- Chimera-users - RBVI Mailing Lists

down arrow goes all the way to empty selection
by Eric Pettersen 17 Nov '09

17 Nov '09

> On Oct 2, 2009, at 1:27 PM, Cathy Lawson wrote: > > > (4) It is great to have the down and up arrow to narrow and broaden > > selection, would be great if a final down arrow would lead to > > clearing the selection. > > After some discussion we have decided to do this, though it won't make > it into the next release since we are already in a feature freeze / > debugging mode for that. > > --Eric This is implemented now and will be in tomorrow's daily build and the eventual 1.5 release. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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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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