- Chimera-users - RBVI Mailing Lists

add custom residues to rotamer library or for swapaa command
by Sabuj Pattanayek 05 Dec '11

05 Dec '11

Hi, How do I add custom residues so that they're usable with swapaa or the rotamer tool? Thanks, Sabuj

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CASTp unable to recognise pdb format
by George Tzotzos 03 Dec '11

03 Dec '11

Hi everybody, I used Modeller to generate a structure which I then saved using Chimera. The CASTp server complains that the structure is not in pdb format. I'm attaching the pdb file to help with the diagnostics. Good weekend to all George

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Cando
by poorvi garg 02 Dec '11

02 Dec '11

Hii.., I have generated the json files by sending it to cando . The files we have generated is opened in UCSF Chimera but I am not able to perform any options or operations of the tool . Could you tell me how to perform operations on bld files of the json file obtained. thanks Regards, Poorvi Garg

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volume calculation
by sdimicco 02 Dec '11

02 Dec '11

Dear Chimera developers, is it possible to calculate the volume of the binding site by the softwere? How can I do it? Thank you in advance. Simone

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Multi-align: retract
by George Tzotzos 01 Dec '11

01 Dec '11

I'd like to retract the previous message. I found a way to edit the protein names. It's a bit roundabout but it works. I saved the alignment in Clustal, opened with an text editor, edited the names and saved. Then I opened the file in Chimera. Regards George

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Multi-align
by George Tzotzos 01 Dec '11

01 Dec '11

Hi everybody, I'm wondering if there's a way to edit the protein names in Multi-align. It seems that protein names are generated automatically. An example is attached. The problem is that in scalable eps, sometimes the names overlap with the line numbers. Reducing the ellipsis in Multi-align preferences truncates the names. Thanks for any suggestions George

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PDB splitting
by Milen Raytchev 30 Nov '11

30 Nov '11

Hi everyone, First, thank you Tom for redirecting me. I am trying to split a long single chain which is contained in a PDB file into several shorter chains, each to be contained in individual PDB files. I have tried Chimera (save as) and PDBEditor.jar software to do that but each approach messes the format somehow and I cannot use it in Chimera later (visualization suffers). Could you recommend me a way to do this splitting properly such that the PDB format is not messed up in the resultant 6 AAA domains and I can use the files further in Chimera. The file is attached if of any use. Thank you in advance and I do appreciate your help. Sincerely, Milen Raytchev

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Ice Crystal Surface
by Nancy 30 Nov '11

30 Nov '11

Hi All, I would like to perform molecular simulations with an ice crystal surface; does anyone know if such a structure file can be obtained online? Thanks, Nancy

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shortest distance
by Bishwajit Das 30 Nov '11

30 Nov '11

How to find out the shortest distance between two atom? help me -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

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help with error message
by Susan Tsutakawa 28 Nov '11

28 Nov '11

I am opening up a pdb that has been generated after MD simulations. Waters have been removed. I am getting an unusual error. I have two pdb files that were generated similarly, but only one gives me the error. Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkgui.py", line 343, in openPath mols = chimera.openModels.open(path, type=ftype) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) error: radius must be positive Error reading bfactor-911_changed.pdb: error: radius must be positive File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) If someone can help, I would appreciate it.

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Error in viewing trajectories
by George Tzotzos 28 Nov '11

28 Nov '11

Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files. The error was "TypeError: Attempt to form duplicate covalent bond." I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour? Best regards George

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EM density fitting
by dhacademic 28 Nov '11

28 Nov '11

Hi, I have an EM density map of a protein, as well as several PDB structures, and want to find the most possible structure with the lowest fitting score. Can anyone tell me know how to calculate the fitting score between the EM-density map and a PDB structure in chimera? Many thanks! Best, Hao

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TypeError: Attempt to form duplicate covalent bond.
by George Tzotzos 27 Nov '11

27 Nov '11

Hi everybody, I'm trying to load a trajectory and I get the error message shown above. I'm attaching the error log in case it's of any help. The problem is that I'm able to load the trajectory in VMD without problems (prefer to work on Chimera, though). Any help on how to troubleshoot this would be most welcome. Have a good weekend George

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3D custom residue labels
by matheus froeyen 22 Nov '11

22 Nov '11

Hi I tried the command mode options to generate a custom hard coded 3D residue label: labelopt resinfo "ARG 167" rlabel offset 0.,0.,20. :151 however get an error in the labelopt command: "resinfo" keyword does not exist (although it is described in the chimera man pages) Then I tried to bypass this by using the atom labeling labelopt info "ARG 167" label offset 0.,0.,20. :151@CA but again no luck, then is displayed the label "none" in the 3D window the default residue labeling works however. How can I use custom labels without using the menus? I use chimera 1.5.3 build 33475 on mac osx. best regards mathy

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2dlabels with solid background
by Tom Goddard 21 Nov '11

21 Nov '11

Hi Gabe, Unfortunately there is no color key command. Here's another creative solution. Make the label background be another label using unicode squares. 2dlabels create b1 text '\u2588\u2588\u2588' color white xpos .5 ypos .7 size 64 This uses the square unicode character, hexadecimal 2588. This solution has the advantage that you can fade out this background together with the label. In order for the text label to appear on top of background label you have to create the text label after creating the background. I'd recommend making all the labels and backgrounds interactive with the 2dlabel dialog and saving them in a session which you use together with your movie script. The script will show and hide the labels that have already been made, sized, positioned. You can cut and paste the unicode square character, say from web page into the 2dlabel dialog. http://en.wikipedia.org/wiki/Box-drawing_characters This solution doesn't make it easy to make an outline around the background box. Elaine suggested that you just make another slightly bigger background in the outline color. That has the problem that the vertical outline edges are thicker than the horizontal ones if the the background is wider than it is tall. To get uniform thickness outline you could make two extra background boxes one square shorter than the normal background and slide them horizontally them to get vertical outline edges of equal thickness. Tom -------- Original Message -------- Subject: 2dlabels From: Gabriel Lander To: Tom Goddard Date: 11/19/11 6:59 PM > Hi Tom, > Again thanks for the volume tracer settings saver - it's been super helpful. > But now I have another question: > I'm currently making a movie that uses lots of labels, and for the most part the current 2dlabels create& acreate commands work really well. But for certain closeup views the text gets lost in the volume density, and I've been trying to figure out a way to get a box to show up behind the labels (like in the attached image). I've figured out I can get something like this if I use the "color key" option, and then offset the text to fit inside the box, but I can't find a "color key" chimera command that I can put it into my movie script. > I tried using the "shape rectangle" command, but it's a bit too tedious to position the rectangles exactly right for all the labels. > Any ideas? > -gabe >

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Calculating and showing the Mass center of Volume Segments
by Schmidt, Claudius 19 Nov '11

19 Nov '11

Hello, I got a volume map that I segmented in 4 parts. Now I wanted to measure how the parts are coordinated to each other. As the Axes/Planes/Centroids menu can only create planes by atoms I wanted to place atoms in the mass- center of each segment. Is there any way to realize that? Or do you have any other way to measure the angles. To explain what I'm trying to measure: Example you have 4 segments, I call them a b c d. I want to measure how the axis that is formed by a and b, forms an angle to c and d, or how ist he angle of the plane formed by a b and c compared to ab and d . All for segments are basically the same objects just turned and rotated. With best regards C. Schmidt

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D-Proline modeling in Chimera
by Raghavender Upadhyayula 18 Nov '11

18 Nov '11

I am using PyMol for modeling a peptide containing D-aminoacid (D-Proline) residue. I could invert the configuration arounf L-Proline to convert it to D-Proline. But, I want the "Phi" of the Proline to adopt a certain value. When i tried using the torsion command by selecting the bond N-CA of the D-Proline residue, there is no change at all. I want the Phi value to change from -60 deg to +60 deg and use this as the model for further analysis. Also, the "Psi" needs to fixed at 120 deg. Is it possible in any way to carry out the same steps and achieve the desired results in Chimera. Any suggestions on how to carry out this would be highly appreciated. -- U.S.Raghavender, PhD Postdoctoral Fellow SRI International 140 Research Drive Harrisonburg, VA 22802 540.438.6643

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Docking box
by George Tzotzos 18 Nov '11

18 Nov '11

Hi everybody, I'm visualising a cavity generated by CASTp. Ideally I'd like to draw and get the coordinates of a box around the cavity to use in docking simulations. Is this possible with Chimera? Your suggestions would be much appreciated. Regards George

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Structure superimposition - RMSD
by Suda Parimala Ravindran 17 Nov '11

17 Nov '11

**Hi all, I have a set of protein structures (about 10) that I need to superimpose. I have used Matchmaker and superimposed by choosing a reference structure. I want to know how to calculate the overall RMSD of the superimposed structures? Where do I lokk out for it? I have checked the Reply log window, but it gets displayed only for some, whereas for others it does not. Please help.. Thanks, -Suda

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Alignment
by bodvael email 15 Nov '11

15 Nov '11

Hi, I have never used Chimera so please bear with me. I have this short peptide sequence (8 aa) that I want to locate in the secondary structure of a protein which I have opened in chimera. Is there a way to highlight the sequence in a particular color in the 3D model and/or only have the aminoacid numbering in this region? Also, I would like to view a linear alignment of the entire protein sequence with my peptide sequence of interest. I was able to do that and see that the peptide sequence falls in a beta-sheet (green color). Is there any way know which strand it is exactly? It is supposed to be in strand 5 but I don't know how to display strand numbers, or verify with certainty that it is indeed strand 5 and not strand 6 for example. Thanks, Bodvael

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van der Waals surface volume
by Jacob Alan Spooner 15 Nov '11

15 Nov '11

Hello chimera-users, I am wondering if and how I can get a volume for the van der Waals surface of my molecule. I know how to generate the vdw surface, and also how the volume and surface area for the solvent excluded surface, however the same method does not seem to work for the vdw surface as it does not show up in my model panel. I tried setting the probe radius of the MSMS to zero but it does not allow this so I am stumped on how I could obtain the volume of my vdw surface. Thanks in advance Jake Spooner

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Chimera issue
by Jason Mears 15 Nov '11

15 Nov '11

I installed Chimera on my linux machine, and there is an issue when I try to open a session (See attached img). It tells me that I need to update the graphics card, but my card is new and I would think is more than sufficient to run Chimera. Any suggestions? Thanks. - Jason -- Dr. Jason Mears Assistant Professor Department of Pharmacology 216-368-3348 jason.mears(a)case.edu <mears.jason(a)case.edu>

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custom label size
by Francesco Pietra 13 Nov '11

13 Nov '11

Hello: Is it possible to increase the letter size of custom labels? I would like to show the residue number only, saving as a stereo pair. As my stereo pair (a protein complex) works nicely for most people only at a reduced size of the figure (14x4 centimeters, or even smaller), larger letter-size is needed for the labels. thanks francesco pietra

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Visualising disulfide bonds
by George Tzotzos 12 Nov '11

12 Nov '11

Hi everybody, I'm trying to find a way to visualise disulfide bonds in AMBER trajectory files to no avail. Any help how to do so will be very much appreciated. Regards George

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Percent Identity for specified parts of a structure
by Victoria James 08 Nov '11

08 Nov '11

Hi there, I don't know if this command already exists, but I can't seem to find it in the Chimera tools or manual. I'd like to be able to calculate the percent identity of specified parts of 2 matched sequences - in my case the individual transmembrane helices of the structures. I wonder if a command already exists or if there is a way of doing this in Chimera without having to make new .pdb files of each of the areas of the proteins that I want to compare? I think it would be a useful command if it does not already exist. Thanks, Vicky

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