[ccp4bb] peak height at mouse click
Dear CCP4 users Is there any easy way of calculating the peak height / number of electrons at a given position, say a mouse click point in coot. Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot. I have some peaks in my map which take water or sodium/magnesium or chlorine atom with out giving out any positive or negative density upon further refinement. The asymmetric unit has about 425 residues and the data resolution is 1.5A. Thanks and regards S. Thiyagarajan Department of Cell and Organism Biology Lund University Sölvegatan 35 Lund, Sweden
Re: [ccp4bb] peak height at mouse click
Hi Thiyagarajan I doubt that what you want can be done easily, if only because of the problem that a mouse click returns only 2-D co-ords (x,y) whereas of course you need the 3-D co-ords (i.e. also z) to identify a point in the map. There is a way however: simply vary the contour level until the peak you're interested in just appears or disappears: that will give you the peak height either as a multiple of the RMSD (in which case you need to find out the RMSD of the map and multiply the sigma level by that) or as an absolute electron density value in electrons/Ang^3. Note that for a difference map if you're using Refmac it doesn't correct the difference coefficients mFo-DFc for phase bias, so you need to multiply either of these results by 2 to get the true electron density (this doesn't apply to a map calculated from the Fourier coefficients 2mFo-DFc which are bias-corrected). I suspect even this doesn't do what you want however: I think you want the total number of electrons contained in a peak to compare with the theoretical value; this can only be obtained by integration of the electron density, which requires peak search/integration software. The peak height is not simply related to the integral, since it clearly depends on the resolution and B factor (both of which make the peaks broader and flatter). I'm not aware of a CCP4 program that will do this, but I could be wrong. Hope this helps! Cheers -- Ian > -Original Message- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of S. Thiyagarajan > Sent: 20 April 2009 11:48 > To: CCP4BB@JISCMAIL.AC.UK > Subject: peak height at mouse click > > Dear CCP4 users > > Is there any easy way of calculating the peak height / number of electrons > at a given position, say a mouse click point in coot. > > Is there any formula to calculate the number of electrons based on sigma > level and peak height, as given in difference map peaks in coot. > > I have some peaks in my map which take water or sodium/magnesium or > chlorine atom with out giving out any positive or negative density upon > further refinement. > > The asymmetric unit has about 425 residues and the data resolution is > 1.5A. > > Thanks and regards > > S. Thiyagarajan > Department of Cell and Organism Biology > Lund University > Sölvegatan 35 > Lund, Sweden > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] peak height at mouse click
Dear Thiyagarajan, To get the peak heights, I would run a peak search on your final electron density map, load the pdb file with the peaks along with the atomic model and click on the peak closest to your spot of interest. If you use the program peakmax, the peakheight is written in the B-factor position. Concerning water/sodium/magnesium/chlorine, if refinement does not give difference peaks you have to use common sense: -Is the B-factor of the unknown ion similiar to B-factors in the neighborhood? If it is similar, your choice of ion could be right, if it is much higher or lower, you should try other ions. -Are there charged residues nearby which would prefer to bind an ion of opposite charge? -What are the distances to nearby atoms (e.g. do they match the expected hydrogen bond/contact distances for a particular ion or water?) -Does the observed coordination geometry match that of the ion of your choice? At 1.5 A resolution, you should be able to make a reasonable guess. Good luck! Herman Schreuder From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of S. Thiyagarajan Sent: Monday, April 20, 2009 12:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] peak height at mouse click Dear CCP4 users Is there any easy way of calculating the peak height / number of electrons at a given position, say a mouse click point in coot. Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot. I have some peaks in my map which take water or sodium/magnesium or chlorine atom with out giving out any positive or negative density upon further refinement. The asymmetric unit has about 425 residues and the data resolution is 1.5A. Thanks and regards S. Thiyagarajan Department of Cell and Organism Biology Lund University Sölvegatan 35 Lund, Sweden
Re: [ccp4bb] peak height at mouse click
Hi Thiyagarajan, the latest version of PHENIX has a command line tool called "phenix.real_space_correlation", that for each atom or residue computes: - map CC (where a user can define any map types, the default: 2mFo-DFc and Fc maps), - 2mFo-DFc map value at atom center, - mFo-DFc map value at atom center. Please let me know if you have question, Pavel. On 4/20/09 3:47 AM, S. Thiyagarajan wrote: Dear CCP4 users Is there any easy way of calculating the peak height / number of electrons at a given position, say a mouse click point in coot. Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot. I have some peaks in my map which take water or sodium/magnesium or chlorine atom with out giving out any positive or negative density upon further refinement. The asymmetric unit has about 425 residues and the data resolution is 1.5A. Thanks and regards S. Thiyagarajan Department of Cell and Organism Biology Lund University Sölvegatan 35 Lund, Sweden
Re: [ccp4bb] peak height at mouse click
Empirically, you can leave out a couple of "average" atoms in the structure, and recalculate the maps. If you leave out a O, N, and C atom, with relatively average B's, then you know how many electrons you should be seeing for each in the difference map. Note that the peak height will vary due to errors in phasing or B-factor. Bernie Santarsiero On Mon, April 20, 2009 11:18 am, Pavel Afonine wrote: > Hi Thiyagarajan, > > the latest version of PHENIX has a command line tool called > "phenix.real_space_correlation", that for each atom or residue computes: > > - map CC (where a user can define any map types, the default: 2mFo-DFc > and Fc maps), > - 2mFo-DFc map value at atom center, > - mFo-DFc map value at atom center. > > Please let me know if you have question, > Pavel. > > > On 4/20/09 3:47 AM, S. Thiyagarajan wrote: >> Dear CCP4 users >> >> Is there any easy way of calculating the peak height / number of >> electrons at a given position, say a mouse click point in coot. >> >> Is there any formula to calculate the number of electrons based on >> sigma level and peak height, as given in difference map peaks in coot. >> >> I have some peaks in my map which take water or sodium/magnesium or >> chlorine atom with out giving out any positive or negative density >> upon further refinement. >> >> The asymmetric unit has about 425 residues and the data resolution is >> 1.5A. >> >> Thanks and regards >> >> S. Thiyagarajan >> Department of Cell and Organism Biology >> Lund University >> Sölvegatan 35 >> Lund, Sweden >> >> >
Re: [ccp4bb] peak height at mouse click
S. Thiyagarajan wrote: Dear CCP4 users Is there any easy way of calculating the peak height / number of electrons at a given position, say a mouse click point in coot. Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot. I have some peaks in my map which take water or sodium/magnesium or chlorine atom with out giving out any positive or negative density upon further refinement. First, go to the coot wiki and pick up the scheme key bindings. If you want density information at a given cursor point: Point at the blob, press the 'g' key (which recentres on the biggest density under the cursor) using the Scheme scripting window: (apply density-at-point (imol-refinement-map) (rotation-centre)) There is no user access to the peak integration code of coot as yet. Paul.
