chimera with the command line to solve this type of stuff. Thank a lot per avance, Richard Bonnet

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Amino acid substitution with Chimera
by Hayeon Kwak 20 May '10

20 May '10

Hi, I am currently working on a homology-modelled protein. How do I mutate a certain amino acid with Chimera? For example, if I wanted to mutate 55N into 55K to look at how the structure changes, what would I do? Any help would be appreciated. Thank you.

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Re: [Chimera-users] weighted distance
by Greg Couch 19 May '10

19 May '10

On 05/19/2010 02:07 PM, Eric Pettersen wrote: > Hi Bala, > > On May 18, 2010, at 2:04 AM, Bala subramanian wrote: > >> 1) When i type help(object) in chimera's python shell, it shows the >> help message, is there any to way to make the help information to be >> displayed in a separate window. I tried in config setting but i >> couldnt make it. > > I don't know of any way to make help() output go elsewhere. > Here's a technique to bring up the help() documention in your web brower: (1) start the IDLE tool in chimera (2) type into the IDLE dialog: import pydoc pydoc.gui() At that point, pydoc brings up a dialog where it says it started up a web server on your computer and you can "open browser" to browse all of the builtin chimera and Python documentation. There are a couple downsides: (1) chimera becomes unresponsive until you press the "quit serving" button and then chimera exits -- so browse the documentation with one chimera and program in another, (2) pydoc fails for some chimera modules, e.g., the important chimera module -- that's a pydoc bug unfortunately. - Greg

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