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

Re: [ccp4bb] Negative electron Density for Zinc

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 giving 0.5 to each of them. I got

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] 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

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] 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

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

? 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] Negative density around C of COO-

. 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 of Molecular Biology HHMI Department

Re: [ccp4bb] Truncated protein structure

The convention for P22121s 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 90

Re: [ccp4bb] PST in refinement

. If 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 541

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] Lower completeness, decent R factors, but low B factor...

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

[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] 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 Molecular Biology

Re: [ccp4bb] refinement of half molecules

, 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] Help sought for problem dataset

%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 intensity distribution in TRUNCATE P222_srf.jpgcumul_intensity_081008.jpgP2_srf.jpg Lijun Liu, PhD Institute of Molecular Biology

Re: [ccp4bb] About system absence in P4222?

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 Institute of Molecular Biology HHMI

Re: [ccp4bb] Fwd: Twinning

, 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/~liulj

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

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

/ Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836 Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158

Re: [ccp4bb] Perfect crystal with weird diffraction pattern

in advance for your inputs. Sincerely, Hui Yang data.rar 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] A strange case of MR

if this is a normal 2fo-fc map. cheers, -ed collins On Jul 18, 2010, at 10:39 PM, 孙庆祥 wrote: Density over model.png 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] Residual densities!

will 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] Residual densities!

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 lijun@ucsf.edu Subject: Re: [ccp4bb] Residual densities! To: CCP4BB

Re: [ccp4bb] Residual densities!

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. No ice ring! Sorry I meant

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

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 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax) Lijun Liu Cardiovascular Research Institute

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

*** 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] embarrassingly simple MAD phasing question (another)

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 lijun@ucsf.edu wrote: When talking about

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

: 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 Lijun Liu Cardiovascular Research Institute University

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] First images of proteins and viruses caught with an X-ray laser

Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** 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] 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] 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!

Re: [ccp4bb] how to run detwin?

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] moelcular replacement with large cell

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] Rfree in similar data set

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 your convergence time. Lijun Liu On Sep 24, 2009, at 10:24 AM

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

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 Liu Cardiovascular Research Institute University of California

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

-- Hmmm...where does the 'electron' in electron density then come from after integration/summation over the structure factors? -- BR Lijun Liu

Re: [ccp4bb] Correct MR solution

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] Why Do Phases Dominate?

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] 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 kristofrg.vanhe...@gmail.com wrote: Dear, I’m struggling with the following (small molecule)

[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

[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

Re: [ccp4bb] Chain ID number limit!

supported in Phenix). Pavel On Mon, Jul 24, 2017 at 5:09 PM, Lijun Liu <lijunli...@gmail.com <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

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

[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 Liu --

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

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

interacting 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] 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

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

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

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