- Chimera-users - RBVI Mailing Lists

residue label
by Bala subramanian 17 Nov '09

17 Nov '09

Friends, I would like to know how to use our own strings with 3D label. suppose if i give 'rlabel :3', residue 3 is labelled as LEU 3. But i want to pass a string that should replace LEU 3. Hope i am clear. I know 2D label can use a string but i wish to use string especially with 3D label. Thanks, Bala

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suggestion/stereo
by Dougherty, Matthew T. 16 Nov '09

16 Nov '09

I am finding that getting the optimal stereo view requires ongoing adjustment of the stereo parameters, particularly when multiple people are observing the structure simultaneously (e.g., depthQ stereo projector). Currently these numbers have to be typed in, requiring me to break my gaze, move a mouse, and type a number. Ideally it would good to have controls similar to binoculars, such that you maintain constant view and adjust by turning knobs. Getting hardware knobs may be impractical, but these improvements could help. 1) two small buttons (+/-) next to each stereo parameter. 2) commands that would do the same (small incremental changes). Then I could have my nostromo n52 USB game box dedicate the dual axis thumb button for stereo adjustment by issuing keyboard commands. Thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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help with raytrace
by Corey Fugate 16 Nov '09

16 Nov '09

I am trying to improve image quality using the raytrace option. The script is below - reset view_1 movie record directory /Users/fugate/Desktop pattern partA_* fformat png raytrace true wait 15 delete :.B move x 1.25 15;wait wait 15 movie stop Everything works fine without "raytrace true". I should note that I do not have the movie encode command because I want to have the individual images ( for a larger Flash project). When I compare the raytrace true images produced from the script to an image generated using the "save image" option under the File menu setting "raytrace with POV" to true. Am I missing something? Corey

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Apply rotation with precision
by Damien Larivière 15 Nov '09

15 Nov '09

Dear Chimera team, Once two pdb structures are opened, the command measure rot #1 #0 give the orientation of one structure with respect to the other one under the form of: Position of 1Wxx_chB1.pdb (#0) relative to 1Wxx_chB1.pdb (#1) coordinates: Matrix rotation and translation 0.99727151 0.01713873 0.07180395 46.50921950 -0.01715871 0.99985272 -0.00033862 3.66357812 -0.07179918 -0.00089436 0.99741871 15.01300748 Axis -0.00376406 0.97263698 -0.23229967 Axis point 231.74603365 0.00000000 -638.91369622 Rotation angle (degrees) 4.23351417 Shift along axis -0.09924878 Let's suppose that I want to decrease the rotation angle from 4.233° to 0.5°: I can use "Movement" and select the model to be rotated in order to do that with the mouse but I will not be accurate. Is there way to do such rotation with precision? Thank for your help Damien

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Re: [Chimera-users] help with raytrace
by Corey Fugate 13 Nov '09

13 Nov '09

Doh! Sorry lack of sleep results in incomplete sentences. The raytrace option in the script looks exactly like the chimera window quality and nothing like an image made using raytrace. Corey On Nov 13, 2009, at 4:12 PM, Thomas Goddard wrote: > You didn't say what was wrong with the raytraced image. So we are > missing something. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] help with raytrace > From: Corey Fugate <fugate(a)hawaii.edu> > To: chimera-users(a)cgl.ucsf.edu > Date: 11/13/09 1:12 PM > >> I am trying to improve image quality using the raytrace option. >> The script is below - >> reset view_1 >> movie record directory /Users/fugate/Desktop pattern partA_* >> fformat png raytrace true >> wait 15 >> delete :.B >> move x 1.25 15;wait >> wait 15 >> movie stop >> Everything works fine without "raytrace true". I should note that >> I do not have the movie encode command because I want to have the >> individual images ( for a larger Flash project). When I compare >> the raytrace true images produced from the script to an image >> generated using the "save image" option under the File menu setting >> "raytrace with POV" to true. >> Am I missing something? >> Corey >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [Chimera-users] Fields in dms format
by Elaine Meng 12 Nov '09

12 Nov '09

No -- that would overcount the area, because it would overlap for neighboring dots. The area is an *estimate* for the piece of surface around the dot that is not assigned to any other dot. If you added up the areas for all the dots for one atom, it would *approximately* equal the surface area for that atom. However, to get the total area for an atom, residue, etc., don't do that -- just use the already existing areaSES (and areaSAS) attributes of atoms and residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces > Elaine On Nov 12, 2009, at 10:34 AM, Yasser Almeida Hernández wrote: > Thanks for your help... > About the estimated surface area in the 8th field, i view this > number as the area enclosed by the neighboring dots, where the > guessing dot is the center of a square formed by this dots. What do > you think about that? > > *-----* > | | > | * | > | <-|-- Area > *-----* >

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Fields in dms format
by Yasser Almeida Hernández 12 Nov '09

12 Nov '09

Hi all... In the .dms format: 1 - What's the meaning of the digit (allways 0) after the SR (or SC, SC)? 2 - What's the meaning of the number in the 8th field? I've read the help of this format, but i don't understand the meaning of these numbers Thanks... -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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nmrclust: linux terminal
by Austin B. Yongye 12 Nov '09

12 Nov '09

Hi everyone, I am trying to use nmrclust to cluster a set of about 5K conformers with the chimera gui. It is been ~5hrs now, and still running. I was wondering whether the algorithm can be run via the linux terminal. I found this posting: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003195.html Could some one please let me know how to use this python code to run the clustering in the linux terminal invoking the python environment? Thanks, Austin-

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Select / Structure / secondary structure / turn broken
by Tom Goddard 12 Nov '09

12 Nov '09

Hi Haixin, I suspect "turn" doesn't just mean not helix and not sheet but I don't know. Others in my lab will know so I've forwarded your question to the Chimera mailing list so they can answer. If you want to select all residues that are neither helix nor sheet you can use the command: select ~ :/isHelix :/isSheet Tom -------- Original Message -------- From: Haixin Sui To: 'Thomas Goddard' Date: 11/6/09 2:27 PM > Tom, > > How have you been? > > This email is to report a small bug I experienced. The "select"-> > "structure"->"secondary structure" -> "turn" function is not working. It > worked for selection of "helix" and "strand". Selection of "turn" is the > only one does not work. I am using chimera alpha version 1.3( build 2577) > 2008/12/09 00:54:36 on a laptop PC running Windows XP. > > While I have a lot of different molecules aligned in a map, this selection > function is very useful for me. Any suggestion? > > Best regards from > > Haixin > > -- > Haixin Sui > Research Scientist IV > Wadsworth Center > Empire State Plaza > P.O. Box 509 > Albany, NY 12201-0509 > > Assistant Professor > SUNY-Albany > School of Public Health > Department of Biomedical Sciences >

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coarse-grained MD
by Francesco Pietra 11 Nov '09

11 Nov '09

I know that questions about coarse-grained MD wit amber have already been raised. However, I wonder whether any plan is going on - if feasible at all - to implement in the ambertools something like the cg builder of vmd. Or ask chimera software if a conjoint effort may allow us amber users to approach cd md "at home", benefitting of the amber's secure code. thanks francesco pietra

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Re: [Chimera-users] Coloring range for residues
by Eric Pettersen 10 Nov '09

10 Nov '09

Hi Ibrahim, I'm glad it helped. I've opened a Trac ticket for your request for restricted rainbow coloring, so you'll get a notification when it gets implemented. It could be quite some time before I get to it, though if others request it also it could happen sooner. --Eric On Nov 9, 2009, at 8:28 PM, Ibrahim Moustafa wrote: > Hi Eric, > > Thank you very much, as usual, I got the help I expected from > chimera team. > > Actually, the conformational change for the structure I have is > dramatic and involves wide range of residues. It is really painful > for the eye to follow the structural change for a certain element. > Coloring the residues in few colors did the job; however, the > rainbow coloring using the script you sent did a much better job. > It would be useful if this command can be added to the chimera!. > > Many thanks, > Ibrahim > > -------------------------------------------------------------------------------------------------------------------------- > Ibrahim M. Moustafa, Ph.D. > Biochemistry and Molecular Biology Dept. > 201 Althouse Lab., University Park > Pennsylvania State University > PA 16802 > > Tel. (814) 863-8703 > Fax (814) 865-7927 > > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Monday, November 09, 2009 7:29 PM > To: Ibrahim Moustafa > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Coloring range for residues > > Hi Ibrahim, > I'm not 100% sure why you want to rainbow the > highlighted part of your structure, rather than use a single color, > or color the rest of the structure dark gray, or make the rest of > the structure semi-transparent, or many other possible highlighting > schemes. > Anyway, there's no way to do it without resorting to > (simple) Python. Put the following in a file that ends in ".py": > > import chimera > residues = chimera.selection.currentResidues() > residues.sort() > for i, r in enumerate(residues): > r.highlightNum = i+1 > > Then select the residues you want highlighted in > Chimera. Run the Python script by opening it with the "open" > command or with the File->Open dialog. Then run this Chimera command: > > rangecolor highlightNum,r min blue mid white max red sel > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Nov 9, 2009, at 11:14 AM, Ibrahim Moustafa wrote: > > > Dear Chimera team, > > I wonder if there is a way to color a certain range of residues > using rainbow. > I tried to use the rainbow command with atom_spec but it applied for > the whole chain. > > What I want to do is to color part of the structure as a rainbow > (from blue-white-red) with an increasing order of residues number. > I just wanted to highlight a region of conformational change so the > eye can follow which part of the structure has changed dramatically. > > > Thanks in advance for your help. > > Ibrahim > > -- > Ibrahim M. Moustafa, Ph.D. > Biochemistry and Molecular Biology Dept. > 201 Althouse Lab., University Park, > Pennsylvania State University > PA 16802 > > Tel. (814) 863-8703 > Fax (814) 865-7927 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Re: [Chimera-users] Coloring range for residues
by Elaine Meng 10 Nov '09

10 Nov '09

Hi Ibrahim, Just thought I would mention that there are some other interesting ways to show conformational changes or conformational variability in a single picture. Some images are attached at the bottom. You can assign attributes to residues, and then show those attribute values on one or more structures with color and/or "worms". If two or more structures are associated with an alignment and you show the alignment "RMSD" header, that automatically creates the residue attribute named mavRMSD, where the values are the alpha-carbon RMSDs for residues in the same column of the alignment. If you only have two structures it boils down to the CA-CA distance between the two residues in each column of the alignment. You are probably thinking "but I don't have an alignment!" -- however, in Chimera it is easy to make one. If you have > 2 structures already superimposed, you can use Match->Align (under Tools... Structure Comparison) to create and display the sequence alignment. If you have 2 structures, you can use MatchMaker to both create the pairwise sequence alignment and superimpose the structures. Here is an example with a G protein in the "on" and "off" conformations, using the command version of MatchMaker: open 1tad open 1tnd del ~ :.a mm #0 #1 show true That will create the pairwise sequence alignment with RMSD header shown. Then in the alignment window, choosing "Structure... Render by Conservation" brings up the dialog for mapping colors and/or worm fatness onto the structures. In that dialog, change the attribute from "mavConservation" to "mavRMSD" to see the histogram of values. Then use the Colors or Worms section in the dialog to map the values. You can do it for either or both structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html… > I attached images for the example above, where mavRMSD is shown with: (a) worms for both structures (b) color on one structure (c) both color and worms on one structure You could also do the coloring with command "rangecolor" instead of with the dialog <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> The example uses two conformations of the same protein, but it will also work with different proteins along as they are similar enough for Matchmaker to create a good alignment. Or instead of using an alignment, you can create your own attribute in a text file and then use "rangecolor" or the "Render by Attribute" tool (under Tools... Depiction), actually the same dialog used above for showing mavRMSD, to show your custom attribute on the structure. There is a description of the file format <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > and example files <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Probably more information than you wanted 8-) 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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Re: [Chimera-users] External SAS calculation
by Yasser Almeida Hernández 10 Nov '09

10 Nov '09

It would be nice that Chimera also compute and save the SAS (like a grid), since there're a few softwares to do this task spacifically. I hope this will avaible in the future... Anywere, thanks a lot for your helps -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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Re: [Chimera-users] problem with surface representation
by Miriam Gochin 10 Nov '09

10 Nov '09

Outstanding! That worked perfectly! Thank you so much, Tom. Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463 ________________________________________ From: Tom Goddard [goddard(a)cgl.ucsf.edu] Sent: Monday, November 09, 2009 10:07 PM To: Miriam Gochin Subject: Re: [Chimera-users] problem with surface representation Hi Miriam, I think the cusps (two points) are just parts of the surface. The surface is obtained by rolling a sphere of a 1.4A radius over the molecule and the surface is all points reached by that rolling sphere. The cusps happen because that sphere does not fit between the residue 36 and 104 HE2 atoms. If you reduce the probe radius to 1.2 A then you get rid of the cusp but the surface is slightly different. You would change probe radius in the same dialog where you changed vertex density. Tom -------- Original Message -------- Subject: Re: [Chimera-users] problem with surface representation From: Miriam Gochin <miriam.gochin(a)tu.edu> To: Tom Goddard <goddard(a)cgl.ucsf.edu> Date: 11/9/09 9:31 PM > Hi Tom, > > Thanks for the suggestions. That does improve things a bit, but not completely. Maybe I just have bad geometry at that position? I attach the pdb file. The residues involved are #36 and #104, if you have time to take a look at it. > > Best, > > Miriam > Touro University - CA > miriam.gochin(a)tu.edu > 707-638-5463 > ________________________________________ > From: Tom Goddard [goddard(a)cgl.ucsf.edu] > Sent: Monday, November 09, 2009 8:50 PM > To: Miriam Gochin > Cc: Chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] problem with surface representation > > Hi Miriam, > > I guess the surface is being divided into two few triangles. You can > increase the number of triangles by increasing the "vertex density" > parameter. To do this, select the surface (ctrl-click it), use > inspection selector (menu Actions / Inspect), set the "Inspect" menu in > the inspector dialog to MSMS Surface, increase the "vertex density" > parameter, say from 2 to 5, and press the Enter key after typing in the > new number. That should give a smoother surface. > > Another step that can improve the lighting of the surface is to enable > glossy lighting in the Lighting panel. Menu Tools / Viewing Controls / > Lighting, quality -> glossy. Some old graphics cards don't support this. > > Tom > > -------- Original Message -------- > Subject: [Chimera-users] problem with surface representation > From: Miriam Gochin > To: Chimera-users > Date: 11/9/09 8:07 PM > >> I am having trouble with some pointed edges to my surface (attached). It only happens in one location - everywhere else the surface is smooth. I appreciate any suggestions. >> >> Thanks, >> Miriam Gochin >> Touro University - CA >> miriam.gochin(a)tu.edu >> >> > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Re: [Chimera-users] External SAS calculation
by Yasser Almeida Hernández 10 Nov '09

10 Nov '09

Hi Tom... I'm actually interested in compute and save the accesible surface as a grid (like DMS). If Chimera doesn't compute the SAS surface (with MSMS code), why it ask for the probe radius in Favorites > Preferences > New Surfaces? Thanks -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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problem with surface representation
by Miriam Gochin 09 Nov '09

09 Nov '09

I am having trouble with some pointed edges to my surface (attached). It only happens in one location - everywhere else the surface is smooth. I appreciate any suggestions. Thanks, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Coloring range for residues
by Ibrahim Moustafa 09 Nov '09

09 Nov '09

Dear Chimera team, I wonder if there is a way to color a certain range of residues using rainbow. I tried to use the rainbow command with atom_spec but it applied for the whole chain. What I want to do is to color part of the structure as a rainbow (from blue-white-red) with an increasing order of residues number. I just wanted to highlight a region of conformational change so the eye can follow which part of the structure has changed dramatically. Thanks in advance for your help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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External SAS calculation
by Yasser Almeida Hernández 09 Nov '09

09 Nov '09

Hi all.. In the Chimera source where is located the sources files for the calculation of SAS. I'm writing a python script for calculate the SAS and i want to call the Chimera's routines to do this task... Best regards -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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access rotation and translation matrices
by Lori Nyland 05 Nov '09

05 Nov '09

Hello, I have been trying to rotate a large volume relative to a reference volume using the vop resample command. The problem is that both volumes are nearly 2GB. However, If I were to bin the volumes (by n) and had access to the rotation R(alpha, beta, gamma) and translation T(x,y,z) matrices I could perform the rotation in an alternate program via R and nT. Thanks! Lori

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How to increase h bond width
by Kshatresh Dutta Dubey 01 Nov '09

01 Nov '09

Dear Users, I want to increase the hydrogen bond width and change bond color. How can i do this ? Any help is heartily appreciated. Regards Kshatresh

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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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problem with SAXS profile
by Stefan Jehle 27 Oct '09

27 Oct '09

Hi, I have to finish very urgently a model of a big oligomer and the SAXS curve utility would be extremely helpfull for me if working properly. Here my problem: I get the following error message after pressing the "Profile" button: Wrote /var/folders/dP/dPWm0vEeFkG9xqa+tbipE++++TM/-Tmp-/tmprnvHi_.pdb Executing command: /Users/stefan/Downloads/Chimera.app/Contents/Resources/share/SAXS/ChimeraExtension.py /var/folders/dP/dPWm0vEeFkG9xqa+tbipE++++TM/-Tmp-/tmprnvHi_.pdb /Users/stefan/Documents/modelling/saxsprofile/abc30mer.dat Error 512 executing command "/Users/stefan/Downloads/Chimera.app/Contents/Resources/share/SAXS/ChimeraExtension.py /var/folders/dP/dPWm0vEeFkG9xqa+tbipE++++TM/-Tmp-/tmprnvHi_.pdb /Users/stefan/Documents/modelling/saxsprofile/abc30mer.dat" First I thought this may be because I have encrypted my cache (using MacOSX Leopard) but the same problem occurs using Win Vista or Windows XP or Windows Vista. I would appreciate your help, if you could provide me a saxs.py file working. Thanks a lot Best Regards Stefan __________________________________ Dr. Stefan Jehle Structural Biology Unit Leibniz Institute for Molecular Pharmacology, FMP Robert-Rössle-Str. 10 13125 Berlin Germany jehle(a)fmp-berlin.de Phone +49 30 94793232 Fax +49 30 94793169

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Error during PDB Fetch
by Bryan Krantz 27 Oct '09

27 Oct '09

Dear Chimera Users: Does anyone know how to resolve this bug. I tried to load a PDB file from the web using the ID 3hvd. Got this error back: Error reading 3hvd: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') I am running this Chimera : Linux 64-bitchimera-1.4-linux_x86_64.exe<https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=linux_x86_64/chimera-1…> Size: 77850528 bytes MD5: 1e05f4607699c88467e81cc249aa4ad1 My OS is Debian Lenny AMD64. Thanks in advance for your help. Yours, bryan -- Bryan Krantz University of California, Berkeley Department of Molecular & Cell Biology Department of Chemistry 476 Stanley Hall #3220 Berkeley, CA 94720-3220 Phone: (510) 666-2788 Email: bakrantz(a)berkeley.edu Lab: 492 Stanley Hall Lab phone: (510) 666-2789 URL: http://mcb.berkeley.edu/labs/krantz/

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Re: [Chimera-users] Terminating Match-align without loosing reply log
by Eric Pettersen 27 Oct '09

27 Oct '09

Hi Mario, There is no guaranteed way. On the Mac or on Linux you may be able to stop the computation by sending Chimera's Python interpreter an INT signal (terminal interrupt) [I don't know of any such option on Windows]. Open a terminal window (on Mac: /Applications/Utilities/ Terminal.app). Find Chimera's Python process via: ps augxww | grep python You'll see something along the lines of: pett 86576 98.7 13.4 1218088 562256 ?? R 11:58AM 2:17.97 /Users/pett/Applications/Chimera-daily-x11.app/Contents/ Resources/bin/python2.5 /Users/pett/Applications/Chimera-daily-x11.app/ Contents/Resources/share/__main__.py The first number (86576) is the process ID of Chimera's Python interpreter. Send it an interrupt signal by: kill -INT 86576 If all goes well, Chimera will bring up an error dialog saying something about KeyboardInterrupt. The Match->Align computation will have stopped with the structures in the same position as they were at the end of the last iteration, the last alignment window will be up, and the Reply Log will be available. On Linux, if you started Chimera yourself from the command line you may be able to just hit control-C (or whatever your interrupt character is) instead of the rigamarole above. --Eric On Oct 27, 2009, at 11:46 AM, Mario Borgnia wrote: > Hi Eric, > > Thanks for the fast response. My other question is how to terminate > the process > in progress without compromising the output of previous iterations. > Thanks!!! > > Mario > > Eric Pettersen wrote: >> Hi Mario, >> The iterations are independent. So you could iterate twice, save a >> session, and then iterate further later. You could use the 'Save' >> button on the Reply Log to save info as needed. >> >> --Eric >> >> P.S. Sorry it's slow. It's all in Python and given how complex it >> is >> it's unlikely it's going to be recoded in C++ anytime soon. >> >> >> Eric Pettersen >> >> UCSF Computer Graphics Lab >> >> http://www.cgl.ucsf.edu >> >> >> >> On Oct 27, 2009, at 7:47 AM, Mario Borgnia wrote: >> >>> Hi, >>> I launched a massive match-align procedure with five iterations >>> without knowing >>> that it would take so long to complete. Is it possible to stop it at >>> iteration 2 >>> without loosing the information computed to that point? Also, is it >>> possible to >>> continue from that point on in a subsequent round? >>> Thanks! >>> >>> Mario

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Chimera slow on Win 7 64-bit system
by Thomas Goddard 27 Oct '09

27 Oct '09

Hi Wen, The slow ribbon and atom rendering must be a graphics driver issue. Surfaces use different OpenGL calls for rendering allowing them to be fast. You can try updating your graphics driver. If you have the most recent you could try poking around with graphics driver settings that trade of speed and quality. We don't have a 64-bit Windows Chimera. Only 64-bit Linux Chimera is available. We'll probably put out a 64-bit Mac Chimera in about 6 months and 64-bit Windows Chimera in about 1 year. Tom -------- Original Message -------- Subject: chimera question From: Wen Jiang To: Tom Goddard Date: 10/15/09 7:54 PM > Hi Tom. > I recently set up a Windows 7 64bit system for Nvision stereo display > and ran into some problems with Chimera. First, the performance for > pdb molecules (ribbon and atoms) is very slow. It seems fine with > volume data (surface). Do you have any clue? Second, there is only > 32bit version for Chimera and it cannot deal with large map. Do you > have a 64bit version for Windows? > Thanks, > > Wen > > Wen Jiang, Ph.D. > Assistant Professor > Department of Biological Sciences > Lilly Hall, B-402A > Purdue University > West Lafayette, IN 47907

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Terminating Match-align without loosing reply log
by Mario Borgnia 27 Oct '09

27 Oct '09

Hi, I launched a massive match-align procedure with five iterations without knowing that it would take so long to complete. Is it possible to stop it at iteration 2 without loosing the information computed to that point? Also, is it possible to continue from that point on in a subsequent round? Thanks! Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

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[Fwd: creating more memory]
by Lori Nyland 24 Oct '09

24 Oct '09

Ooops forgot attachment. Here it is.

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problem with chimera 1.4
by lionel nauton 23 Oct '09

23 Oct '09

Hi everyone, I'm using chimera 1.4 since few days on Fedora 11 (leonidas) with a nvidia card (8600 gts), and it's working very fine. but just one problem, when we have more than one model displaying, every informations like distances, H-bond, labels, doesn't move with models during rotation or translation. this problem don't exist with just one model. best regards, ____________________________________ Mr NAUTON Lionel Ingénieur d'étude CNRS Laboratoire SEESIB UMR6504 Université Blaise Pascal Campus des Cézeaux Bâtiment Chimie 4 et Chimie 3 RDC 24 avenue des Landais 63177 AUBIERE Cedex France Tel : 0473405506 http://seesib.univ-bpclermont.fr/Nouveau_site/pages/

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creating more memory
by Lori Nyland 23 Oct '09

23 Oct '09

Hello, I have attached an image that shows the command line and the command where I am trying to save an image map of one volume relative to another. I received an error when the operation was executed. The error code is in the image. I noticed that there was an error in memory allocation (toward bottom of error script). So I think I need to allocate more memory. How do I do that? Thanks so much! Lori

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problem with chimera 1.4
by lionel nauton 23 Oct '09

23 Oct '09

thank's for your answer Victor Sure that the Action Mark is active, my problem is for the distance, label or H-bond printing, they stay fixed when the models are moving.

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trying to process 1000 proteins via Chimera
by Bisn 21 Oct '09

21 Oct '09

Hello, We are Chimera users trying to process 1000 proteins, e.g., add hydrogen and charge. We want to do this via a Chimera for DOCK preparation. I know that Chimera accepts command line, but this is not realizable for processing 10000 molecules. Have you any idea of the task? Thanks! Jian Chen

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Calculation of RMSD between 2 PDB structures automatically
by Sumitro Harjanto 21 Oct '09

21 Oct '09

Hi, I have about 150 peptide structures in PDB format. I would like to compare each of them with a Template Structure (also in PDB format) and obtain an RMSD measurement for each comparison. These peptides are similar in structures to the template but may have very low sequence similarity/conservation. So my question is: 1. what is the command I should use given this scenario..? I was quite confused with the many different commands such as: rmsd, match, ensemblematch, matchmaker,... can anyone enlighten me on the differences among them. I would like to find one which can align/superimpose 2 peptides and calculate RMSD (Ca or backbone) 2. Is there a way to automate the process through scripting..? I'm still young with CHIMERA so please pardon my ignorance. =] Cheers, Sum

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Re: [Chimera-users] using CHIMERA to measure RMSD for large number of short peptides against a template structure
by Elaine Meng 21 Oct '09

21 Oct '09

On Oct 21, 2009, at 6:45 AM, Sumitro Harjanto wrote: > > Background: > Basically I would like to compare peptide to peptide and obtain the > RMSD between the two peptides using CHIMERA. These peptides may > have different lengths (eg 9-mer vs 10-mer) and they are not > conserved at all, in fact, they can be quite different in sequence. > They however have similar structures. > > Problem: > I have a dilemma in choosing which alignment method to use. If I > use matchmaker, which is based on sequence alignment, only selected > amino acid pairs will be measured (since the peptides are not > conserved); if I use match instead, the peptides have to be of > equal length, but they are not. Is there way to get around this > dilemma..? > I need the RMSD value to be exported from CHIMERA. I understand > that CHIMERA kept a log (replylog) for each session. Is there a way > for me to extract the content of this file? Or is there any other > way to keep a record of the RMSD values (since I would need to > automate this process to calculate RMSD for many pairs of peptides. > Thanks, > Sumitro Hi Sumitro, Matchmaker does not require the sequences to be identical, but generally it is intended for homologous proteins with at least partly conserved sequences and secondary structures. If you are working with short peptides, I agree that matchmaker will probably not give the matches that you want, so "match" would be the way to go. The "match" command does not require that the overall structures have the same number of atoms, only that you tell it to use equal numbers of atoms from the two models. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> For example, model 0 could be some protein with residues 1-500 in chain A and residues 1-250 in chain B, while model 1 is your peptide that only has 10 residues. In the match command you just say exactly which atoms and residues should be used. When the residues are of different types, you would normally just use their backbone atoms instead of the whole residues, which could have different numbers of atoms. Examples: match #1:1-10@ca #0:1-10.a@ca match #1:1-10@n,ca,c,o #0:425-434.b@n,ca,c,o match #1:2-9@ca #0:4.a,6-9.a,8-10.b@ca The RMSD values will be reported in the Reply Log (under Favorites menu). You can copy the text in it and paste to a file. Or, if you are running Chimera in "nogui" mode, this information can be redirected to a file as described in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/ 003064.html> For more about scripting to process multiple structures, see previous posts such as: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003261.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003262.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

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Chimera 1.4 release candidate
by Elaine Meng 21 Oct '09

21 Oct '09

Hi everybody, Candidate builds for the Chimera 1.4 production release are now available. <http://www.cgl.ucsf.edu/chimera/download.html> As detailed in the release notes, <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html> many new features have been added since the 1.3 release. Please try the candidate and report any problems. 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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Incompatibility between --nogui and viewdock scripting ?
by Aurelien Grosdidier 20 Oct '09

20 Oct '09

Dear all, I'm trying to create a minimal chimera script that loads a PDB structure, then loads docking results (Dock format), saves the result and exits, as follows: open mystructure.pdb viewdock myresult.dock4 "Dock 4, 5 or 6" save result.py stop This works perfectly, when I launch Chimera (1.4rc 32-bits on Kubuntu 9.04 AMD64) : chimera --script mkview.com However, when I try to get rid of the display by adding the --nogui switch, chimera crashes with the following stack trace: ...Traceback (most recent call last): File "CHIMERA/share/chimeraInit.py", line 425, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1439, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 32, in func File "CHIMERA/share/Midas/midas_text.py", line 101, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 132, in _processFile File "CHIMERA/share/Midas/midas_text.py", line 64, in makeCommand File "CHIMERA/share/ViewDock/ChimeraExtension.py", line 42, in cmdViewdock File "CHIMERA/share/ViewDock/base.py", line 97, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 523, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 244, in __init__ File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI TclError: invalid command name "tix" Error while processing mkview.com: TclError: invalid command name "tix" File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI See reply log for Python traceback. Any idea / workaround ? Cheers, -- Aurélien Grosdidier Molecular Modeling Group Swiss Institute of Bioinformatics PS: I already tried Xvfb with no luck (segfault, this might be a *buntu bug, though).

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minimize without addh and without GUI
by richardbonnet 19 Oct '09

19 Oct '09

Dear users Would you give me the best way to minimize the hydrogens in ligands with chimera used without GUI and without addh? I use : chimera --nogui --nostatus ligand_1.mol2 ./script.py here is script.py : from chimera import runCommand runCommand("select @H=") runCommand("minimize freeze unselected nsteps 1000") runCommand("write format mol2 0 out.mol2") However, chimera add wrong hydrogen because of the load of addh with minimize. I have a lot of ligands to process and I can not use GUI. thank you much for your help, Richard Bonnet Universite Auvergne

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Running chimera in Intel Core 2
by Dimitrios Evangelopoulos 19 Oct '09

19 Oct '09

Hi everyone, Just a question regarding running chimera on a Intel Core 2 cpu. Do you know if it is running propeprly? I just show that you mention that Chimera uses the Intel Pentium instruction set so wondering before download it. Thanks in advance. Best regards, Dimitrios Evangelopoulos, PhD student

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chimera 1.4 and Windows 7
by Boaz Shaanan 19 Oct '09

19 Oct '09

Hi, Has the latest production release (1.4) been also tested under Windows 7 ? Does it work OK ? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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bond order
by Dan Gurnon 19 Oct '09

19 Oct '09

I was wondering if there are plans to enable the display of bond order in ball and stick mode? -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] 3D-glassen
by Dan Gurnon 16 Oct '09

16 Oct '09

Thomas, I've been using the Quadro fx 380 for a couple weeks now, and I would say that the results are marginally better than with the fx 4500. There is still some occasional flickering, and for some reason, the card has trouble resetting to the normal windows aero after I close chimera with the view set to sequential stereo. I also have occasional issues when using stereoplayer or Pymol, so it looks like Nvidia still has to work out some driver issues with their 3Dvision. On Fri, Oct 2, 2009 at 4:23 PM, Thomas Classen < Thomas.Classen(a)uni-duesseldorf.de> wrote: > Thank you for your help. > > > > > > > > --------------------------------- > > Thomas Classen, M. Sc. Biochemie > > Thomas.Classen(a)uni-duesseldorf.de > > > ------------------------------ > > *Von:* doublehelix00(a)gmail.com [mailto:doublehelix00@gmail.com] *Im > Auftrag von *Dan Gurnon > *Gesendet:* Freitag, 2. Oktober 2009 16:28 > *An:* Thomas Classen > *Cc:* chimera-users(a)cgl.ucsf.edu > *Betreff:* Re: [Chimera-users] 3D-glassen > > > > Tom, > I use the 3D vision system with Chimera. Note that in order for the > 3Dvision to work you'll either need a 100Hz or better CRT or a 3D-ready > 120Hz LCD from Samsung or Viewsonic. It won't work with standard LCDs. > You'll also need to be running Vista or Windows 7. > http://www.nvidia.com/object/3D_Vision_Requirements.html > > You're also going to want a Quadro card, not the GTX285 geforce card you > have listed below. The Geforce cards can't do sequential stereo in windowed > mode, and I'm not sure if Chimera would even allow sequential stereo even in > full screen mode with a geforce (but I haven't tested it with a geforce > card). > > In my experience, the sequential stereo with the Nvidia hardware has been > just "ok"...its nice when it works, but it hasn't always worked. I really > think my issue has been my hardware...I have a Quadro FX 4500, which is an > older (albeit expensive!) card with an onboard DIN-connector. I just found > out that its not supported by the 3D vision drivers, so thats hopefully why > I'm having occasional display problems. Here's a list of compatible quadro > cards: > > http://www.nvidia.com/object/quadro_pro_graphics_boards.html > > The nice thing about Nvidia's 3D vision is that you don't need to buy one > of the very expensive Quadro cards with stereo output through an onboard > DIN-connector (the fx 3000 series and up). In fact, I just ordered a Quadro > Fx 380 for about $125, which I hope will solve the issues I'm having with > the fx 4500. It should be here next week- I'll let you know how it goes. > > > Dan > > On Fri, Oct 2, 2009 at 4:12 AM, Thomas Classen < > Thomas.Classen(a)uni-duesseldorf.de> wrote: > > Dear colleaques; > > > > I want to use 3D-glasses of nVidia for the sequential stereo view in > chimera. Are there any experiences with that system in combination with > chimera? > > Or are there some problems with that kind of technology known? > > > > Wanted hardware > > - nVidia GF 3D Vision 3D-Glasses > > -nVidia graphicboard; GTX285 Series min. 1024MB > > > > Additional hardware: > > - Intel 2 Duo Quad Prozessor; Q9650; boxed > > - 8GB DDR2 RAM PC1066 > > > > > > Thanks for your help from germany > > Tom > > > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > ____________________________ > > Daniel Gurnon, Ph. D. > Assistant Professor of Chemistry > DePauw University > Greencastle, IN 46135 > > p: 765-658-6279 > e: danielgurnon(a)depauw.edu > -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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questions about volume tracer
by Jean-Francois Menetret 16 Oct '09

16 Oct '09

I have a few questions about *volume tracer*: Is it possible to add marker(s) in an existing marker set ? Is it possible to change the marker note of an existing markers ?

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Re: [Chimera-users] Hydrodynamic radius
by Tom Goddard 14 Oct '09

14 Oct '09

Hi Sudheer, I don't know if the theoretical hydrodynamic radius Rhyd defined on the wikipedia page http://en.wikipedia.org/wiki/Hydrodynamic_radius is a good approximation to the Stokes' radius. The Stokes' radius depends on both shape and hydration details. I've added a request for this calculation in Chimera to our feature request page (item 220). http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests This is much more specialized than typical Chimera features and I would not expect it to be implemented any time soon. If you wished to implement it I could probably show you how to get out of Chimera a list of grid points within a displayed contour level that would be the input to the calculation. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Hydrodynamic radius From: Sudheer To: goddard(a)cgl.ucsf.edu Date: 10/14/09 2:03 PM > Hi Tom, > > Im interested in the optical properties of a protein. Yes, "the > hydrodynamic radius for a uniform solid bounded by a contour surface > of your map would be useful". Yes, Stocks radius. Actually I'm running > Dynamic light Scattering experiment to find the variation in the size > distribution of a protein with change in Temperature. (I mean im > trying to find at what temperature the protein forms monomer and > dimer...!) I already have Cryo-EM map of the dimer and so just thought > of comparing the Hydrodynamic radius between the cryo-map and the DLS > result. > > I hope you got my interest in finding the Hydrodynamic radius of my > protein. > > Thank you very much for your help, > Sudheer. > > > Date: Wed, 14 Oct 2009 13:54:03 -0700 > > From: goddard > > To: Sudheer > > CC: chimera-users(a)cgl.ucsf.edu > > Subject: Re: [Chimera-users] Hydrodynamic radius > > > > Hi Sudheer, > > > > Chimera isn't able to compute hydrodynamic radius of maps or > > molecules. Are you primarily interested in diffusion properties or > > optical properties of your structure? Do you think the hydrodynamic > > radius for a uniform solid bounded by a contour surface of your map > > would be useful? Do you mean Stokes' radius or the R_H defined on the > > wikipedia page? > > > > http://en.wikipedia.org/wiki/Hydrodynamic_radius > > > > The latter looks like a pretty simple calculation. > > > > Tom > > > > -------- Original Message -------- > > Subject: [Chimera-users] Hydrodynamic radius > > From: Sudheer > > To: chimera users > > Date: 10/14/09 1:05 PM > > > Hi, > > > > > > Can I measure the Hydrodynamic radius a Cryo-EM density map using > Chimera? > > > > > > Thank you, > > > Sudheer Molugu. > > > > ------------------------------------------------------------------------

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Hydrodynamic radius
by skmolugu＠miners.utep.edu 14 Oct '09

14 Oct '09

Hi, Can I measure the Hydrodynamic radius a Cryo-EM density map using Chimera? Thank you, Sudheer Molugu.

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Running Chimera on Ubuntu
by Claudio Saracini 12 Oct '09

12 Oct '09

Hello, I installed Chimera on my MacBook Pro with Unix OS (Ubuntu). When I try to run the program from the bash I get: Bash: Chimera: Command not found I'm a newbie of Linux. I guess I forgot to do something after having installed Chimera. I would appreciate your help. Claudio *************************************************** Claudio Saracini Kenneth D. Karlin Research Group Department of Chemistry The Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218 E-Mail: claudio.saracini(a)jhu.edu Group Website: http://www.jhu.edu/~chem/karlin/ ****************************************************

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Protein secondary structure
by Beale, John 08 Oct '09

08 Oct '09

I realize that this is probably simple, but I haven't been able to work this problem out. Is there a way to read a single pdb file into Chimera and then have the program show me what amino acid sequences of the protein are alpha helices, what are beta sheets, and what are 3,10 helices, etc? Thanks! John John M. Beale, Ph,D, Associate Professor of Medicinal Chemistry St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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Pseudobonds
by David Chenoweth 08 Oct '09

08 Oct '09

Hi, I am trying to delete/hide a single pseudobond in a group of pseudobonds. Can anyone tell me how to do this, or to specify a set of new pseudobonds which doesn't include the one I would like to remove. I tried to do this in the pseudobond panel but didn't get anywhere. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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