February 2012 - Chimera-users - RBVI Mailing Lists

fly command
by rswett＠chem.wayne.edu 14 Feb '12

14 Feb '12

Is anyone else having issues with the fly command lately? Seems like since RC 1.5ish flying to a savepos ignores the # of frames it's set to fly over. i.e. fly 50 in (where in is a saved position) does the fly in one frame, appearing the same as fly in or fly 1 in Additionally fly in 50 has the same effect. Has anyone else run into this? I have a few saved sessions i'd like to animate, and the older versions are having none of it. Suggestions? ~Rebecca

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Re: [Chimera-users] meaning of the ANISOU PDB parameters
by Eric Pettersen 13 Feb '12

13 Feb '12

On Feb 10, 2012, at 1:55 PM, Julian Chen wrote: > hi Eric, > > First of all, hello, I was in Stroud's lab for many years, until > 2003, when I left SF. Hi Julien! > I am in a rather interesting situation where we have been dealing > with neutron and X-ray refinement, and we have been able to do > anisotropic refinement on selected hydrogen atoms, from having high > resolution neutron data. I've been using Chimera. > > I am still somewhat confused as to the meaning of the six ANISOU > terms, I understand that the first three describe the three > orthogonal axes of the ellipsoid, and that the last three somehow > relate this to the coordinate space. The six terms actually describe a 3x3 matrix that is symmetric about the diagonal. The eigenvectors and eigenvalues of that matrix are the atomic displacement axes and the mean squares of the displacements respectively. The first thing to know is that the values shown in the ANISOU records are scaled by 10**4. The other thing to know is that the six numbers correspond to these positions in the matrix: 1,1 2,2 3,3 1,2 1,3 2,3. Since the eigenvalues are mean squares, one typically works with the square roots of the eigenvalues. > Specifically, I want to look at the ANISOU for the H/D atoms, and > want to try to correlate it to its bonded neighbor (the C or the N > or the O). If possible, I'd like to extract some vector for the > 'directionality' of the aniso atoms and relate them to one another. > I want to see if the vibrational motions of the hydrogen are > correlated to the vibrational motions of its bonded neighbor. Is > there anything in CHIMERA that could do something like this, or some > appropriate mathematical formula that could output the right sort of > information? The ellipsoids option in the program gives a > qualitative description, but I'd like to get something a bit more > quantitative in nature. Depending on how comfortable you are with programming in Python, you could either write your own external code based on the info above, or write something that runs in Chimera. The latter does have the advantage of you not having to write PDB-parsing code an so on. In Chimera, atoms with corresponding ANISOU records have an 'anisoU' attribute which is a 3x3 matrix (the matrix is often referred to as 'U' in the literature, hence ANISOU record). This code snippet (basically copied from the Chimera's Aniso module) will extract the eigenvectors/values for an atom and take the root of the values: from numpy.linalg import svd ignore, lengths, axes = svd(atom.anisoU) from numpy import sqrt lengths2 = sqrt(lengths) Let me know if you need more info or help with scripting. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Visualising AutoLigand affinity points
by George Tzotzos 09 Feb '12

09 Feb '12

Hi, I'm attaching a jpg image of ligand affinity map fill points generated by AutoLigand. My question is whether there's a way to depict these fill points as "disconnected" spheres. Actions/spheres generates something like I'd like to see but the size of the spheres is too large. Regards George

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pi-cation interaction
by Bishwajit Das 09 Feb '12

09 Feb '12

how to find cation pi-interaction in a docked molecule.......plz help me -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* *

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How to select
by Bishwajit Das 09 Feb '12

09 Feb '12

suppose i want so select ARG 188 and TRP 144 and also want to see the distance between them ....how i do this in chimera..please help me. -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* *

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Re: [Chimera-users] Rotamer copying- Specific Residues only
by Eric Pettersen 08 Feb '12

08 Feb '12

On Feb 8, 2012, at 8:27 AM, Ahir Pushpanath wrote: > Eric, although the script is highly useful for what I previously > asked, I have come to the realisation that simply copying all the > apo chi angles to the holo form may not be ideal for me in this > particular situation. I noted that of around 200 residues modelled, > around 90 of them are modelled different to the apo, the rest are > modelled similar to the apo form. Of these 90, only around half are > truly changed in the holo form(literature evidence from homolog), > therefore I do require a script that is able to accept an input of > which residues to copy the chi angles for, I think this will be > useful for other users who want to copy chi angles from apo-holo > forms and other applications, and probably could be included in > later build versions of chimera, under structure editing. > > Do you think you could help me with this? I am only learning python > now, so my scripting is not at a good level for these types of things. I've attached a modified script that will only copy the chi angles for residues that are selected in the lowered-numbered model. It's up to you to select them somehow. :-) > On another note, do you have any experience with using chimera to > model apo-holo transitions any other way without using Modeller? I don't. Maybe others on the list will have suggestions... ? > Also, does chimera have the ability to do docking of ligands, i.e. > given you know the apo crystal structure, can you tell it to dock a > ligand and change conformation of protein,(similar to autodock)? Currently Chimera cannot dock ligands. If our next 5 years of funding gets approved by the NIH, we have proposed interfacing Chimera to an Autodock Vina web service that would allow docking to be carried out directly from Chimera. Right now all you can do is prepare the input for / analyze the output of external docking programs in Chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to find hydrophobic interaction
by Bishwajit Das 08 Feb '12

08 Feb '12

how to find hydrophobic interaction in a docked protein structure......please help me.... -- BISHWAJIT DAS +91-9433237920 KOLKATA,West Bengal INDIA* *

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how to setup a default settings for a new pdb model?
by Xing Zhang 07 Feb '12

07 Feb '12

Hi, I have many different pdb models that need to be displayed at exactly the same settings, including color, background, stick scale and so on, so I want to set all these settings for the first model, and then apply these settings to a newly opened pdb model. Is there any way to save and load a default setting for a new pdb model? Thanks much. Xing

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Rotamer copying
by Ahir Pushpanath 07 Feb '12

07 Feb '12

Hello there, I have a question regarding MODELLER in Chimera and the ability of chimera to adjust the model using some inbuilt features quickly(i.e. automatically, instead of interactively) Firstly, I am trying to model the "holo" form of an enzyme with known apo-form structure. I did this usinig the two independent domains of the apo form as a template (in a bid to get the domains accurate) and for the holo-form closure I used a very similar homologue that has been solved in the holo form. The results were good and I got a decent model that had closed up like the homolog. However, I noticed that in the model a lot of the sidechains have not been modelled with the right rotamer. This is odd, as I gave it the two independent domains as a template, so it had all the information it needed to get that perfectly right. Either way, this means, I need to manually "copy" the rotamers from the apo form onto the "holo model", which is time consuming. I know from the homolog that only two or three residues in the active site change rotamer upon apo-holo conformational change. So, I just want an easy way to edit the rotamers in the holo-model to copy the rotamers of the apo-form for all residues. Is there an easy way to do this, is it possible to this with a script? I have no idea how to script, mind you! Ahir

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associating multiple structures and sequences
by Uppal, Karan 07 Feb '12

07 Feb '12

Hi, I am writing a custom extension based on MultiAlign Viewer that highlights regions in a multiple sequence alignment based on numerical values stored in an external file. I modified the RegionBrowser.py script, and added a function that works just like "showSS". It works fine for one structure and sequence combination. However, I am trying to associate multiple copies of the same protein structure and its sequence. So, the structures are identical and so are the sequences in the sequence alignment, but each copy represents different information. My problem is that the sequences in the alignment viewer dialog box are highlighted in a random fashion. And, I want the sequences to be highlighted in an ordered fashion starting from first sequence to last sequence since we want to be able to map the highlighted regions back to the external file. Is there a way to control the order in which the sequences are highlighted in the alignment viewer dialog? Or is there a way to get the model # associated with a particular sequence and using the model # to highlight the alignment viewer? I would highly appreciate your help. Thank you, Karan Uppal Application Developer Emory University ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Chimera-users February 2012