[ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

Dear all - I'm working with a PDB file with explicit hydrogens where many of the histidines are in protonated form due to crystallization at low pH. Unfortunately, although the additional protons are present in the model for the positively charged histidines, the residues in question are indi

[ccp4bb] Test system for binding energy predictions

Dear crystallographers - I've been trying without success to find a suitable system to test a method for predicting change in binding energy (delta-delta-G) due to mutations of protein-protein complexes that result in a change in net charge. In particular I'm looking for a system with the fol

Re: [ccp4bb] pdbset

Hi Charlie - I'm not able to reproduce your issue. I tried this with a random PDB and, although the symmetry operation wasn't appropriate for that particular structure, I got normal-looking cartoon representations. One thing to consider might be that, if there are abnormalities in the numberi

Re: [ccp4bb] 1.how to use pymol to choose all the residues that have polar contacts in the complex 2.how to draw a residues-DNA interaction picture

Hi Weifei - The first image looks like it was drawn using a vector drawing program like Adobe Illustrator or Inkscape. If you're looking for something automatically generated, two of the first hits from a Google search for "protein interaction diagram" are LigPlot+ (http://pubs.acs.org/doi/abs

Re: [ccp4bb] off topic: pymol

Hi Almu - It's actually even easier than what Vincent wrote as well. :) You don't need to create multiple objects or worry about backbone selections--PyMOL has some built-in settings that will do this for you. # the PDB from your example fetch 3bwp # color however you like color blue, resi

Re: [ccp4bb] Adding a residue with an insertion code

text editor; 3) pdbset xyzin old.pdb xyzout new.pdb renumber increment –1 102 to 500 chain A !move everything up starting from 102 end You can make a little shell script file for step 3, to save some typing/typo. (see attachment for an example) Zhijie From: Sam

[ccp4bb] Adding a residue with an insertion code

Along the same lines as Dialing’s recent post about inserting a residue, I’d like to ask: Is it possible to insert a residue with an insertion code in the residue number? For example, what’s the best way to insert residue 100A between residues 100 and 101? This situation arises frequently for

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

Greetings all - My interest in the rest of the discussion of experimental precision and error notwithstanding, and at the risk of stating explicitly what some might consider obvious, it seems to me that no one has actually (intentionally) asserted that they have determined the unit cell to 10^-

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

Hi Meisam - We do this frequently, using pieces of spongy foam to pad the inside of a sturdy styrofoam shipping box, which keeps the temperature from fluctuating too much. This is then carried in a reusable grocery bag by one person whose sole responsibility it is to ensure it isn’t subjected

Re: [ccp4bb] Kabat, insertion codes & refinement

Hi David - Your input files for Refmac (I’m not sure about Buster) should have LINKR records of the form: LINKRGLY L 95 THR L 95A gap This has worked fine for me in the past. The file I happened to excerpt here was refined with Refmac 5.6.0117 a

Re: [ccp4bb] negative density around disulfide bond

Hi Eze - I’m glad to see you solved your problem. On Jun 2, 2014, at 9:07 PM, Eze Chivi mailto:ezech...@outlook.com.ar>> wrote: Thanks to everyone for the useful information. I refined my structure in the reduced form (using the method suggested by Pavel). Negative density disappeared, and als

Re: [ccp4bb] HisTrap Trap

Hi Bernhard - Like Zhijie, we have also been using a Tangential Flow Filtration (TFF) system to address this same issue with serum-free 293 Freestyle media. Ours is the Minimate TFF system from Pall; there is also the Millipore Labscale system, and I’m sure others as well. I’ve done only limit

Re: [ccp4bb] [PyMOL] Farewell

Jason - I’d also like to express my appreciation for all you’ve done to benefit the PyMOL community. You have, time and again, proven yourself to be an extremely responsive and helpful leader both in developing the software and in enabling others to learn to use it. Like many on these lists,

Re: [ccp4bb] PyMol and Schrodinger

In addition to what has been mentioned by others, Open-Source PyMOL installation instructions for various platforms are available on the PyMOL Wiki: http://pymolwiki.org/index.php/Linux_Install http://pymolwiki.org/index.php/MAC_Install http://pymolwiki.org/index.php/Windows_Install Cheers, Jare

Re: [ccp4bb] coloring by RMSD

Hi Tim - There is a script on the PyMOL Wiki that does just this: http://pymolwiki.org/index.php/ColorByRMSD. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jan 29, 2014, at 12:43 P

Re: [ccp4bb] making high res image in pymol

Hi Alex - You can also try reducing the value of `hash_max` (e.g. `set hash_max, 50`). The default value is 130; a lower number reduces the memory PyMOL tries to obtain for ray tracing. The trace will take longer, but hopefully will get you throug

Re: [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units

Hi Gabriel - If the crystal contacts really are all the same, it sounds to me like your MR program may have just placed the monomers in different but equivalent symmetry-related positions between the two structures. Try moving the outlying monomers to the symmetrically related positions that

Re: [ccp4bb] how to get off a mailing list

In particular, selecting the option in your favorite email program to "view all headers" should reveal the following lines: List-Help: , List-Unsubscribe:

Re: [ccp4bb] Extracting .pdb info with python

Hi Grant - In addition to the other good suggestions, there is also the Biopython project's PDB parser. http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc148 Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th

Re: [ccp4bb] Best practice for transformed PDB coordinates?

Hi James - If you need the transformed coordinates in the original form for another program, this may not help, but if you just want to compare the packing between structures, have a look at PyMOL's matrix_copy command (http://pymolwiki.org/index.php/Matrix_copy). # load your files load file1.

Re: [ccp4bb] Any tool to calculate surface accessible by ... another protein?

Hi Emmanuel - You might consider using MSMS. If you wish to visualize it, there is a PyMOL script available: http://pymolwiki.org/index.php/Msms. Relatedly, one should keep in mind that, while a 10 or 50 Angstrom probe will give you a general idea of accessible surface, if there is any shape

Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window

Terrific! I always thought it was X11-related as well. Thanks to Paul and Bernhard for the fix. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Nov 7, 2012, at 1:53 PM, Jon Agirre

Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window

I agree, this is a frustrating "feature." I tend to work around this by pressing Cmd-` (back-tick) to cycle through the X11 windows (this works for other applications as well), or by running Coot from within the directory containing the PDB file and using Ctrl-S to save with auto-incremented (e.

Re: [ccp4bb] Stereo Microscope

Our setup is an Olympus SZX-10 with both 1x and 2x objectives and 10x eyepieces. It's nice having the different objectives for different things--a close up look at a tiny crystal requires the 2x, but the 1x is less bulky and has better depth-of-field, so it's better for freezing crystals. The

Re: [ccp4bb] information received through the AFC: iycr2014

I particularly enjoy that the U.N.'s declaration of the International Year of Crystallography comes in the form of a "resolution." Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jul 4,

Re: [ccp4bb] NCONT chain selection issue

Thanks to Pius for the tip that I can use more than one "source" keyword. ncont xyzin my.pdb

[ccp4bb] NCONT chain selection issue

Hello all - Short version: NCONT from CCP4 v6.2.0 doesn't properly recognize comma-separated chain IDs with the source or target keyword. I'm trying to use NCONT to determine contacts between antibody chains and their bound epitope as part of a programmatic workflow. I'm using a Biopython Bio

Re: [ccp4bb] Off topic: vector map editing and DNA sequence alignment software

Hi Florian - I've used Geneious for a few years now and been pleased with it. Also a "freemium" business model: Basic version is free, and Pro version price depends on the term and type of license (student, academic/government, or commercial). I find the Basic version suits my limited molecul

Re: [ccp4bb] Coot "Bad magic number" errors

\:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5\:||g' > /Library/Coot/bin/coot > > and that will fix it. > > I'll make a new one. > > Bill > > > On Mar 10, 2011, at 7:55 AM, Sampson, Jared wrote: > >> Hi all - >&g

Re: [ccp4bb] Coot "Bad magic number" errors

Hi Ben and Pete - I did think about deleting (or moving) the .pyc files, but in the newer of the two students' computers (3 weeks out of the box), there wasn't a site.py file in that directory, only .pyc and .pyo, so I figured I'd better not mess with it. Thanks for the suggestions so far. I'l

[ccp4bb] Coot "Bad magic number" errors

Hi all - Two of the grad students in our structural biology course are having similar problems installing Coot on their Mac computers using the stand-alone packages from Bill Scott's Crystallography on OS X website. I've paste

Re: [ccp4bb] Stereo Microscope advice

Hi Kevin - 1) I can only imagine that LEDs would produce vastly less heat than halogen lamps. In general, they are small, efficient, long-lasting and don't produce a lot of heat. Here's a start for more information http://en.wikipedia.org/wiki/Light-emitting_diode . Also, a quick search got

Re: [ccp4bb] pyMol--set up view through one axis of the unit cell

Hi Jerry, If your protein has an NCS symmetry axis parallel to a cell edge, you can try using the “orient” command. http://www.pymolwiki.org/index.php/Orient Best, Jared On 9/3/10 7:31 PM, "James Stroud" wrote: On Sep 3, 2010, at 4:03 PM, Jerry McCully wrote: It is a Pymol question. How