- Chimera-users - RBVI Mailing Lists

display comsia contour maps
by Joern Lenz 08 Feb '10

08 Feb '10

hi there, i am wondering if it is possible to display contour plots for 3d qsar (comsia) made by sybyl in chimera. any help is much appreciated, cheers, jorn

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Aligning planes with principal planes
by Dipl.-Ing. Thomas Mitterfellner 05 Feb '10

05 Feb '10

Hello! Is there a command in Chimera that turns a molecule in a way that a plane (explicitly created or just the selected atoms defining the plane) is parallel to the xy or the other principal planes? Thank you, Thomas

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SDF partial charges
by Elaine Meng 04 Feb '10

04 Feb '10

Hello, An additional follow-up to Nancy's question from Jan 31. <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004754.html > Daily builds (version 1.5) dated Feb 4 or newer will now automatically read the partial charges in 3D SDF files obtained directly from the PubChem database. <http://pubchem.ncbi.nlm.nih.gov/release3d.html> However, I wanted to caution everybody that the protonation states of the resulting molecules are not what you would expect at physiological pH. The functional groups that would generally be charged near pH 7 are neutralized, at least from the few examples that I've examined: carboxylic and other acids fully protonated rather than formally negative, aliphatic amines neutral rather than formally positive. For example, alanine is given as H2N-CH(CH3)-COOH rather than + H3N- CH(CH3)-COO - If that is the case for all of the 3D SDFs obtained directly from PubChem (Nancy, you may want to take a closer look at a sample of your structures), I would not recommend them for docking. Instead, you may want to get small molecule structures from some place that has attempted to put them in reasonable charge states, such as the ZINC database. <http://zinc.docking.org/> Best, 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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Calculating sigma level for EM map
by Thomas Goddard 04 Feb '10

04 Feb '10

Hi Andy, I don't know any convention defining the sigma value for an EM map. For x-ray maps there is a convention because the density is periodic you can just take the root-mean square density value across a whole unit cell. Note that that isn't a measure of noise level -- it's just a reproducible value describing the typical density levels across the unit cell. That isn't useful in EM maps because the value depends on how big the box is that contains the non-periodic structure. A bigger box contains more grid points outside the structure (values near zero) that make the root-mean square value (RMS) smaller. So such an RMS value isn't a reproducible measure of density values since it depends on the box size. I think when sigma is mentioned in EM papers they tend to mean the noise level. I don't know of any standard protocol for determining the noise level. If you knew the sigma level you wished to use, Chimera is still not able to display density values in sigma units. That is on our feature request list. Currently you have to take the values Chimera displays and divide by the sigma value yourself. I haven't added this capability yet because the notion of sigma does not seem to be well defined in EM work. Since Chimera map analysis is primarily used for EM, not x-ray, showing sigma units has not been a high priority. Tom -------- Original Message -------- Subject: Re: Threshold From: Anindito Sen To: Tom Goddard Date: 2/4/10 1:09 AM > Hi Tom > > I should have been more specific- my reconstruction is a EM density map > of a helical biopolymer. In that case what should be the correct > approach to calculate the threshold. Can you site any reference which > may be useful in this regard? > > Do we have the option of directly obtaining sigma value for the > threshold in Chimera ? > > Dr. Anindito Sen (Ph.D) > > --- On *Thu, 4/2/10, Tom Goddard* wrote: > > > From: Tom Goddard > Subject: Re: Threshold > To: "Anindito Sen" > Date: Thursday, 4 February, 2010, 9:29 > > Hi Andy, > > That may be right. But there are many issues. If your map is for > a crystal unit cell then that seems reasonable. In other cases > where the map is not a crystal unit cell then the RMS of the whole > map will depend on what the boundaries are of the map. For > instance, for an EM single particle reconstruction the RMS will > depend on how much padding of zeros there is, ie how big the box > is. If it is an x-ray map but not a unit cell again the RMS will > vary depending on what part of the map is taken. > > Tom > > > -------- Original Message -------- > Subject: Threshold > From: Anindito Sen > To: Tom Goddard > Date: 2/3/10 7:23 PM >> * >> >> Hi Tom >> >> I am "cropping" out high electron dense region from my >> density map to determine the volume of that region. The value of >> the Level in my Volume viewer is 438 (Range -618- 1024). The other >> factors are : >> >> f15_volume035.brix: mean = 23.123, SD = 137.14, RMS = 139.07 >> >> Therefore following your email, can I say, threshold is 438/139.07 >> = 3.1s >> >> Thanks for your help. >> >> Best Wishes >> >> Andy >> >> >> >> Tom Goddard* >> /Tue May 20 15:54:10 PDT 2008/ >> ------------------------------------------------------------------------ >> Hi Dave, >> >> Chimera can report the mean, standard deviation and root mean square >> map value using menu entry >> >> Tools / Volume Data / Volume Mean, SD, RMS >> >> The values using whatever normalization the map file has. If you divide >> the threshold level you set in the volume dialog by the RMS value you >> will get a sigma value. Actually I'm not sure if that is correct -- >> depends on the definition of sigma. Maybe you have to take the volume >> dialog number, subtract the mean and divide by the SD. The reported SD >> and RMS differ only in that the SD is the standard deviation of the map >> about the mean while the RMS is the standard deviation about 0. >> >> Allowing the volume dialog to show the sigma values directly is on our >> requested features list (item 88) but has not yet been implemented. >> >> http://www.cgl.ucsf.edu/chimera/plans.html >> >> Tom >> >> >> David Chenoweth wrote: >> >/ Hi! >> />/ >> />/ Can you please let me know if there is a way to report or set the >> />/ sigma value for an electron density map from a high resolution crystal >> />/ structure. I am using a ccp4 FWT.map and DELFWT.map file for >> />/ structures <1.2 angstrom resolution. Can I somehow find the sigma >> />/ value that corresponds to the Level setting in the Volume viewer? >> />/ >> />/ Thanks, >> />/ Dave Chenoweth >> />/ >> / >> >> ------------------------------------------------------------------------

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Smooth Surface
by sudheer molugu 03 Feb '10

03 Feb '10

Hi, I've installed the latest chimera version. I wanted take pov-ray pictures of a cryo-EM map. I would greatly appreciate if you can help me in make the map surface smooth. I couldn't find the option for smooth surface. Thank you, Sudheer.

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Mac 64-bit Chimera for large data sets
by Tom Goddard 02 Feb '10

02 Feb '10

A 64-bit Mac Chimera daily build is now available for Mac OS 10.6. It will not run on Mac OS 10.5. http://www.cgl.ucsf.edu/chimera/download.html#daily If you work with EM maps larger than 1 Gbyte or molecular models of several hundred thousand atoms the larger addressable memory in the 64-bit version will help avoid out-of-memory errors and crashes. The 32-bit Mac Chimera versions can only address 4 Gbytes of memory and because libraries, stack and other uses of memory the practical working data size limit for 32-bit versions of Chimera is about 1 Gbyte. You should have more than 4 Gbytes of memory installed in order to benefit from the 64-bit version. The 64-bit Mac Chimera is in early testing so will have more bugs than usual. I've tested the 64-bit Mac Chimera running Gaussian filtering on a 2048 by 2048 by 800 map requiring about 3.2 Gbytes for the floating point result and 0.8 Gbytes for the original map. This worked correctly (took about 3 minutes on a machine with 6 Gbytes of memory) but failed with 32-bit Mac Chimera. We are also working on a 64-bit Windows Chimera that will work with Windows 7. This may be available within a month if no serious obstacles are encountered. A 64-bit Linux Chimera has been available for a few years. Tom

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alter volume data with python
by Michael Zimmermann 02 Feb '10

02 Feb '10

Dear Chimera users, I cannot find a way to search the chimera-users archive, so I appologize if this has been asked already. I wish to alter some volume data in specific ways; delete (zero out) all volume values that do not meet certain density criteria. The following code modifies the matrix values, but I can't figure out how to update the map that is being displayed in the volume viewer. I would like to be able to do something like: opened[0].full_matrix = H Then I would only see the swath that I "selected" with the following code. # ------------------------------------------------------------------------ source = '1R0A_antigen_6A_8s_0.425f_inv.mrc' opened = chimera.openModels.open(source) em = opened[0] H = em.full_matrix() s = H.shape for k in range(0,s[2]-1): for i in range(0,s[0]-1): for j in range(0,s[1]-1): if(H[i,j,k] >= -.28) and (H[i,j,k] <= -0.001): H[i,j,k] = H[i,j,k]+1 else: H[i,j,k] = 0 # ------------------------------------------------------------------------ Thank you, -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University

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SDF Partial Charges
by Nancy 01 Feb '10

01 Feb '10

Hello, I am performing protein-ligand docking simulations, and the preferred ligand input file format is Mol2. I obtained some of my ligand structures from PubChem in SDF format, and I noticed that the SDF files contain partial charges ("PUBCHEM_MMFF94_PARTIAL_CHARGES"). Is there a way to preserve the charges in Chimera when converting to Mol2 file format? Thanks in advance. Nancy

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Converting SDF to Mol2: Errors
by Nancy 01 Feb '10

01 Feb '10

Hi All, When I convert an SDF file to Mol2 format using UCSF Chimera, I noticed that some valence errors were introduced. I can correct these errors for individual molecules, but doing so for large sets becomes cumbersome; is there any solution to this problem? Thanks in advance. Nancy

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Re: [Chimera-users] [Chimera] #8137: undesirable window placement (was: Chimera bug report submission)
by Eric Pettersen 01 Feb '10

01 Feb '10

Guy Nimrod wrote: > When I do an action that opens a new window (e.g. ‘file’ -> ‘save > session as’ or ‘file’-> ‘fetch by ID’), it seems that the new window > is located in a random position. Sometimes it is out of the borders > of the screen which is very problematic. Hi Guy, I think the new window-placement behavior is an improvement for most people. Nonetheless, it seems to be a problem for you so I've changed it into a preference (with the new behavior as the default). Starting with tomorrow's daily build there will be a preference in the General category called "Try to avoid placing dialogs over main window" which you can change to "false". Unfortunately the daily build for Windows hasn't been working lately, so it may be a few days before you can get a version with this preference available... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] holle,sir!
by Elaine Meng 30 Jan '10

30 Jan '10

On Jan 29, 2010, at 10:14 PM, gytjyb wrote: > holle,sir! nice to send a letter to you! > (1) about FindHBond .I can find out some HBond between ligand and > receptor,by chimera. I also use Accelrys Discovery Studio to find > out some HBond . but Accelrys Discovery Studio find out HBond to be > more than chimera. why?which one result is ture? > (2)what is meaning about Clashes/Contacts?what is useful for Finding > Clashes/Contacts > (3)how can i find out interaction between ligand and receptor and > classify displaying. > (4)can i use this software to publicate my paper ,directly? > best wishes for you ! (1) FindHBond vs. other programs. Different programs use different methods and cutoffs, and there is no reason to expect exactly the same results. The world of science does not agree on one exact definition of H-bond. Each program should explain its own method, as we have in the FindHBond documentation. Click "Help" on the FindHBond dialog or go here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon… > Also, this same question was discussed 2 days ago on the chimera-users list, see: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004746.html > (2) What are clashes and contacts? This is explained in the Find Clashes/Contacts documentation. Click "Help" on the Find Clashes/Contacts dialog or go here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas… > (3) use FindHBond and Find Clashes/Contacts. The "Structure Analysis and Comparison" tutorial is one example of using these tools: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> (4) yes, you can use images and calculation results from Chimera in your paper, but please remember to credit Chimera as described here: <http://www.cgl.ucsf.edu/chimera/docs/credits.html> 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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H Bonds in MD simulation
by snoze pa 29 Jan '10

29 Jan '10

Dear Chimera Users, I am analyzing a MD trajectory in chimera. After selecting H binds when I am playing the trajectory, then it always shows the hydrogen bond. Though some of the bonds are broken during the simulation but it always connect the step 1 h bonds connected.. How can I show the h bonds which breaks during the simulation. Thank you very much for your help. S

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Re: [Chimera-users] Rename atoms...and chains, residue numbers
by Jonathan Sheehan 28 Jan '10

28 Jan '10

On Mon, Jan 25, 2010 at 4:25 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > This is actually a little trickier than it really should be in the current > builds. As of tomorrow's daily build the following will work without any > issues to set the name of selected atoms to 'X1': > from chimera import runCommand > runCommand("setattr a name X1 sel") > --or-- > from chimera import selection > for a in selection.currentAtoms(): > a.name = "X1" Hi- Following up on this, I'd like to offer a feature request regarding structure editing. Two of the most common tasks I need to do when constructing a model are: renaming the chains in the structure, and renumbering stretches of residues. I can imagine two menu items similar to "Actions->Atoms/Bonds->Delete" named "Set chain ID..." and "Renumber residues from..." that could operate on the current selection. I suspect these menu options (or something similar, maybe under "structure editing"?) would be helpful to many folks. It could be a lot faster / easier than generating the right awk line or venturing into Emacs' PDB-mode. :-) Would this be difficult to implement? Thanks for considering it, -Jonathan -- Jonathan Sheehan, Ph.D. Comput. Biol. Educ. and Outreach Vanderbilt Univ. Ctr. for Struct. Biol. 5138 MRB3, 465 21st Avenue S. Nashville, TN 37232-8755

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Re: [Chimera-users] Chimera-users Digest, Vol 81, Issue 21 - chopped ccp4 maps in chimera
by Boaz Shaanan 28 Jan '10

28 Jan '10

Hi, The possible reason for the chopped ccp4 maps when they are displayed in Chimera (whereas they're fine Coot) may have to do with the fact that as far as I know Chimera does not apply the crystallographic symmetry operations to the ccp4 map (at least that's how it used to be in v1.3), whereas Coot does. So if the map is defined for the asymmetric unit only, it has to be expanded in order to cover all the region which one wants to display before being read into Chimera. There could of course be other reasons for the chopped maps. Cheers, Boaz ----- Original Message ----- From: chimera-users-request(a)cgl.ucsf.edu Date: Thursday, January 28, 2010 21:11 Subject: Chimera-users Digest, Vol 81, Issue 21 To: chimera-users(a)cgl.ucsf.edu > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Chimera movie question (Tom Goddard) > 2. Contouring ED Map: Sigma versus Chimera > thresholds (Veer Bhatt) > 3. Re: Contouring ED Map: Sigma versus Chimera thresholds > (Elaine Meng) > 4. Contouring ED Maps (Hector Viadiu) > 5. Re: Contouring ED Maps (Tom Goddard) > 6. H Bonds in MD simulation (snoze pa) > 7. Re: H Bonds in MD simulation (Elaine Meng) > > > ----------------------------------------------------------------- > ----- > > Message: 1 > Date: Wed, 27 Jan 2010 12:51:19 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > To: Bridget Carragher <bcarr(a)scripps.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Chimera movie question > Message-ID: <4B60A747.5030705(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Bridget, > > I put an example animation on the Chimera web site in the > animation > gallery called "Herpes virus slices". There is also a link > to a command > script which makes this movie. You just use File/Open... > in Chimera to > run the command script. > > > http://www.cgl.ucsf.edu/chimera/animations/animations.html > Tom > > > > > > OK, thanks Tom. Any tips on how to do all three planes > at once - or > > > rather keep the others constant while eating though the side > plane. I > > > have sen movies like this but can;t seem to figure out how > to do it in > > > Chimera. > > > Bridget > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 27 Jan 2010 19:12:31 -0500 > From: Veer Bhatt <veer82(a)gmail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Contouring ED Map: Sigma versus Chimera > thresholds > Message-ID: <C41C6E8E-343B-4FA1-BB71-49BAADB32DF2(a)gmail.com> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > Hi, > This in context of using Chimera to view *ccp4 format > electron > density maps. How does Chimera 'Threshold Level' ('Level' in > Volume > viewer) equate or relate to sigma level reported by some > other > programs. For example a 'Level' of 0.4 seems like a map > contoured at > 1.5 sigma or so. > I was wondering if someone could point out how these two are > related, > more precisely. > > Thanks > > Veer Sandeep Bhatt > >

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Contouring ED Map: Sigma versus Chimera thresholds
by Veer Bhatt 27 Jan '10

27 Jan '10

Hi, This in context of using Chimera to view *ccp4 format electron density maps. How does Chimera 'Threshold Level' ('Level' in Volume viewer) equate or relate to sigma level reported by some other programs. For example a 'Level' of 0.4 seems like a map contoured at 1.5 sigma or so. I was wondering if someone could point out how these two are related, more precisely. Thanks Veer Sandeep Bhatt

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lighting in Chimera
by Dan Gurnon 27 Jan '10

27 Jan '10

I wanted to tell you all that I love the new "glossy lighting" feature- now its easy to see the difference between the inside and outside of a surface when you use the per-model clipping tool. Without it, I had a hard time getting a sense of depth when a surface was clipped. But with the improvement glossy lighting brings, I have begun to wonder if other improvements in coloring and lighting are in the works or are possible. For instance, I use radial coloring with a grey palette to help my students pick out tunnels and pockets in a surface, but a better method would ambient occlusion on-the-fly. I've seen it in the molvis program "Qutemol", though the program does little else. Alternatively, is it possible to change the quality of shadows enabled in the effects window? And on a separate note, is it possible to change the inside color of a surface (something like "ribinsidecolor" for surfaces?) Thanks Dan -- ____________________________ 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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running command scripts
by Michael Zimmermann 27 Jan '10

27 Jan '10

Dear Chimera users, I am getting to know Chimera a bit more and was just going through the scripting tutorial here: http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Scr… For the command line script 1gfl.com, the tutorial just says "run it" but does not say how. I just typed "run 1gfl.com" in the chimera command line, but I get a syntax error in the script. I can't seem to copy the error text, so a screenshot is attached. Is this an issue with the script or how I am running it? I use chimera v. 1.4 on win XP - 64bit. Thank you, Mike Z

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Rename atoms...
by Yasser Almeida Hernández 25 Jan '10

25 Jan '10

Hi.. How can i rename atoms? How would be the script python syntax? Thanks Best regards -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 246 ---------------------------------------------------------------- Correo FENHI

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Fitting a structure to a DAMMIN/SAXS model/volume
by Byrd, Robert A. (NIH/NCI) [E] 25 Jan '10

25 Jan '10

Chimera Team & users, We have been using SAXS data and the DAMMIN software from the Svergun group. The bead model that DAMMIN produces approximates the shape and volume of the molecule. If one has a three dimensional structure of the molecule, then it becomes valuable to do a best superposition of the structure into the bead-model shape. Chimera is our preferred molecular display & analysis software, and we would like to perform this fitting in Chimera. Do you have any experience in how to display the bead-model output of DAMMIN and to fit or superimpose the bead model with a known structure? Thanks Andy Byrd

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Re: [Chimera-users] Failed surface calculation
by Elaine Meng 25 Jan '10

25 Jan '10

Hi Ibrahim, First, make sure you set the New Surfaces preference value before showing the surface for the first time -- it would not affect a surface that already exists (even if it is hidden when you set the preference). If the surface already exists, you could change it to single-component by changing its attributes, such as with the command given in my previous message. However, if the Reply Log says there is only one component of the surface in both sets of parameters, I think it is still possible for a surface area to decrease when the VDW radii increase. I'm imagining a case where there is a lot of concavity. Similar to the situation of an inside bubble shrinking or disappearing, a concave part of the surface could become shallower or much less extensive as the VDW radii are increased. This is just a case I'm imagining. If you feel there is an error, please use "Help... Report a Bug" in the Chimera menu and be sure to describe exactly what you did to get the two area measurements, what two values you are comparing, and attach the PDB file of the structure (or just include the PDB ID in your description if it is taken directly from the Protein Databank). 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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Failed surface calculation
by Ibrahim Moustafa 23 Jan '10

23 Jan '10

Dear Chimera, I¹m trying to calculate the surface for a protein but I get an error ²Surface calculation failed, mscalc returned code 5². I tried to change the probe size from 1.4 to 1.5 or 1.7 but still getting the same error. I know there is some issue with The code that calculates the surface (if I¹m not wrong) but I wonder if there is a way to get around this. For some smaller pdb files I don¹t have this problem. I¹m not sure if the size of the protein is a factor here. The protein having the problem is a single chain protein with 880 amino acids. Any advice? Thanks for help. Ibrahim

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Compatibility of Chimera with MacOS 10.4.11. PPC
by Arwid.Bierbach 22 Jan '10

22 Jan '10

Ldies and Gentlemen, The Chimera version Mac OS X (Aqua, PowerPC) chimera-alpha-osx_ppc_aqua.dmg Size: 73241868 bytes MD5: 39623fa9e0d9f4a869a4c985d45223bb Jan 22, 2010 is not compatible with G4 PPC Mac OS 10.4.11. Do you plan to quit the G4 PPC OS 10.4.11. - Compatibility ???? With best regards, Dr. Arwid Biebach, Germany

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Massive superposing...
by Yasser Almeida Hernández 22 Jan '10

22 Jan '10

Hi... I'm performing a massive superposing of aminoacids in different conformations. The first model is a arginine "template" reference structure that is the fixed model in all matching iterations. I've loaded 236 models and i want to match the arginine guanidine group on the template guanidine. In each iteration i execute two matching, with different atoms selections. The first selection is the "right" selection: CD,NE,CZ,NH1,NH2 and the second is the "inverse" selection: CD,NE,CZ,NH2,NH1. I run the two superpositions, and i want to show that with the minimal RMSD between the guanidine groups. This is the code: import chimera from chimera import runCommand right = "@CD,NE,CZ,NH1,NH2" inverse = "@CD,NE,CZ,NH2,NH1" for i in range(2,328): print "Superposing..." runCommand("match #"+str(i)+right+" #0"+right+"; close 1") right_rmsd = runCommand("rmsd #"+str(i)+right+" #0"+right+"; close 1") runCommand("match #"+str(i)+right+" #0"+right+"; close 1") inverse = runCommand("rmsd #"+str(i)+inverse+" #0"+right+"; close 1") if right < inverse: print "Minimum RMSD =",right,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") elif right > inverse: print "Minimum RMSD =",inverse_rmsd,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") In principle this script should show the matching with the minimum RMSD, but it doesn't work. Please, help... Thanks -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 246 ---------------------------------------------------------------- Correo FENHI

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Measuring Distances in Chimera
by Beale, John 21 Jan '10

21 Jan '10

Hello, I am trying to measure distances between atoms using the Tools -> Structure Analysis -> Distances routine. Chimera is requesting that two atoms must be selected in the main graphics window for this to work. I can't figure out how to select the atoms. Can someone help me? John

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Ligand Binding to Homodimeric Proteins
by Nancy 17 Jan '10

17 Jan '10

Hi All, I am performing molecular docking simulations of a ligand binding to a homodimeric protein, to determine a potential binding site(s). Due to the symmetrical nature of a homodimer, I would expect that the binding site(s) on one protomer would be identical on the other protomer. Therefore, a ligand should bind with equal probability and affinity to both sides of the protein. However, when I perform a molecular docking simulation (using an X-Ray crystal structure), the ligand preferentially binds to one side of the homodimer. Is this outcome likely the result of errors inherent in the X-Ray crystal structure, as one would expect identical binding to both sides? Thank you very much. Nancy

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