Re: [ccp4bb] happy/sad maps

what about if you run a 2-D FFT rather than 2-D FFT, if your hand drawing map in on a 2-D paper? > On Apr 28, 2023, at 10:48 AM, James Holton wrote: > > Its still April, but this one isn't a joke. > > The smiley-face electron density in the left panel of the attached image has > the remarkabl

Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

If data processing to be ok and all possible monoclinic and orthorombic SG gave unreasonable high Rs, maybe good to give a try with p1 space group?  Since the p-lattice indexing gave same a and  b also very close alpha and beta, it could not exclude the possibility of p1 then twinned (also together

Re: [ccp4bb] To Trim or Not to To Trim

from my iPhoneOn Mar 19, 2023, at 11:30 PM, Lijun Liu wrote:James:Sent from my iPhoneOn Mar 19, 2023, at 2:37 PM, James Holton wrote: They say one test is worth a thousand expert opinions, so I tried my hand at the former. The question is: what is the right way to

Re: [ccp4bb] To Trim or Not to To Trim

James:Sent from my iPhoneOn Mar 19, 2023, at 2:37 PM, James Holton wrote: They say one test is worth a thousand expert opinions, so I tried my hand at the former. The question is: what is the right way to treat disordered side chains?: a) omit atoms you cann

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

racting side chains will almost certainly have different orientations, > which necessitates a twinning of the whole structure. > Best, > Herman > > Von: CCP4 bulletin board Im Auftrag von Lijun Liu > Gesendet: Freitag, 27. August 2021 14:22 > An: CCP4BB@JISCMAIL.AC.UK >

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

I believe it is a twin from P32. Not like the assignment of double conformations with partial occupancies to small part of asu, for examples, a side chain of lysin or a small fragment of a protein, which have both conformations stayed in the same specific asu at the same time. For this p3221 a

[ccp4bb] Citation of REFMAC!

r. D74, 215-227 = Obviously, the Journal information of the two got swapped.  Also, for the top one, Author Carlon A.'s name was missing. You guys did great job, and deserve correct citations! Best regards, Lijun Li

Re: [ccp4bb] [OT] Structure-related pun needed urgently

Not sure if it is of the taste but I sometimes joked like: == It is a complex that it is a complex when a ligand rather than a water binds there. I worry about data security when running TLS, so to computer security when using TNT. I keep solving important structure

Re: [ccp4bb] Chain ID number limit!

(both supported in Phenix). Pavel On Mon, Jul 24, 2017 at 5:09 PM, Lijun Liu <mailto:lijunli...@gmail.com>> wrote: Hi: this must be an old problem but I would like to know if there are other ideas to make things easier. I solved a structure that contains 240 helices of identical

[ccp4bb] Chain ID number limit!

Hi: this must be an old problem but I would like to know if there are other ideas to make things easier. I solved a structure that contains 240 helices of identical sequences in the asymmetric unit. Handling so many chains is really a headache as pdb contains only a single column for chain ID

[ccp4bb] superpose bug?

tried to generate an input script from ccp4i running. Unfortunately, running with the particular "superpose using S-S-M" option did not generate an input card (other options OK, what a bad luck). I appreciate a working script (ccp46.4.0) or a "debugged" source code for compilation. Thanks. Lijun Liu

Re: [ccp4bb] Twinning in space group Pc

Hi, Pc may not be the space group for your crystal, if the molecule is chiral. Seems like the data were forced to be reduced to a mirror_related SG. Lijun On Aug 13, 2014 2:00 AM, "Kristof Van Hecke" wrote: > Dear, > > I’m struggling with the following (small molecule) problem: > > We are tryin

Re: [ccp4bb] Strange density

F000 contributes to the whole map as a level (F000/V). If calculated with a only difference of with or w/o F000, should the sigma levels of the two maps be the same? That is why we could rely on maps for modeling that are calculated w/o F000 item. Lijun On Nov 28, 2012, at 2:30 PM, Pavel

Re: [ccp4bb] Negative electron Density for Zinc

sure. Changing occupancy of Zn may not be reasonable in this regard even though it does erase negative peaks. Lijun Liu@Kansas On Tue, 2012-08-28 at 12:07 -0700, Deepthi wrote: > Hi Everybody > > > Thank You very much for your suggestions. I did play around with > Zinc occupancy by

Re: [ccp4bb] refining large region with multiple conformers

Hi, ~1/3 of a chain that show substantial difference suggests a possibility that may deserve a check---the symmetry is actually lower and the 2 conformations belong to two occ=1 mols (unless the SG is already P1). I had a case that the apo SG was P1 and ligand-bound (soaked) SG was P1 t

Re: [ccp4bb] My protein precipitates at r.t and dissolves at 4 oC

Min-Kyu, This sounds like to be a hydrophobicity ~ temperature issue (as Kevin pointed out, pH gets involved too). If your protein is sensitive in this regards, it could form different oligomerization states at diff temp, associated with diff solubility. You may want to crystallize it at diff

Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser

stassis Perrakis> >> wrote: >>>> >>>> Anyway, I thought that was a cool idea, but like so many other cool >>>> things, it had to be cut from the Nature paper. Admittedly, the problem >>>> has >>>> not actually been solved yet.

Re: [ccp4bb] Space group vs. gap between Rwork and Rfree?

http://kolda.webz.cz Lijun Liu 555 Mission Bay Blvd South CVRB Room 482, MBox 3122 University of California, San Francisco San Francisco, CA 94158 Phone: (415)514-2836

Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

d I choose f000 over f010 or whatever else? Since I have no access to f000 experimentally, isn't it strange to define its phase as 0 rather than some other reflection? JPK On Wed, Oct 13, 2010 at 7:27 PM, Lijun Liu wrote: When talking about the reflection phase: While we are on embarrass

Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

There is no point a shift on this value is applied, but a counter balance for this shift will have to be applied during the calculation later if a shift had been applied. no any merits for this! Lijun JPK On Wed, Oct 13, 2010 at 7:27 PM, Lijun Liu wrote: When talking about

Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836

Re: [ccp4bb] Summary : [ccp4bb] embarrassingly simple MAD phasing question

. Thanks again for everyone's help. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (o

Re: [ccp4bb] Residual densities!

y making a map with resolution limited to 2.3 A. If that looks ok, extend the resolution in small steps through the 2.1A range. If you layers suddenly returns with one of these steps, you could eliminate a thin shell, or narrow it down to the particular spot and eliminate that. -ed- Lijun Liu wrote: No.

Re: [ccp4bb] Residual densities!

pattern to address this---I used the wrong nomenclature to address the same thing, I think. Lijun Could any of those strong spots at 2.1 be ice? Original message Date: Tue, 20 Jul 2010 16:13:31 -0700 From: Lijun Liu Subject: Re: [ccp4bb] Residual densities! To: CCP4BB@JISCMAIL.AC.

Re: [ccp4bb] Residual densities!

l not modify your original data in any way. Let me if using PHENIX map calculation tools does not help. Cheers, Pavel. On 7/20/10 3:19 PM, Lijun Liu wrote: Hi all, I solved a structure and the refinement is close to complete. However, some residual density puzzles me. The SG is P212121

Re: [ccp4bb] A strange case of MR

the statistics if this is a normal 2fo-fc map. >cheers, >-ed collins > >On Jul 18, 2010, at 10:39 PM, 孙庆祥 wrote: > >> > 您想拥有和网易免费邮箱一样强大的软件吗？ Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836

Re: [ccp4bb] Perfect crystal with weird diffraction pattern

Sorry, I think my reply was not case in the attached images! I happened to have the problem to see the image but I could now see all of them. I think Tim was correct, the patterns are not the same at all. Lijun On Jul 16, 2010, at 12:23 PM, Lijun Liu wrote: Dear Hui, About the so

Re: [ccp4bb] Perfect crystal with weird diffraction pattern

ly appreciated. Thank you very much in advance for your inputs. Sincerely, Hui Yang Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836

Re: [ccp4bb] Is it possible to mutate a reversible epimerase into an inreversible one?

epartment of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: m-schm...@uwm.edu http://users.physik.tu-muenchen.de/marius/ Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94

Re: [ccp4bb] Is it possible to mutate a reversible epimerase into an inreversible one?

hmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: m-schm...@uwm.edu http://users.physik.tu-muenchen.de/marius/ Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836

Re: [ccp4bb] Why Do Phases Dominate?

give very positive density contribution at some specific spots in the cell, just because of the phases. Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836

Re: [ccp4bb] Why Do Phases Dominate?

, 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] Correct MR solution

ion (P2 or P212121)? 2) How should we proceed further in case like this? Thanks in advance for the suggestions. Bob Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836

Re: [ccp4bb] units of f0, f', f''

de to that for a free electron. -- Hmmm...where does the 'electron' in electron density then come from after integration/summation over the structure factors? ---------- BR Lij

Re: [ccp4bb] units of the B factor - resolved?

le go away. Marc and Ian I imagine will tell me that cycle = 1 and hemi = 1 and therefore we have Angstrom^2 and they are more than welcome to do that in their papers, but I think it important here to clarify exactly what "one B factor unit" means. -James Holton MAD Scientist Lijun L

Re: [ccp4bb] Rfree in similar data set

quot; (I mean you are going to stop) of a smooth refinement, switching test sets should not be a "huge" problem, or the model is too wrong! Back to Mike's question: I suggest you keep the same test set, since your data were from the exactly same crystal. At least it saves y

Re: [ccp4bb] moelcular replacement with large cell

ething else for binning, especially in the early time for refinement package development. RESOLUTION BINNING might not be a have-to? :D Best regards. Lijun Liu, PhD http://www.uoregon.edu/~liulj/

Re: [ccp4bb] moelcular replacement with large cell

sults from CNS and Molrep differs so much. 4. Any other suggestions on the molecular replacement are appraciated. Thanks. Wei Zhang PKU Lijun Liu, PhD Institute of Molecular Biology Department of Physics University of Oregon Eugene, OR 97403 541-346-5176 http://www.uoregon.edu/~liulj/

Re: [ccp4bb] how to run detwin?

y Facility Manager Department of Structural Biology 3501 Fifth Avenue, Pittsburgh, PA 15260 412-383-5839 lab...@pitt.edu Lijun Liu, PhD Institute of Molecular Biology Department of Physics University of Oregon Eugene, OR 97403 541-346-5176 http://www.uoregon.edu/~liulj/

Re: [ccp4bb] low UV reading on AKTA prime

Hi Matt, AKTA system does allow you check the how-good percentage of the UV lamp, so if the UV lamp is new, and it gives low percentage (I do not mean the 20%) then your AKTA system may have the problem like Scott said or other thing in the Optical path. There are other possibilities, however! F

Re: [ccp4bb] images

Now that there is possibility that images could be fake, which means the first and automatic FFT in crystallography could be falsified. All those depositions later than this would be just nothing but wrong, if images were fake. To keep the first and most important FFT not contaminated, I would su

Re: [ccp4bb] Fwd: Twinning

ght angle, derived from your P21 cell constants (a, c and beta angle) (if they were well determined), implying this may not be the case. Good luck! Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-5176 http://www.uoregon.edu

Re: [ccp4bb] About system absence in P4222?

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 Lijun Liu, PhD

Re: [ccp4bb] Help sought for problem dataset

81.1% 1% 0.7072144 total 131556 16015 16144 99.2% 5.4% 5.6% 131514 26.34 5.7%10.6% 0% 0.758 13597 Attached figures: Data scaled in P2, self-rotation function in MOLREP Data scaled in P222, self-rotation function in MOLREP Cumulative inte

Re: [ccp4bb] low B factors

Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-5176

Re: [ccp4bb] refinement of half molecules

rster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-5176

Re: [ccp4bb] Classic density map drawing!

Hello, Thank you all for replying to the question about the old-fashioned drawing of electron density map. It should be able to work with one or combination of 1) Gerard's USF scripts 2) Chain 3) CCP4's Thanks also to other alternate suggestions. Lijun Liu, PhD Institute of Molecul

[ccp4bb] Classic density map drawing!

from writing and debugging codes. Thanks a lot! Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-4080

Re: [ccp4bb] Lower completeness, decent R factors, but low B factor...

sometimes the overall scaling struggles to get a reasonable fit.. Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-4080

Re: [ccp4bb] D-Amino acids to L-Amino acids

Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany - This mail sent through IMP: http://horde.org/imp/ Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-4080

Re: [ccp4bb] simple rule for spot overlap?

899-909, but it is a detailed simulation rather than a single formula. Richard Gillilan MacCHESS Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-4080

Re: [ccp4bb] PST in refinement

the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403

Re: [ccp4bb] Truncated protein structure

The convention for "P22121"s is P21212, which is used by both CNS and CCP4 and many else, if not all. The unit cell needs to be reindexed (a-b-c --> b-c-a in your case). Then please try again. Lijun > Thank you for your suggestions. > 1. The unit cell of my crystal is 47.41 99.67 114.97 90 90

Re: [ccp4bb] Negative density around C of COO-

int out if I am wrong. This "assignment" of free radicals to damage is often made (flippantly) in the literature, but I feel a strong need to point out that there is NO EVIDENCE of a free radical diffusion mechanism for radiation damage below ~130K. Lijun Liu, PhD Institute

[ccp4bb] Crystallization and cryo with Li at high concentration!

0 M? Thanks a lot. Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-4080

Re: [ccp4bb] twinned?

you received this information in error, please contact the Compliance HelpLine at 800-856-1983 and properly dispose of this information. Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-4080

Re: [ccp4bb] cns and refmac refinement

20.088 178 0.273 0.3700.683 81567.80.010 1.3710.088 179 0.273 0.3710.682 81568.00.010 1.3740.088 180 0.273 0.3700.683 81565.70.010 1.3720.088 Lijun Liu, PhD Institute of Molecular Bi

Re: [ccp4bb] Mosflm P21 integrating issues

If the number ~75% was ALWAYS true for all datasets, while not a SG error, not cracks/twinning, not a mosaicity problem and not here and there, then I would BET the REAL oscillation angle for each img for all datasets should be 4 times as what what input while the steps stayed correct. (For instanc

Re: [ccp4bb] How to improve the density of another molecule in Asymmetric unit

, the density is much worse than the first one. Are there any ways to improve the density of the second molecule, such as some kinds of averaging? Why that happens? Thank you very much for your help! Sincerely, Sun Tang [EMAIL PROTECTED] Never miss a thing. Make Yahoo your homepage. Lijun

Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?

in advance Brenda Lijun Liu, PhD Institute of Molecular Biology HHMI & Department of Physics University of Oregon Eugene, OR 97403 541-346-4080