Re: [ccp4bb] str solving problem

2013-06-21 Thread Francis E. Reyes
and struggle is on the peak... There are a number of ccp4bb postings about crystal reproducibility or crystal diffraction improvement. Search the archives for these. F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

Re: [ccp4bb] PILATUS data collection

2013-05-08 Thread Francis E. Reyes
Graeme and Bob, Wow... It's great to learn from actual experiences. Thanks much for this write up. If this were stackoverflow, +1. F On May 8, 2013, at 12:32 AM, Graeme Winter graeme.win...@gmail.com wrote: A couple of extra comments on top of Bob's rather comprehensive

Re: [ccp4bb] Strange density in solvent channel and high Rfree

2013-03-15 Thread Francis E Reyes
...@gmail.com wrote: I/Isig.=4.4 - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

Re: [ccp4bb] a challenge

2013-01-13 Thread Francis E Reyes
Ok, I'll bite. I dare anyone who considers themself an expert macromolecular crystallographer to find a way to build out of this map. I put emphasis on this map. Short of actually cheating (see below), there doesn't seem to be any automated way to arrive at a solved structure from these

Re: [ccp4bb] NCS from electron density

2012-12-12 Thread Francis E Reyes
to another). Thanks for your help, Nicolas - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

Re: [ccp4bb] NCS from electron density

2012-12-12 Thread Francis E Reyes
On Dec 12, 2012, at 2:55 PM, Francis E Reyes wrote: I've had good experience with GETAX if you have a self rotation peak. Be careful about moving the NCS operator from program to program. Phenix/DM/RAVE all have specific formats for how it should be presented. F On Dec 12, 2012

Re: [ccp4bb] Nobel Prize 2012

2012-10-10 Thread Francis E Reyes
- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

Re: [ccp4bb] How to output water molecules with Phaser?

2012-10-02 Thread Francis E Reyes
Hi Randy When you say carried along are you saying that they are used as part of the molecular replacement search? Or are they temporarily put aside and them simply added to the PDB in frame with the molecular replacement solution (but are not part of the weighted structure factors output in

Re: [ccp4bb] Tricky MR problem

2012-10-01 Thread Francis E Reyes
[1] In addition to using lower resolution data, you should check a variety of RMSDs as well. In fact constructing an RMSD / high resolution contour plot would be beneficial to determine the optimum set of parameters. (That is if you're using PHASER). [2] You say you suspect two molecules

Re: [ccp4bb] dmmulti cross-crystal averaging question

2012-09-21 Thread Francis E Reyes
crystals have one domain that is the same in each. We'd like the average the one domain between the crystals, but leave the other domains unaveraged. How do we describe that to dmmulti? thanks, Dave -- - Francis E. Reyes PhD 215 UCB

Re: [ccp4bb] DM with twinned data

2012-09-02 Thread Francis E Reyes
With DM errors, it would be best to supply the input you used for DM as well as DM's complete error output. On Sep 2, 2012, at 9:59 PM, Sofia Caria wrote: Dear all, Recently I have been playing with some twinned data (Britton alpha 0.447). Phasing was done by MR and since I have

[ccp4bb] CNS compliant addition of hydrogens to structure?

2012-07-17 Thread Francis E Reyes
Anyone know of a util that'll add hydrogens in a naming scheme consistent with CNS? (reduce doesn't do this). Thanks! F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Large unit cell, overlaps

2012-07-16 Thread Francis E Reyes
E. Reyes PhD 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Large unit cell, overlaps

2012-07-16 Thread Francis E Reyes
of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 17/07/2012, at 2:53 PM, Francis E Reyes wrote: The cell predictions look like they're

Re: [ccp4bb] how to get phase of huge complex

2012-06-12 Thread Francis E Reyes
Do you have crystals? Do they diffract? If so, to what resolution? What resolution do you require to answer your biological question? F On Jun 12, 2012, at 7:46 PM, LISA science...@gmail.com wrote: Hi all, My work is to solve huge complex containing 4 different proteins and total

Re: [ccp4bb] DNA/RNA modeling

2012-05-23 Thread Francis E Reyes
For the RNA I recommend Eric Westhof's Assemble. F On May 23, 2012, at 9:32 AM, jens j birktoft wrote: Hi everybody, Does anyone know of a (non-commercial) software that are suitable for modeling DNA/RNA structures. Coot is great, however I am looking something that allows more

Re: [ccp4bb] phaser: high z score but no sol

2012-04-20 Thread Francis E Reyes
P21.. You sure about this space group? (very high confidences for space group and laue group in pointless?) F On Apr 19, 2012, at 12:20 AM, LISA wrote: Hi all, I am trying to solve one structure by molecular replacement with phaser in CCP4. This a complex of a multi-domain domains

[ccp4bb] Disorder or poor phases?

2012-04-10 Thread Francis E Reyes
in this region because of disorder or bad model phases? Would love people's thoughts on this one, F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Disorder or poor phases?

2012-04-10 Thread Francis E Reyes
for most crystallographic refinement packages). F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] mtz2cif capable of handling map coefficients

2012-04-05 Thread Francis E Reyes
It seems that deposition of map coefficients is a good idea. Does someone have an mtz2cif that can handle this? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

2012-04-02 Thread Francis E Reyes
I'm now preparing for the flood of 'unsubscribe ccp4bb' requests On Apr 2, 2012, at 9:15 AM, Bernhard Rupp (Hofkristallrat a.D.) wrote: Guys, http://www.youtube.com/watch?v=CobZuaPMQHw second 9 in this 22 sec video -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] about heavy atom derivatization

2012-03-30 Thread Francis E Reyes
is there? thanks in advance for help and suggestions.. regards Shanti Pal Gangwar - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Defining beamstop and error during indexing- moslfm

2012-03-22 Thread Francis E Reyes
. Perhaps a screen shot of one of the images where this is happening would be helpful. So we can judge the quality of the diffraction / whether the space group is correct, etc. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Using intrinsically bound Zn atoms for phasing

2012-03-06 Thread Francis E Reyes
http://skuld.bmsc.washington.edu/scatter/AS_form.html Maybe useful to you. However, I would advise to do a fluorescence scan over the range given in the graph and then use chooch to provide the precise energies for your peak and inflection. If you have a large crystal don't expose all of

Re: [ccp4bb] sudden drop in R/Rfree

2012-03-02 Thread Francis E Reyes
data if we consider the difference. I appreciate your valuable suggestions. Thanks Raj - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] effects of salt on twinned crystals

2012-02-22 Thread Francis E Reyes
in the same drop. Thanks for any input. - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] proper or improper ncs?

2012-02-21 Thread Francis E Reyes
of peaks on the self rotation maps). Any help would be appreciated. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] offtopic : Signed binaries in the next OS X

2012-02-16 Thread Francis E Reyes
). Or the user can go rogue and 'Ctrl-Click' install any application. http://www.apple.com/macosx/mountain-lion/security.html Personally I'll probably choose Mac App Store and identified developers. (I imagine this will be the default). - Francis E

Re: [ccp4bb] offtopic : Signed binaries in the next OS X

2012-02-16 Thread Francis E Reyes
(for free) and then distribute your public key to the community, in case you want to do something similar. [FUD] OS X won't trust those keys, only the ones that come from apple [/FUD] F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] choice of wavelength

2012-02-15 Thread Francis E Reyes
Acta Cryst. (1997). D53, 734-737[ doi:10.1107/S0907444997007233 ] The Ultimate Wavelength for Protein Crystallography? I. Polikarpov, A. Teplyakov and G. Oliva http://scripts.iucr.org/cgi-bin/paper?gr0657 may give some insights. To the OP, have you solved the structure? In some cases,

Re: [ccp4bb] Freezing crystal

2012-02-07 Thread Francis E Reyes
not a surprise to me and if you have not tried small crystals from the same batch well then you missed 50% of your chances to solve s structure with the first light the crystals saw. J├╝rgen - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Soaking Kinase Crystals with ATP analogues

2012-02-01 Thread Francis E Reyes
crystals diffract? Do you see the analogue? F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] No diffraction

2012-01-26 Thread Francis E Reyes
. Any suggestions to improve diffraction would be welcome. Thanking you in advance. Theresa - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Merging data collected at two different wavelength

2012-01-20 Thread Francis E Reyes
in Crystallography and Biophysics University of Madras Chennai,India - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Merging data collected at two different wavelength

2012-01-18 Thread Francis E Reyes
atoms for each ) were used in phasing. Aren't analyzing the differences (independent of source) the important bit anyway? F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Choice of heavy atom derivatives

2012-01-11 Thread Francis E Reyes
at home. If it kills your crystals, move to more toxic things... Thanks in advance, Federica Cheers, F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] At what resolution is (individual,group,one per residue, two per residue) appropriate? was Re: [ccp4bb] Structure Determination combining X-ray Data and NMR

2012-01-06 Thread Francis E Reyes
- I'll have to check out the details of how phenix handles it, and give it a try. Pete - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] live streaming of ccp4 study weekend

2012-01-05 Thread Francis E Reyes
/events/CCP4_2012/programme.html . All details are accessible from the ccp4 homepage (http://www.ccp4.ac.uk). Charles Ballard CCP4 - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] model building at 3.2 A

2011-12-08 Thread Francis E Reyes
On the other hand, shooting a lower resolution crystal may get you the conformation of the disordered domain. Surprising at first thought, but was true in p97/VCP from the Brunger Lab. F On Dec 7, 2011, at 11:47 PM, atul kumar wrote: Dear all I have crytals which diffract up to

Re: [ccp4bb] Protein-DNA complex crystallization

2011-11-21 Thread Francis E Reyes
to set drops, only DNA crystals. Kindly suggest me, what could be done. Thanks Regards, Umar Farook.S - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] raw data deposition

2011-10-28 Thread Francis E Reyes
is different. I could test my hypothesis by reprocessing the data were it available. and thank you for providing yours . F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] IUCr committees, depositing images

2011-10-27 Thread Francis E Reyes
for improvement of a group II intron structure. Acta Crystallogr D Biol Crystallogr (2010) vol. 66 (Pt 9) pp. 988-1000 F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] raw data deposition

2011-10-27 Thread Francis E Reyes
sure this has to be done, but consensus in this area is equally important. - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] solvent mask from one crystal form applied to the other second ...

2011-10-24 Thread Francis E Reyes
at similar features in both maps and using lsqkab to get the transformation matrix; but this approach would probably need tuning to get a good alignment. Good luck, Pete Francis E Reyes wrote: Hi all I'm using dmmulti and one of my crystal forms seems to have a better solvent mask (after

[ccp4bb] how to input O-style rotation matricies in dmmulti?

2011-10-23 Thread Francis E Reyes
). Is there some formatting error I'm not seeing? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] Ice rings...

2011-10-11 Thread Francis E Reyes
algorithm by those programs during integration, or is it up to the scaling/merging (by SCALA for example) step to deal with them? Thanks! F inline: PastedGraphic-1.tiff - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] off topic: Adobe demos deblur of photos...

2011-10-11 Thread Francis E Reyes
density maps. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] XDS suggestions: Frame.cbf shows white circles in the beamstop...

2011-10-08 Thread Francis E Reyes
I already started with an ellipse... should I extend with a rectangle down the shaft of the beamstop?(this is FRAME.cbf after integration) inline: PastedGraphic-2.tiff Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado

Re: [ccp4bb] Linux vs MacOS for crystallographic software

2011-09-30 Thread Francis E Reyes
Scott wrote: she asked were a few questions about a specific computer (HP Z210 8 GB with a low end Quadro Nvidia 400 512 MB) running any Linux, and a specific computer (IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB) - Francis E. Reyes M.Sc

Re: [ccp4bb] Linux vs MacOS for crystallographic software

2011-09-30 Thread Francis E Reyes
better than then drives from 2007. I doubt it though. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] neutron diffraction 'difference' map?

2011-09-13 Thread Francis E Reyes
you want to use it as a tool to verify the location of a ligand binding site. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] refmac and DNA (and now RNA)

2011-09-12 Thread Francis E Reyes
specific to my setup? Cheers, Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs - Francis E. Reyes M.Sc. 215

Re: [ccp4bb] refmac and DNA (and now RNA)

2011-09-12 Thread Francis E Reyes
residue names, however pdb may use only one of them. - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] How to handle b-factors at low resolution and very incomplete model?

2011-08-23 Thread Francis E Reyes
body or very restrained ( secondary structure | reference structure | etc ) refinement of the coordinates for helping the fit. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] Modeling ligands in binding pockets when the density is weak.

2011-08-23 Thread Francis E Reyes
this and subsequent refinement still does not produce the expected density for the chains. or [3] Your solution here. If this situation has been discussed before, please let me know . F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] COOT library

2011-08-17 Thread Francis E Reyes
are not compatible. I'm trying to build an RNA molecule by the way. Any suggestions? Eric - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] Good performing low resolution iterative model building programs?

2011-08-11 Thread Francis E Reyes
- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] anomalous scatterer

2011-08-09 Thread Francis E Reyes
at the Ir peak and Ir at the Co peak. Use both to cross validate your model (when you get to it) and calculate experimental phases using both (dual SAD or 2wl MAD for each heavy atom). So no it's not surprising. F - Francis E. Reyes M.Sc. 215 UCB

[ccp4bb] Multi crystal averaging : data on same scale before averaging?

2011-07-14 Thread Francis E Reyes
to scale) ? Am I interpreting this correctly? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] Way off topic.. less than 96 well culture plates in black?

2011-06-27 Thread Francis E Reyes
them to be black on the walls. I'm looking for a supplier / catalog number of such plates. To save bb spam, I'll take replies privately. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

2011-06-16 Thread Francis E Reyes
Never had problems with evaporation (and this is in the relatively dry climate of Denver, CO, especially in the winter when the relative humidity is in the low 20%). Using the Thermo Scientific Nanodrop 2000c. We use it also as a prerequisite for ITC, which can be very sensitive to proper

[ccp4bb] confused about ncs in this xtal and local correlation maps with maprot.

2011-05-27 Thread Francis E Reyes
of the data is about 3.1A). The unit cell is: 142.0500 142.0500 137.9200 90. 90. 120. P6422. Any ideas appreciated, Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] Where is multillog for dmmulti?

2011-05-04 Thread Francis E Reyes
Can someone return their full path of the location of multilog (used for browsing dmmulti output)? I can't find it in my ccp4-6.1.13 installed from Mr Scott's distrib. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[ccp4bb] early (incomplete model) refinement if you had the location of a bound (highly occupied) anomalous scatterer

2011-04-01 Thread Francis E Reyes
position with respect to your protein. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] molecular replacement solution

2011-03-15 Thread Francis E Reyes
I doing wrong? Please help me with suggestions Many thanks Careina - Francis E. 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

[ccp4bb] molrep NOSG=-1 (space group checking)

2011-03-15 Thread Francis E Reyes
that explains how 'Scor' is computed? [2] Based on the results above, it seems that P 21 21 21 is the correct s.g.? [3] Why the failure? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu

[ccp4bb] inverse beam integration/scaling protocol

2011-02-01 Thread Francis E Reyes
Hi all Is there a walkthru/tutorial for processing inverse beam images with imosflm/scala? Googling a few things didn't get me anywhere. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu

Re: [ccp4bb] CCP4 SW Web Broadcast

2011-01-06 Thread Francis E Reyes
. Our apologies for the inconvenience. Best wishes, Ronan Ronan Keegan CCP4 Group - Francis E. 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] Mg2+ or water

2010-12-20 Thread Francis E Reyes
it with water refines perfectly with no indication of positive difference density even at 2.0 sigma cut off. Should I modelled this density as water or as Mg2+. Your opinions are appreciated. JL test.png.odp - Francis E. Reyes M.Sc. 215 UCB University

Re: [ccp4bb] off topic: advice for crystallography workstation/server

2010-12-15 Thread Francis E Reyes
Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG Groningen, The Netherlands - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC

[ccp4bb] ncs operator confusion...

2010-12-01 Thread Francis E Reyes
- -0.1051 -0.9808 0.1642 shift - invert - -108.0451 47.655 -17.5654 end Can someone supply me with the correct matrix to input into DM (and what convention it is?) Thanks F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg

Re: [ccp4bb] ncs operator confusion...

2010-12-01 Thread Francis E Reyes
Oops It pays to view the pdbset log as it gives the right matrix. F On Dec 1, 2010, at 10:41 AM, Francis E Reyes wrote: Hi all I'm trying to figure out rotation matricies for ncs averaging in DM. Except the conventions have got me confused. The following input script for pdbset

[ccp4bb] limit for number of files for CAD...

2010-11-03 Thread Francis E Reyes
CCP4'ers, Are 9 datasets the maximum for an mtz file? or a single run of cad? The manual (http://www.ccp4.ac.uk/html/cad.html) seems to suggest that 9 is the limit per cad run but not for a given mtz. F - Francis E. Reyes M.Sc. 215 UCB

[ccp4bb] Crystal lattice builder (educational)

2010-11-01 Thread Francis E Reyes
Hi all Are there any online/offline 3D crystal lattice builders to explore symmetry relationships in the unit cell given say a space group and unit cell parameters? I need one for an educational opportunity. Thanks! F - Francis E. Reyes M.Sc

[ccp4bb] Radiation damage with crystals containing metal centers (TaBr people chime in?)

2010-10-04 Thread Francis E Reyes
one backsoaked. Thanks F - Francis E. 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] difficult P1 crystal

2010-09-30 Thread Francis E Reyes
, alpha=119, beta=119, gamma=90), - Francis E. 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

[ccp4bb] Lousy diffraction at home but fantastic at the synchrotron?

2010-09-28 Thread Francis E Reyes
Hi all I'm interested in the scenario where crystals were screened at home and gave lousy (say 8-10A) but when illuminated with synchrotron radiation gave reasonable diffraction ( 3A) ? Why the discrepancy? Thanks F - Francis E. Reyes M.Sc

[ccp4bb] offtopic: effect of compound impurities on ITC?

2010-08-24 Thread Francis E Reyes
never are able to completely get rid of Y. How does this affect the analysis of determining the derivative's affinity by ITC? References or personal experience is appreciated! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg

[ccp4bb] offtopic: adjustable vertical sequencing gels.

2010-07-21 Thread Francis E Reyes
to be able to accommodate 35 cm (wide) by 26-30cm (height) plates. Please reply privately. F - Francis E. 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] Stuck refinement

2010-06-23 Thread Francis E Reyes
Sorry a late comer to this thread but the OP mentioned tweaking the error model in HKL2000. I have heard this before.What's the validity in this? Does it actually help or does it only help the integration numbers but you'll pay for it during refinement? FR On Jun 23, 2010, at 8:25 AM,

[ccp4bb] Charge flipping.

2010-05-22 Thread Francis E Reyes
Hi all I've been playing around with charge flipping for macromolecular substructure determination with pretty promising results. I'm particularly attracted to the fact that it solves structures in P1, with no space group assumptions and curious how it would handle some of the

[ccp4bb] odd request: add phase error linearly with resolution

2010-03-19 Thread Francis E Reyes
Hi all I'd like to add a phase error to my PHIB's and FOM's (experimental phases) that increases linearly with higher resolution.. it's akin to taking good phases and making them bad. Any approaches on how this can be done? Thanks FR - Francis Reyes

[ccp4bb] self rotation education

2010-03-18 Thread Francis E Reyes
Hi all I have a solved structure that crystallizes as a trimer to a reasonable R/Rfree, but I'm trying to rationalize the peaks in my self rotation. The space group is P212121, calculating my self rotations from 50-3A, integration radius of 22 (the radius of my molecule is about 44). I can see

[ccp4bb] density in LLG maps for heavy atoms sit on xtal axes?

2010-03-03 Thread Francis E Reyes
Is this a cause for concern? FOM's are over 0.5 and Phasing Power is over 2.0. 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

[ccp4bb] low resolution phasing protocols

2010-03-02 Thread Francis E Reyes
Hi all I'm in search of literature *detailing* low resolution [4-5A] phasing protocols. Heck I'll take detailed thesis chapters (since they tend to be more detailed than pubs anyway). If you ribosome people are on this board I'd love to hear from you. [sarcasm]Searching for 'grasping at

[ccp4bb] how to supply the following twin operator to detwin?

2010-02-01 Thread Francis E Reyes
Hi All I'm having trouble with the following ... title [No title given] operator -1/2*h+1/2*k-l, 1/2*h-1/2*k-l, -1/2*h-1/2*k labin I(+)=I_Unspecified(+) SIGI(+)=SIGI_Unspecified(+) I(-)=I_Unspecified(-) SIGI(-)=SIGI_Unspecified(-) end I keep getting symmetry operator error. Thanks FR

[ccp4bb] Omit maps in cases of NCS?

2010-01-26 Thread Francis E Reyes
How does one calculate a simulated annealing omit map in cases of non crystallographic symmetry? The omit map is being used to identify the presence and configuration of a ligand and surrounding residues. The omit region therefore will contain the ligand and residues within hydrogen

[ccp4bb] Experience with experimental phasing in P21 with c cos Beta = - a/2 ?

2010-01-14 Thread Francis E Reyes
Or know of any references besides Declercq and Evrard, 2001 ? I'd love to hear from you. Please PM me. Cheers FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640

Re: [ccp4bb] Reindexing P21.. the process?

2010-01-13 Thread Francis E Reyes
+1 phenix FTW FR On Jan 13, 2010, at 3:28 PM, Peter Zwart phzw...@lbl.gov wrote: try using phenix.reflection_file_converter data.sca --change_of_basis=h,-k,-h-l --sca=reindex.sca or something like that HTH Peter 2010/1/13 Francis E Reyes francis.re...@colorado.edu: Hi all I have

Re: [ccp4bb] How to reduce R-factor and Free-R

2009-12-18 Thread Francis E Reyes
What is the space group? Is there unmodeled density? Are all residues in your construct built? What is the refinement protocol? FR On Dec 18, 2009, at 6:47 AM, james09 pruza james09x...@gmail.com wrote: Dear All, I am trying to solve a 2.55 A resolution data set. The R-factor is

[ccp4bb] optimizing ncs masks in DM + interpreting output

2009-11-10 Thread Francis E Reyes
Hi all I have a rotation + translation component for the 2-fold given to me by GETAX using low resolution low quality experimental maps. I understand that these are input into DM for NCS averaging. What are signs of progress as well as how does one usually optimize the mask? When doing

[ccp4bb] offtopic: screening compounds libraries for binding via crystallography

2009-10-28 Thread Francis E Reyes
Hi All I'm interested in screening small molecule libraries against my xtal for potential binders. There are many papers that cover this (http://www.nature.com/nbt/journal/v18/n10/abs/nbt1000_1105.html , for example). If you have had experience in this field, please email me privately as

[ccp4bb] fix or scale bfactors during processing?

2009-10-27 Thread Francis E Reyes
Hi all I have pretty low res data (4-4.5A) and was wondering what's the suggestion for allowing the bfactors to vary or keep them fixed during scaling. If I fix them, xtriage reports wonderful anomalous signal whereas if they are varied, the anomalous signal is gone. I have natives and

[ccp4bb] Using own orientation matrix with imosflm.

2009-10-23 Thread Francis E Reyes
Hi All I have a predetermined matrix from labelit, how can I use it with imosflm? I add the matrix file under 'Images', but I cannot integrate. Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver

[ccp4bb] multiple datasets in Xds

2009-09-29 Thread Francis E Reyes
Hi all Can XDS take in additional images that have a different template name and reside in a different directory? The reason is that I have high res images and then low res images in different directories that I want XDS to consider. Thanks! FR

[ccp4bb] Interpretation of wilson statistics and pseudosymmetry in R32.

2009-09-28 Thread Francis E Reyes
Hi all I'm working on a structure of an RNA. Phases were obtained via SAD and the structure was refined to 21/26 % on R and R-free with a resolution of 2.8A, single molecule in the ASU. 7 residues were missing in a disordered loop out of a total of 54 residues in the asu. The cell was

[ccp4bb] Using SAXS data for phasing at mediocre resolution.

2009-09-14 Thread Francis E Reyes
Hi all I'm looking for anyone who has had (practical) experience using SAXS data to phase 4.2 A crystals. Please email me. FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2

[ccp4bb] suggestions for SIR with strong diffraction anisotropy in the derivative

2009-08-26 Thread Francis E Reyes
Hi all I'm trying SIR on my crystal both are C222. Native Cell Dimensions: 97.66 243.45 87.62 90 90 90 Resolution: 4.3 Derivative Cell Dimensions: 96.9100 244.66 87.61 90 90 90 Resolution: 4.7 . I plan to scale together using FHScal. Ctruncate says that my derivative has strong

[ccp4bb] strange pattersons

2009-08-19 Thread Francis E Reyes
Hi All Im receiving some strange patterns in my pattersons. Space group is C222 with no confidence (due to resolution) of systematic absences to transform to C2221. Thanks! FR pattersonmap.pdf Description: Adobe PDF document - Francis Reyes

[ccp4bb] a simple question: how is redundancy measured?

2009-08-11 Thread Francis E Reyes
For a given reflection (h,k,l) how much does each situation increase the redundancy ? and which maximizes the ability to measure anomalous differences? (so assume we're separating friedel pairs here) a) measuring the same reflection again b) measuring a symmetry related reflection c) both

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