Re: [ccp4bb] In CCP4 6.1.1 import_scaled isn't reading a dataset_name?
Hi Francis There is a fix for this on the CCP4 problems page: http://www.ccp4.ac.uk/problems.php#6.1.1-ccp4i (item 7). Norman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Francis E Reyes Sent: 17 April 2009 18:55 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] In CCP4 6.1.1 import_scaled isn't reading a dataset_name? Despite setting a dataset name in the dialog box, i get the following in the log file. $TEXT:Warning: $$ comment $$ WARNING: PROJECTNAME not assigned $$ $TEXT:Warning: $$ comment $$ WARNING: CRYSTALNAME not assigned $$ $TEXT:Warning: $$ comment $$ WARNING: DATASETNAME not assigned $$ Which ultimately fails in... #CCP4I TERMINATION STATUS 0 Error from script /sw/share/xtal/ ccp4-6.1.1/ccp4i/scripts/import_scaled.script: can't read "dataset_name": no such variable #CCP4I TERMINATION TIME 17 Apr 2009 11:49:17 #CCP4I MESSAGE Task failed Despite the fact that http://www.ccp4.ac.uk/dist/html/ scalepack2mtz.html says : Specify the project, crystal and dataset names for the output MTZ file. It is strongly recommended that this information is given. Otherwise, the default project, crystal and dataset names are "unknown", "unknown" and "unknown" respectively (where is the date, with no spaces). So there seems to be two broken things here. Any ideas? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] Reindexing Orthorhombic
Mo;lecular replacement can choose any suitable origin so you cant predict. The easiest way is to run "superpose molecules" Match all residues to each other. You should get a rotation matrix -1 0 0 0 0 1 / 0 1 0 with some translation which sjould be very c;lose tpo components of 0, or 1/2 along all the axes.. ie -x+dx z+dz Y+dy where the dx dy and dz are 0 or 1/2 Eleanor and that is what you want James Stroud wrote: Update: The pounding I am beginning to feel in my head is reminiscent of a pounding I felt while working in p43212 a while ago. I think this is an alternate origin issue. Now I just need to figure out how to redefine the origin. James On Apr 16, 2009, at 9:38 PM, James Stroud wrote: Hello All, I have two crystals (that I'll call "data set 1" and "data set 2") that seem to be isomorphic, but y and z are transposed between the two data sets. Reindexing data set 2 with the operators h => -h k => l l => k makes the axes match data set 1, but running MR with the previous data set 2 solution on the newly reindexed data set 2 yields a solution rotated 180 about z with respect to the data set 1 solution. What is the operation to reindex such that real space is rotated 180 about z? These are in P212121. James
[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
[ccp4bb] Refmac 5.5 and B-factors in a DNA model
Dear ccp4bb, I have noticed I get strange results when I have been attempting to refine a protein-DNA complex in refmac 5.5.0088. I see a large variation in the B-factors of connected atoms for the DNA while the protein atoms all seem to refine to sensible values, for example, before refinement ATOM 2160 P Ad Z 2 26.238 -46.384 -6.900 1.00132.37 P ATOM 2161 O1P Ad Z 2 26.966 -46.846 -8.102 1.00132.16 O ATOM 2162 O2P Ad Z 2 26.972 -45.589 -5.892 1.00132.16 O ATOM 2163 O5* Ad Z 2 24.935 -45.563 -7.357 1.00132.09 O ATOM 2164 C5* Ad Z 2 25.029 -44.404 -8.207 1.00131.15 C ATOM 2165 C4* Ad Z 2 23.809 -43.486 -8.137 1.00130.50 C ATOM 2166 O4* Ad Z 2 22.628 -44.204 -8.584 1.00130.90 O ATOM 2167 C1* Ad Z 2 21.474 -43.738 -7.912 1.00132.14 C ATOM 2168 N9 Ad Z 2 20.586 -44.878 -7.656 1.00132.86 N ATOM 2169 C8 Ad Z 2 20.874 -45.936 -6.844 1.00133.05 C ATOM 2170 N7 Ad Z 2 19.931 -46.841 -6.773 1.00133.11 N ATOM 2171 C5 Ad Z 2 18.942 -46.347 -7.599 1.00133.07 C ATOM 2172 C4 Ad Z 2 19.319 -45.140 -8.155 1.00133.06 C ATOM 2173 N3 Ad Z 2 18.567 -44.410 -9.004 1.00133.19 N ATOM 2174 C2 Ad Z 2 17.383 -44.993 -9.259 1.00133.13 C ATOM 2175 N1 Ad Z 2 16.883 -46.154 -8.797 1.00133.05 N ATOM 2176 C6 Ad Z 2 17.673 -46.856 -7.946 1.00133.00 C ATOM 2177 N6 Ad Z 2 17.231 -48.008 -7.459 1.00132.98 N ATOM 2178 C2* Ad Z 2 21.949 -43.038 -6.641 1.00130.70 C ATOM 2179 C3* Ad Z 2 23.473 -42.943 -6.745 1.00129.56 C ATOM 2180 O3* Ad Z 2 24.028 -41.608 -6.453 1.00127.12 O ATOM 425 N TRP A 70 22.973 -26.906 -0.217 1.00 76.89 N ATOM 426 CA TRP A 70 22.385 -26.863 -1.557 1.00 77.16 C ATOM 427 CB TRP A 70 23.469 -26.569 -2.611 1.00 76.94 C ATOM 428 CG TRP A 70 22.947 -26.097 -4.000 1.00 76.52 C ATOM 429 CD1 TRP A 70 22.021 -25.123 -4.252 1.00 75.29 C ATOM 430 NE1 TRP A 70 21.839 -24.989 -5.603 1.00 75.65 N ATOM 431 CE2 TRP A 70 22.660 -25.868 -6.259 1.00 75.66 C ATOM 432 CD2 TRP A 70 23.380 -26.580 -5.281 1.00 75.71 C ATOM 433 CE3 TRP A 70 24.299 -27.554 -5.691 1.00 75.33 C ATOM 434 CZ3 TRP A 70 24.476 -27.779 -7.056 1.00 75.47 C ATOM 435 CH2 TRP A 70 23.750 -27.051 -8.009 1.00 75.84 C ATOM 436 CZ2 TRP A 70 22.837 -26.092 -7.634 1.00 76.15 C ATOM 437 C TRP A 70 21.647 -28.154 -1.886 1.00 77.50 C ATOM 438 O TRP A 70 22.270 -29.143 -2.316 1.00 77.24 O (The residues in the pdb as output from coot 0.5.2) after refinement ATOM 4339 P A Z 2 26.115 -46.360 -6.953 1.00161.28 P ATOM 4340 O1P A Z 2 26.825 -46.773 -8.177 1.00115.03 O ATOM 4341 O2P A Z 2 26.880 -45.599 -5.929 1.00 80.54 O ATOM 4342 O5* A Z 2 24.826 -45.511 -7.390 1.00127.62 O ATOM 4343 C5* A Z 2 24.963 -44.268 -8.095 1.00500.00 C ATOM 4346 C4* A Z 2 23.717 -43.401 -7.975 1.00225.44 C ATOM 4348 O4* A Z 2 22.559 -44.187 -8.350 1.00156.09 O ATOM 4349 C1* A Z 2 21.406 -43.694 -7.694 1.00104.26 C ATOM 4351 N9 A Z 2 20.510 -44.825 -7.408 1.00104.67 N ATOM 4352 C8 A Z 2 20.744 -45.842 -6.524 1.00254.53 C ATOM 4354 N7 A Z 2 19.785 -46.733 -6.464 1.00117.22 N ATOM 4355 C5 A Z 2 18.849 -46.275 -7.373 1.00 93.98 C ATOM 4356 C4 A Z 2 19.271 -45.104 -7.969 1.00 96.16 C ATOM 4357 N3 A Z 2 18.583 -44.406 -8.898 1.00500.00 N ATOM 4358 C2 A Z 2 17.410 -44.988 -9.198 1.00215.48 C ATOM 4360 N1 A Z 2 16.872 -46.121 -8.708 1.00102.77 N ATOM 4361 C6 A Z 2 17.597 -46.787 -7.774 1.00122.19 C ATOM 4362 N6 A Z 2 17.111 -47.910 -7.255 1.00116.30 N ATOM 4365 C2* A Z 2 21.891 -42.938 -6.457 1.00297.54 C ATOM 4368 C3* A Z 2 23.418 -42.883 -6.565 1.00170.10 C ATOM 4370 O3* A Z 2 23.994 -41.570 -6.268 1.00179.14 O ATOM 846 N TRP A 70 22.483 -26.850 -0.143 1.00 59.32 N ATOM 847 CA TRP A 70 22.017 -26.748 -1.526 1.00 59.25 C ATOM 849 CB TRP A 70 23.181 -26.454 -2.468 1.00 59.30 C ATOM 852 CG TRP A 70 22.781 -26.038 -3.869 1.00 59.32 C ATOM 853 CD1 TRP A 70 21.994 -24.979 -4.207 1.00 59.49 C ATOM 855 NE1 TRP A 70 21.884 -24.891 -5.573 1.00 59.57 N ATOM 857 CE2 TRP A 70 22.613 -25.897 -6.147 1.00 58.75 C ATOM 858 CD2 TRP A 70 23.200 -26.637 -5.110 1.00 58.53 C ATOM 859 CE3 TRP A 70 24.009 -27.725 -5.439 1.00 58.37 C ATOM 861 CZ3 TRP A 70 24.205 -28.036 -6.786 1.00 58.38 C ATOM 863 CH2 TRP A 70 23.611 -27.282 -7.790 1.00 58.88 C ATOM 865 CZ2 TRP A 70 22.808 -26.210 -7.493 1.00 59.39 C ATOM 867 C TRP A 70 21.365 -28.043 -1.920 1.00 59.50 C ATOM 868 O TRP A 70 22.020 -28.969 -2.411 1.00 59.13 O A bit more background is probably needed, the data resolution is 3.0 Angstrom and the protein is dimeric so I have applied tight NCS restraints to the protein chains and the DNA bases have been made to strictly obey Watson-Crick geometry by the use of LINK records, I have not use NCS restraints for the DNA. I have also refined using TLS for the protein chains (1 per chain), but not the DNA followed by individual isotropic B-factors. I am running ccp4-6.1.1 on a linux box running centos-5.3. I still get the same B-factors if I do not refine using tls or if I remove the LINK records. I have tried reducing the sigma-values for
[ccp4bb] Refmac refinement with two ligands
Dear CCP4 community, I would like to refine a structure with two bound ligands using Refmac. However, the Rafmac GUI allows only one library to be read in. How can I combine or synthesise two .cif/.lib files (originating from the Dundee DRG server) and circumvent this problem? Many thanks in advance, Alex
Re: [ccp4bb] Refmac refinement with two ligands
Alex, The CCP4i 6.1.1 refmac allows you to combine multiple .cif using Merge LIBINs. Have you tried that? Joe aber...@mrc-lmb.cam.ac.uk wrote: Dear CCP4 community, I would like to refine a structure with two bound ligands using Refmac. However, the Rafmac GUI allows only one library to be read in. How can I combine or synthesise two .cif/.lib files (originating from the Dundee DRG server) and circumvent this problem? Many thanks in advance, Alex
[ccp4bb] Refmac refinement with two ligands -- Sorted! --THANKS VERY MUCH!!!
merge monomer libraries under refinement does the trick (amongst others like combing the textfiles of the cif files) Thanks, Alex
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
[ccp4bb] Postdoctoral Research Associate positions in X-ray Crystallography
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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 >> >> >
[ccp4bb] largest distance between atoms
Hey all, is there a script out there that computes the longest extent of a molecule and determines which atoms define the 'space diagonal'. In other words, I'm looking for the two atoms in a molecule that are most distant from each other. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] largest distance between atoms
Andreas,
In PyMOL:
print cmd.get_extent(selection)
where selection is the name of the molecule you'd loaded.
Note that the set of coordinates which define an XYZ extent do not necessarily
correspond to only to atoms.
To find the two atoms most distant from one another, you could iterate over all
pairs of coordinates. This is possible in PyMOL as shown below, but is
impractically slow for large structures due to the N^2 dependence.
# PyMOL Script: longest_diagonal.pml
# takes 5-10 seconds with a 1,600 atom structure
# (1) extract all coordinates into a temporary array "xrd"
xrd = []
iterate_state 1, all, xrd.append( ((x,y,z), model+"`"+str(index)) )
python
from chempy import cpv
xrd_len = len(xrd)
# (2) measure all diagonals and keep the longest
diag = (-1.0,"none","none")
for i in range(xrd_len):
for j in range(i+1,xrd_len):
dst = cpv.distance(xrd[i][0], xrd[j][0])
if dst > diag [0]:
diag = (dst, xrd[i][1], xrd[j][1])
# (3) draw the longest diagonal
cmd.distance("diag", diag[1], diag[2])
python end
Cheers,
Warren
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Andreas Förster
> Sent: Monday, April 20, 2009 10:25 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] largest distance between atoms
>
> Hey all,
>
> is there a script out there that computes the longest extent of a
> molecule and determines which atoms define the 'space diagonal'. In
> other words, I'm looking for the two atoms in a molecule that are most
> distant from each other.
>
> Thanks.
>
>
> Andreas
>
>
> --
> Andreas Förster, Research Associate
> Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
> http://www.msf.bio.ic.ac.uk
>
>
>
Re: [ccp4bb] largest distance between atoms
Warren DeLano wrote: To find the two atoms most distant from one another, you could iterate over all pairs of coordinates. This is possible in PyMOL as shown below, but is impractically slow for large structures due to the N^2 dependence. # PyMOL Script: longest_diagonal.pml # takes 5-10 seconds with a 1,600 atom structure Doing it in fortran shaves that to 93 ms for 1600 atoms, but n^2 catches up rapidly: 32657 atoms takes 29 s. http://sb20.lbl.gov/berry/for/pdbdistmax.for (compiles w gfortran, not tested extensively, author takes no responsibility, etc) Ed
[ccp4bb] Low-level disable ccp4i database...?
Panic, I'm trying to configure ccp4i for a tutorial (i.e. multiple clueless
students about to descend on the same user account), but the DB handler is
somehow not responding, nor will it let me get to System Administration to turn
it off. ("I'm sorry Dave, I'm afraid I can't do that.")
(Ref Ronan Keegan's reply on 18 March 09 on the BB.)
What is the low-level way to turn it off? It must be either in the
installation directory, or in ~/.CCP4 somewhere, but I couldn't find it.
Hope someone's solved this before...
phx
Re: [ccp4bb] Low-level disable ccp4i database...?
Well, the guys may have distributed a phx-specific configure file, but
otherwise, I think it is USE_DBCCP4I_ON_STARTUP in ~/.CCP4/unix/configure.def
At least it worked for me after the briefest of tests of the Windows equivalent.
Cheers
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Frank Von Delft
Sent: Mon 4/20/2009 11:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Low-level disable ccp4i database...?
Panic, I'm trying to configure ccp4i for a tutorial (i.e. multiple clueless
students about to descend on the same user account), but the DB handler is
somehow not responding, nor will it let me get to System Administration to turn
it off. ("I'm sorry Dave, I'm afraid I can't do that.")
(Ref Ronan Keegan's reply on 18 March 09 on the BB.)
What is the low-level way to turn it off? It must be either in the
installation directory, or in ~/.CCP4 somewhere, but I couldn't find it.
Hope someone's solved this before...
phx
[ccp4bb] X-ray fluorescence: numbers for fluorescence lifetime and quantum yield
Hello Crystallographers, Is the assumption correct that x-ray fluorescence is exactly the same process as occurs in the UV-vis range, but simply with higher-energy photons? If so, does anybody know of a source for numbers like fluorescence lifetime and quantum yield for the "usual suspect" heavy atoms (Se, Hg, etc.). This might be quite helpful to me... Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] X-ray fluorescence: numbers for fluorescence lifetime and quantum yield
On Monday 20 April 2009 16:33:57 Jacob Keller wrote: > Hello Crystallographers, > > Is the assumption correct that x-ray fluorescence is exactly the same > process as occurs in the UV-vis range, but simply with higher-energy > photons? Yes. > If so, does anybody know of a source for numbers like fluorescence > lifetime don't know > and quantum yield http://www.csrri.iit.edu/periodic-table.html > for the "usual suspect" heavy atoms (Se, Hg, > etc.). This might be quite helpful to me... -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] Low-level disable ccp4i database...?
Yes, I was framed. Thanks for the quick response.
Okay, question 2:
There is no ~/.CCP4/unix/configure.def, because it's the first time ccp4i is
run on this account. What do I do?
And question 3:
How can I set it up for all users? Somewhere in $CCP4? (Turns out home
directories are local on every machine.)
And question 4:
Will this be multi-user in the upcoming release that will not need overriding
(alla Ronan Keegan's email)? Oh please let it be, there are so few single-user
labs...
phx
>>> "Winn, MD (Martyn)" 21/04/09 0:15 >>>
Well, the guys may have distributed a phx-specific configure file, but
otherwise, I think it is USE_DBCCP4I_ON_STARTUP in ~/.CCP4/unix/configure.def
At least it worked for me after the briefest of tests of the Windows equivalent.
Cheers
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Frank Von Delft
Sent: Mon 4/20/2009 11:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Low-level disable ccp4i database...?
Panic, I'm trying to configure ccp4i for a tutorial (i.e. multiple clueless
students about to descend on the same user account), but the DB handler is
somehow not responding, nor will it let me get to System Administration to turn
it off. ("I'm sorry Dave, I'm afraid I can't do that.")
(Ref Ronan Keegan's reply on 18 March 09 on the BB.)
What is the low-level way to turn it off? It must be either in the
installation directory, or in ~/.CCP4 somewhere, but I couldn't find it.
Hope someone's solved this before...
phx
Re: [ccp4bb] Low-level disable ccp4i database...?
On 03:44 Tue 21 Apr , Frank Von Delft wrote:
> Okay, question 2:
> There is no ~/.CCP4/unix/configure.def, because it's the first time
> ccp4i is run on this account. What do I do?
>
> And question 3:
> How can I set it up for all users? Somewhere in $CCP4? (Turns out
> home directories are local on every machine.)
>
> And question 4:
> Will this be multi-user in the upcoming release that will not need
> overriding (alla Ronan Keegan's email)? Oh please let it be, there
> are so few single-user labs...
Try the same variable in ${CCP4I_TOP}/etc/configure.def.dist (or without
the .dist).
--
Thanks,
Donnie
Donnie Berkholz
P. Andrew Karplus lab
Oregon State University
pgpq9dGnAUi5j.pgp
Description: PGP signature
[ccp4bb] open mask with coot
hello Crystallographers I have generated a solvent mask by CNS ,how can I open the .mask file with COOT? The mask file generated by CNS is different from CCP4. The mask fomat of CCP4 is mask.msk,and I can choose open map to open it in COOT. but I cann't open CNS format .mask with COOT, it did not recoganize the fomat. Thanks and regards! Xiaowei 2009-04-21 Xiaowei Pan
