Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?
Dear colleagues, Thank you to everyone who responded. Here is a short summary: 1.Refmac using isotropic B-factors with tight restraints 2. Add a TLS in refinement may help. Best wishes, chenzhonghao...@163.com From: Tom Peat Date: 2024-01-07 10:57 To: CCP4BB Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group? Hello All, I think we are all in agreement that it depends on resolution, or more specifically the amount of experimental data one has versus how many atoms one has in the model to refine. There is also no question that structures have become better over the decades due to more and better restraints added into the refinement process, and of course people paying more attention to such things. In terms of guidance to questions, such as when to apply grouped, isotropic or anisotropic B factors, it would be nice to have something concrete to respond with. We have plenty of 'rules of thumb' or heuristics that might be valuable to the community that don't have that many years of experience under the belt. My approach, which may or may not be approved by all, is to say that for those dealing with lower resolution structures (3.0 or worse) or with data to parameter ratios less than 4, is to try something that groups B factors instead of refining every atom with its own B factor. There aren't many ways to do this and it would be nice if there were TLS type implementations that allowed one to avoid the individual B factors. There are plenty of data sets out there that fall into this category, so it might be nice to have more tools to apply in these cases. This isn't to say that adding more restraints can't help the refinement, but it isn't necessarily the best initial course of action when starting out with limited data. For very limited data, one might start with a single overall B factor and only do rigid body refinement of a model. I think the results from Pavel's experiment would be interesting and it would be useful to see the resolution bins that fell out for the various categories. cheers, tom From: CCP4 bulletin board on behalf of Pavel Afonine Sent: Sunday, January 7, 2024 11:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group? You don't often get email from pafon...@gmail.com. Learn why this is important Hi All, I believe it depends on the resolution. At sufficiently low resolution, it may not be too unreasonable to assume that the main chain atoms of a residue have the same B factors, and its side chain atoms also share the same B factor (different from the main chain). Why? Simply because your low-resolution data cannot resolve the B-factor difference between, for example, CA and C atoms! This is much like expecting low to almost zero deviations from ideal bonds and angles at low resolution, because your low-res data simply cannot resolve a fraction of an Angstrom deviation in bond lengths. The bottom line, in my opinion, is that there is no black-and-white answer to the "grouped vs. individual" B-factor refinement question. Depending on a) the data resolution, and b) your experimentation with both individual and group options, you may choose one over the other. Back in the day (when working on the implementation of B-factor refinement in phenix.refine), I conducted a test where I re-refined a sample, consisting of about 50,000 models from the PDB, using 1) individual, 2) group with one B per residue, and 3) group with two B per residue (one for the main and one for the side chain). There were clear clusters of results where each of the three parameterizations outperformed the others, and this was heavily resolution-dependent. I regret not publishing that result, mostly because I thought I could always re-do it any time later.. but as Ben said "Don't put off until tomorrow what you can do today"! Regarding TLS, since someone mentioned it, I prefer to see TLS as a more physically realistic atomic vibration model, rather than a magic solution to reduce R-factors or a way to decrease the number of refinable parameters (which, in fact, is not the case because normally residual isotropic B factors are always refined on top of TLS anyway, in Phenix at least). All the best! Pavel On Sat, Jan 6, 2024 at 3:41 PM Robbie Joosten wrote: Hi Tom, I think restraints do change the data/parameter ratio, but how much is not straightforward. In, at least, the context of the Hamilton test restraints change the degrees of freedom which translates into a change of the effective data/parameter ratio. It is treated as adding extra observations albeit with some unknown weight. Ethan Merritt's way of handeling this unknown weight (which we implemented in bselect) is setting an upper limit for the weight and thus bracketing the value. Lets assume we have glycol. Adding individual B-factors instead of one overall B adds 3 extra
Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?
Dear Prof. Dr. Dodson and all CCP4 community, Thanks for your reply. Just now, I used baverage. I found that it can average the B factor but not refine it. This function does not fit my requirement, because my resolution is low as 3 A. Many people said that Refmac5 overrefines the structure if I used isotropic temperature refinement. Did refmac5 or other programs in CCP4 have similar functions like one_adp_group_per_residue or two_adp_groups_per_residue in Phenix? Any help would be highly appreciated! chenzhonghao...@163.com From: Eleanor Dodson Date: 2024-01-05 23:48 To: CCP4BB Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group? Hmmm - I am not sure about the value of this - one expects the longer floppier side chains to have very different B values for the CB than the OE2.. The program BAVERAGE gives you a plot of mean B value residue by residue.. baverage - averages B over main and side chain atoms SYNOPSIS¶ baverage XYZIN foo_in.pdb RMSTAB foo_out1.tab XYZOUT foo_out2.pdb [Keyworded input] DESCRIPTION¶ A very simple minded program to read a PDB file, tabulate to RMSTAB the average B values residue by residue (main chain and side chain separately) and the RMS deviation of the B values from this mean. It also outputs a PDB file with outlying B factors reset to lie within the given range. On Fri, 5 Jan 2024 at 03:08, chenzhonghao...@163.com wrote: Dear CCP4 community, I found that Refmac5 refined the temperature factor only by four modes (see the bottom of the attached figure). However, no grouped B-factor (one or two per residue instead of one per atom) was found. Actually, PHENIX and CNS can do it. But we are not familiar with both software. I want to know whether Refmac5 refines one or two group B per residue (for side and main chains) grouped temperature factor? Any help would be highly appreciated Thanks in advance. best, Zhonghao Chen To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Can Refmac5 refine temperature factor residue by group?
Dear CCP4 community, I found that Refmac5 refined the temperature factor only by four modes (see the bottom of the attached figure). However, no grouped B-factor (one or two per residue instead of one per atom) was found. Actually, PHENIX and CNS can do it. But we are not familiar with both software. I want to know whether Refmac5 refines one or two group B per residue (for side and main chains) grouped temperature factor? Any help would be highly appreciated Thanks in advance. best, Zhonghao Chen To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ <>
Re: [ccp4bb] Electron density map for publications
Dear Raj, Usually, fo-fc is the best way to show. best, chenzhonghao...@163.com From: raj kumar Date: 2017-12-19 13:07 To: CCP4BB Subject: [ccp4bb] Electron density map for publications Hi Which electron density map (fo-fc or 2fo-fc) should I use for representing the density of the bound ligand? Thanks Raj
Re: [ccp4bb] A challenging Molecular replacement
Dear Dr.Richard, Your paper gave a good example for us. Is it possible that you send me all the related files? It will be very helpful for students to learn the detail of solving difficult protein structures. Thanks in advance! best, Zhonghao Chen China agricultural university. chenzhonghao...@163.com From: Tanner, John J. Date: 2017-07-18 00:34 To: CCP4BB Subject: Re: [ccp4bb] A challenging Molecular replacement Richard, I can’t help you with 5XQL. However, I can point out a recent structure from my group that might be useful for teaching. The structure was solved by MR with a search model that had 33% sequence identity and represented only 46% of the target structure. The Methods section of the paper has a detailed description of the phasing procedure. We used BALBES, then did autobuilding in phenix from the BALBES/REFMAC map. https://www.ncbi.nlm.nih.gov/pubmed/28420730 John J. Tanner Professor of Biochemistry and Chemistry Chair, Biochemistry Department Graduate Admissions Committee Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-5635 Email: tanne...@missouri.edu http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A On Jul 17, 2017, at 11:01 AM, CDaddy <2295867...@qq.com> wrote: I am a structural biologist who is teaching X-ray crystallography. Recently I noticed that BrlR structure (5XQL) was solved using molecular replacement with a search model of very low similarity. I am very interested in this structure because I think this a very good example to show students how to solve phase problem using molecular replacement, especially when the model and the target protein share a low sequence identity. However, when I downloaded the data from PDB, I found that I cannot solve the phase problem using Phaser as mentioned by the authors. During this procedure BmrR (PDB:1R8E) was used as the search model. I tried to consult the authors for help but receive no response by now. Since the description of this issue in the literature is very brief, could anyone please spend a little time on this molecular replacement and give me some advices on this issue? I like to learn some valuable tricks. Your assistance will be highly appreciated. All the best, Richard.
[ccp4bb] How to download PROMOTIF v 2.0
Dear all, I want to download PROMOTIF v 2.0 from your ftp server(IP address 128.40.46.11). However, I can not visit it (ftp://128.40.46.11) because the ftp server was shut down. Moreover, I also sent emails to g...@uk.ac.ucl.bioc.bsm or thorn...@uk.ac.ucl.bioc.bsm. However, both emails were returned because the email address were not available. Would anyone like to tell me how to download it or tell me the right net address or email me the problem? Thanks in advance. best, Website: http://www.uoxray.uoregon.edu/local/manuals/promotif/document_2.html The program is freely available for academic users. Industrial users should contact the authors directly. The files can be down loaded from our anonymous ftp server (IP address 128.40.46.11). The files are in the /pub/promotif/v2.0 directory. Please read the LICENSE file, sign it and return it to the authors. If you experience problems in accessing the files by ftp contact the authors via e-mail at one of the following addresses: g...@uk.ac.ucl.bioc.bsm or thorn...@uk.ac.ucl.bioc.bsm . Zhonghao Chen
Re: [ccp4bb] coot fragment translation for nucleic acids
Dear Schulze-Gahmen, Which version of coot did you use? For me, Coot 0.8.4 works well in windows 8.1 system. It does not have a question in optimizing nucleic acids. best, Zhonghao chenzhonghao...@163.com From: Ursula Schulze-Gahmen Date: 2017-03-25 04:35 To: CCP4BB Subject: [ccp4bb] coot fragment translation for nucleic acids Although I have used Coot a lot for modeling protein structures, I have little experience using it for nucleic acids. I am trying to translate fragments of nucleic acid using the rotate/translate zone option in Coot. But I am unable to select a zone; instead the whole chain is selected when I am clicking on 2 atoms in the chain. Any suggestion how to get around this would be appreciated. Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491
