October 2009 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Grouping models
by Tom Goddard 23 Dec '09

23 Dec '09

-------- Original Message -------- From: Thomas C. Marlovits To: Tom Goddard Date: 9/22/09 2:04 AM > HI Tom, > > I was wondering, whether one can "group" a few models in chimera. At > the moment, I have more than 40 models open simultaneously, some of > which I would like to group in order to make coloring, selection, etc > ... more easily. It might be that the feature is present, but > couldn't spot it so far. > The other thing that I would appreciate, if there is a simple way to > assign the model nr manually (at the moment it is done automatically, > and it appears that the order is somewhat random ...) > Best, > Tx, > -T. > Hi Thomas, You can used "named selections" to give a short name to several models or to any combination of selected items. Use menu entry Select / Name Selection... You can use the names in Chimera commands or use the "Select / Named Selection / name" menu entry. I don't know of a command to name a selection. Is there such a command (other Chimera developers)? You can set the model number if you open your models with a command, for example, open 5 twisty.pdb to open a model as model number 5. After the model number has been assigned it unfortunately cannot be changed. Tom

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how to create surface from volume tracer path
by jinghua＠ucsd.edu 16 Dec '09

16 Dec '09

When I try to create a tube by tracing two planes, the surface it makes is more like a cone. Do I need connect all the markers from two different planes? Thank you for your help! Jinghua

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File conversion question
by Miriam Gochin 12 Dec '09

12 Dec '09

I have a series of docked ligands produced by AutoDock (as .dlg files, containing more than one conformer per ligand) and I would love to be able to view these ligands using the ViewDock utility in Chimera. Is there a file conversion protocol? Thanks so much, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

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classifying contact interactions
by M. Shahid 31 Oct '09

31 Oct '09

Dear All, I have a question regarding the contact interactions between a protein-ligand complex. I can retrieve the contacts by the findclash command in --nogui mode as below: chimera --nogui protligcomplex.pdb clash.com and similarly I can find the hbonds. The output I am getting is as below: -------------------------------------------------------------------------------- 32 contacts atom1 atom2 overlap distance LIG 1 H ALA 265.A O 1.045 1.435 LIG 1 O ALA 265.A O 0.550 2.430 LIG 1 N GLU 169.A OE2 0.439 2.666 LIG 1 H GLU 169.A CD 0.116 2.584 LIG 1 O ASN 253.A 1HD2 0.094 2.386 LIG 1 H ALA 265.A C 0.090 2.610 LIG 1 C ALA 265.A O 0.059 3.121 LIG 1 N ASN 253.A OD1 -0.037 3.142 LIG 1 C ALA 265.A O -0.039 3.219 LIG 1 N GLU 169.A HG3 -0.072 2.697 LIG 1 C PHE 168.A HB2 -0.081 2.781 LIG 1 N GLU 169.A CG -0.113 3.438 LIG 1 N GLU 169.A CD -0.125 3.450 LIG 1 N GLU 169.A CD -0.128 3.453 LIG 1 C MET 270.A HG2 -0.140 2.840 LIG 1 N PHE 168.A CD2 -0.163 3.488 .......... .... ... .. . -------------------------------------------------------------------------------- Now I want to further classify these contact interactions into more other types: Aromatic and Ionic (anion < - > cation). Is there any way in Chimera to achieve this? Or if I want to do it with some scripting, which atoms I would say are involved in ionic and aromatic interactions considering the distance value as well? I would be very much grateful if someone suggest me a way to do this. Thanks, Best regards, -- Shahid.

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Help Installing Chimera
by Muhammad Ahmad Chaudary 30 Oct '09

30 Oct '09

Hi, I am trying to install chimera on Fedora 11 and i am running into problems. After config i tried running make and got the following error. #first i got the error evp.h not found Even though yum said openssl was installed. Anyway i downloaded openssl and tried to install it manually. But i still got the same error. So then i copied the openssl header files folder to /usr/include This got me past this error. #Next i got this error gcc -g -O2 -o sha1_keygen sha1_keygen.o -L/home/ahmad/chimera/src -lchimera -lpthread -lcrypto /usr/bin/ld: cannot find -lcrypto collect2: ld returned 1 exit status make[1]: *** [sha1_keygen] Error 1 I just installed openssl with the default options. Any ideas what i am doing wrong here! Ahmad

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binning large volumes
by Lori Nyland 28 Oct '09

28 Oct '09

Hello, I have two volumes with the same dimensions and each are nearly 2GB. I can use the vop resample command in a 64 bit Chimera for Linux and reassign one volumes coordinates relative to the other. However, it is slow to execute, but it does work. In order to speed things up is there a way to bin the volumes (to use less space), place it through the vop resample command, and then un-bin the volume without losing information? Thanks! Lori

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script for
by lorenzo 28 Oct '09

28 Oct '09

Dear all, I'm trying to write a script to interpolate between two structures and save the intermediate conformations as pdb files. I need a script since I have to repeat this procedure several times. As far as importing the structures and interpolating is concerned I have no problem: open A.pdb open B.pdb morph start #0 morph interpolate #1 frames 6 (I need 5 intermediates) What I don't manage to figure out is how to save the intermediate configurations. Figuring out that morph interpolate was generating a trajectory stored as the model #2 I tried write format pdb trajectory #2 out.pdb but it didn't write anything I also unsuccessfully tried with perframe write format pdb out.pdb but I still got no output. Does anybody have any suggestion? Regards Lorenzo Bongini

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problems display a mrc or ccp4 file
by maillist＠dejung.net 27 Oct '09

27 Oct '09

Hi all, I have problems diplaying a 3D map in chimera. I recognized this problems with .mrc and .ccp4 maps. And only at my system. When I load a map, I get an image like this: http://download.dejung.net/chimera.png My version of chimera is: $ chimera --version chimera snapshot version 1.4 (build 28596) 2009-08-20 19:46:50 GMT I tried also other versions (chimera alpha version 1.3 (build 2577)) but they will not start at all. Tell me there is a segmentation fault at the beginning without any molecule, map or other things. Just exits directly at start up. Friends of mine told me, it will be maybe the wrong graphic driver, but I all ready tried different ones. At the Moment I use nvidia drivers 185.18.14 on a Linux 64 bit system. I have no idea now, so hope someone can help me at this point... Best regards! Mario

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Chimera-users October 2009