Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
MathType is a Microsoft Word plugin (on both Windows and Mac OSX). It worked very well for me. http://www.dessci.com/EN/products/mathtype/ Best, Steven On Wed, May 20, 2015 at 6:09 PM, James Stroud xtald...@gmail.com wrote: I didn’t see the following solution in any other responses. It’s probably the most reasonable one given the constraints of collaboration and publishing. In the absence of using the best software, I found it practical to write the equations in MathType and save them as MathType PDF equations and then add these equations to the document. It is a portable, cross-platform-ish solution. Others only need to install a MathType player, which is free. The advantage is that if your equation gets hosed in the document, you still have the original, editable equation in the PDF. In such cases, you must re-embed it in your document, but it’s better than fully rewriting it. With that said, if you want to work behind a full-featured word processor and have access to the wonders of TeX typesetting, LibreOffice (OpenOffice) + TexMaths is the best for the author during preparation of a manuscript. At this point it is bug free (to my experience), embeds vector equations (SVG) or raster (PNG), is editable, and looks spectacular both when editing and when publishing/printing. The downside is that you have to collaborate with people you can’t force into using the best software. Worse, journals seem to use proprietary publishing software and they want MathType or equation editor with Microsoft word, hence my first solution. James On May 18, 2015, at 5:10 AM, Keller, Jacob kell...@janelia.hhmi.org wrote: There is the possibility of using one of the open-source versions, like openOffice, but those I guess also have their issues. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read Sent: Monday, May 18, 2015 4:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Equation Editor woes with Office 2011 for Mac Rather off-topic, but maybe someone on the list has found a way to work around this! There's a problem with the Equation Editor in Office 2011 for Mac (i.e. the one that is based on a stripped-down version of MathType, which you get with Insert-Object-Microsoft Equation). You can insert an equation, re-open it and edit it several times, and then suddenly (and seemingly randomly) the equation object will be replaced by a picture showing the equation, which can no longer be edited. I'm writing a rather equation-heavy paper at the moment, and this is driving me crazy. This seems to be a known bug, which has existed from the release of Office 2011. Apparently it happens, unpredictably, when an AutoSave copy of the document is saved, so you can avoid it by turning off the AutoSave feature. The last time this drove me crazy, several years ago, I did try turning off AutoSave. For a while, I was very good about manually saving frequently, but I got into bad habits and eventually Word crashed after I had worked for several hours on a grant proposal without manually saving. So I turned AutoSave back on. At the moment, the least-bad solution seems to be to turn off AutoSave while I'm working on a document with lots of equations and then (hopefully) remember to turn it back on after that document is finished. But it would be great if someone has come up with a better cure for this problem. No doubt someone will suggest switching from Word to LaTeX, but I need to be able to collaborate on paper-writing, and even though I might be willing to invest the effort in learning LaTeX, I can't really expect that of my collaborators. Most people in our field do use Microsoft Word, regardless of its failings. I've also tried using the professional version of MathType, but that requires your collaborators to install it as well - and I don't think that cured the equation to picture problem anyway. Thanks! - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk -- Steven Chou
Re: [ccp4bb] on openning the PDB file and the mtz file by Coot
Hi Smith, Both PDB and MTZ have records on their headers to specify the cell dimensions and space group. And for an MTZ, once the cell dimension and space group are fixed, its coordinate origins can also be fixed. For a PDB, its CRYST1 record specifies its unit cell dimensions and space group. The position of each atom (X,Y, Z) with respect to the coordinate origins is specified by the ATOM records. To place your pdb in the right position in the map, you need to edit the CRYST1 record (one line) and the ATOM records (many many lines). It's very easy to edit the CRYST1 record with a text editor, but very difficult (almost impossible) to edit the ATOM records manually. You can follow Carlos's advice to edit ATOM with Coot. All the best, Steven On Thu, Mar 19, 2015 at 2:20 AM, Smith Liu smith_liu...@163.com wrote: Dear All, When we by Coot open the PDB fle and the mtz file from the same refinement, the protein backbone (and the sidechains) and the electron density always fit automatically. Will you please tell me the mechanism of the Coot how the PDB file automatically fit the mtz file in its graphical window? Suppose I have a PDB file and a mtz file (PDB file from protein A, mtz file from protein B, which is a homology protein of protein A) which are not from the same refinment (thus not fit automatically in Coot), will you please tell me what modification I should make on the files in order to have the Coot to fit the protein bakbone (and the sidechains) and the electron density? I am looking forward to getting your reply. Smith -- Steven Chou
Re: [ccp4bb] A basic question about Fourier Transform
I would say you cannot measure the diffraction pattern of a single biological molecule accurately thus far, because biological molecules are not strong scatters and can be damaged easily. For other molecules, actually you can! In high-resolution electron microscopy, the diffraction pattern in the back focal plane is actually the diffraction pattern of a projection of your sample, which is usually composed of one to several hundred biological molecules. For biological molecules, this pattern usually is dampened to almost zero at a resolution between 30A-4A (actual resolution, not theoretical); for some metal compounds, the resolution can reach up to 1 A, or even better. The diffraction pattern in the back focal plane is the Fourier transform (achieved by a convex lens) of the a 2D projection of your sample. If you apply another Fourier transform (using another convex lens) to the diffraction pattern, you can get the 2D image of your sample (which contains both amplitude and phase). That is, in single particle EM (imaging mode), people don't have the phase problem. In diffraction mode (2D electron crystallography), only the diffraction pattern (intensity) is recorded, so they also have the phase problem. HTH, Steven On Tue, Jan 20, 2015 at 10:18 PM, Chen Zhao c.z...@yale.edu wrote: Dear all, I am sorry about this slightly off-topic question. I am now a graduate TA for crystallography course and one student asked me a question that I didn't ask myself before. I don't have enough knowledge to precisely answer this question, so I am seeking for help here. The question is, as I rephrased it, assuming we are able to measure the diffraction pattern of a single molecule with acceptable accuracy and precision (comparable to what we have now for the common crystals), is it better than we measure the diffraction spots from a crystal, given that the spots are just a sampling of the continuous pattern from a single molecule and there is loss of information in the space between the spots that are not sampled by the lattice? Of course this is more of a thought experiment, so we don't need to consider that all measurement is discrete in nature owing to the limitation of the pixel size. I kinda agree with him and I have a feeling that this is related to the sampling theorem. I do appreciate your valuable comments. If this is not true, why? If this is true, what is its effect on electron density? Thank you so much for your attention and your help in advance! Best, Chen -- Steven Chou
Re: [ccp4bb] Why the phases from sftools are flipped?
Thank all of you for your inspiring information! Now I understand that actually axis order permutation and phase flipping can have the same effect on the map. All the best, Steven On Wed, Oct 15, 2014 at 4:48 AM, Ian Tickle ianj...@gmail.com wrote: The signs of the phases will depend on the permutation order of the axes. Maybe when you created the map you inadvertently reversed the hand? What do you see if you run mapdump on the map? Cheers -- Ian On 15 October 2014 01:53, Steven Chou stevezc...@gmail.com wrote: Dear All, I used 'sftools (in CCP4)' to convert a map (in CCP4 format) to structure factors (.mtz). However the phases were flipped. I back converted it into a map file and compared it with the original one. The back converted one was just the mirror of the original one. To get the right phase, I had to convert the structure factors to a text format (CIF or XPLOR) and edit it with script. Their relationship is: CorrectPhase = 360 - phaseFromSftools. I also used CNS to do the same conversion. The phases from CNS were correct. sftools set spacegroup P1 set cell 200 200 200 90.00090.00090.000 mapin input.map MAP map2sf resol 3 column F_prot PHI_prot write output.mtz exit Was sftoold designed in this way? Thanks! Steven -- Steven Chou -- Steven Chou
Re: [ccp4bb] Command line tool for RMSD calculation
Hi Chen, I used SUPPOSE previously. It worked very well. The compositions of the structures have to be the same! It works on Linux. http://structbio.vanderbilt.edu/~jsmith/suppose/ If the compositions of your structures are different, you may first load them to PyMOL, then align them use its commandline. http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ If the compositions/sequences of your structures are very very different, but their overall structure are similar, you can do the alignment using a PyMOL plugin called 'cealign'. It works on both Mac and Linux. http://pymolwiki.org/index.php/Cealign Here is my note on how to run SUPPOSE. remove the outputs from the previous runs rm -rf *.rot.pdb mean.pdb all.pdb # if the input file names are XXX.pdb, those of the output files are XXX.rot.pdb and a mean.pdb fit the structrue models based on the CA atoms, and then calculate the RMSD of the backbone atoms suppose -mat -rot -mean -fit :11-52,85-97:CA -calc :11-52,85-97:C,CA,N restrt_*.pdb # 0.639 fit the structrue models based on the CA atoms, and then calculte the RMSD of the heavy atoms suppose -mat -rot -mean -fit :11-52,85-97:CA -calc :11-52,85-97:C*,N*,O*,S* restrt_*.pdb # 1.23 # Do not visulize the rotated pdb files with molmol at this step, because molmol will shift the individual files. # That is, the output files have already been perfectly supperimposed, # but molmol gives an illusion that they have not been rotated correctly. join the pdb with the AWK script ./joinpdb -o all.pdb *.rot.pdb # input files: *.rot.pdb # output file: all.pdb display the rotated pdb with molmol now. molmol all.pdb # molmol can only display the combined pdb (i.e., 20 models in one file) correctly!!! HTH, Steven On Wed, Oct 15, 2014 at 4:05 PM, Chen Zhao c.z...@yale.edu wrote: Dear all, I am just wondering whether there is a simple command line tool for RMSD calculation between two aligned structures? I just cannot find a good answer online, and ccp4bb can always impress me. Thank you so much in advance, Chen -- Steven Chou
[ccp4bb] How to create a mask with specified pixel size in CCP4?
Dear All, I'm trying to generate a mask from a pdb coordinate file using the 'Ncsmask' utility of CCP4 (Map Mask Utilities = Create/Edit Masks). The parameters I used are: = Radius for building mask from atoms 10.0 angstrom. Space group P1 Set map extent x 0.0 307.2, y 0.0 307.2, z 0.0 307.2 Set map grid x=128 y=128 z=128 Cleanup mask to have 1 contiguous region Trim maks to minimum box = I want to have a mask with pixel size of 307.2/128 =2.4, and box size of 128. But the mask I got has a pixel size of 1 A/pixel, and box size of 308. Is there anything wrong with my parameters? It seems that the mask generated by Ncsmask always has a pixel size of 1. Thanks in advance! Steven
[ccp4bb] Why the phases from sftools are flipped?
Dear All, I used 'sftools (in CCP4)' to convert a map (in CCP4 format) to structure factors (.mtz). However the phases were flipped. I back converted it into a map file and compared it with the original one. The back converted one was just the mirror of the original one. To get the right phase, I had to convert the structure factors to a text format (CIF or XPLOR) and edit it with script. Their relationship is: CorrectPhase = 360 - phaseFromSftools. I also used CNS to do the same conversion. The phases from CNS were correct. sftools set spacegroup P1 set cell 200 200 200 90.00090.00090.000 mapin input.map MAP map2sf resol 3 column F_prot PHI_prot write output.mtz exit Was sftoold designed in this way? Thanks! Steven -- Steven Chou
