[ccp4bb] DIALS spot finding
Dear all, I am just switching from HKL3000 to DIALS for processing data collected at EIGER detectors because it is too slow for the HKL300 to handle over 1000 images per dataset. Our crystals are not perfect and you would expect split spots or spots of multiple crystals in most cases. Sometimes we are lucky enough to extract spots of one lattice by playing with the spot-finding parameters in HKL 3000 and find an solution during the index step (changing spot size, more spots, fewer spots, restraining the resolution, etc.). However, it seems very difficult to adjust these parameters in the dials.find_spots step of DIALS. The DIALS tutorial suggest checking the spots using "dials.image_viewer" after the spot findin step. By inspecting the images, it seems that most split sports were not included into the list of "strong spots" for indexing. What options do you have during the step of spot finding (especially fins strong spots for indexing) using DIALS? Thank you in advance. Best, Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] FFT map coefficients only for certain chains
Herman, Thanks for clarifying the difference between map coefficients and map files for me. What I really need are only map files, and I could generate those masked maps by following Paul's suggestion. Yu 2012/2/20 Paul Emsley paul.ems...@bioch.ox.ac.uk Like Herman, it was not apparent to me what exactly you want wanted. If you want a map that covers only [1] or excludes [2] a particular atom selection then you can do that in Coot. Extensions - Maps... - Mask Map by Atom Selection, e.g. to show only the A chain, use an atom selection of //A. You can then export the map using: Extensions - Maps... - Export Map or Extensions - Maps... - Export Local Map Fragment... If you really want structure factors from that then you can use sfall (MODE SFCALC MAPIN). Paul. [1] use mask inversion [2] don't use mask inversion -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKCCP4BB@JISCMAIL.AC.UK] *On Behalf Of *zhang yu *Sent:* Sunday, February 19, 2012 11:47 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] FFT map coefficients only for certain chains Dear CCP4ers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The isomesh command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of FFT tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] FFT map coefficients only for certain chains
Dear CCP4ers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The isomesh command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of FFT tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand
Thanks, I appreciate all the help from you guys. A brief summary, As Sabine, Paul and Ed pointed, change the _chem_comp.group in data_comp_list to DNA is the key for coot to recognize it. As Alan said, ExtensionModelingReplace Residues could also insert BRU into DNA chain without any modification of cif file. 在 2011年10月24日 上午3:52，Alan Cheung che...@lmb.uni-muenchen.de写道： Whoops, i meant Extensions Modelling Replace Residue and not replace fragment. On 24/10/2011 09:43, Alan Cheung wrote: Hi Yu - we regularly model BrdU in our DNA chains with the replace residue function in coot. Model a normal thymine in the required position and then centre on the thymine. Then select : Extensions Modelling Replace Fragment and type BRU into the dialog box. (see 5.17.3 of http://biop.ox.ac.uk/coot/doc/coot/Mutation.html#Mutation ) It will also add a superfluous OP3 atom to the BRU phosphate atom upon residue replacement which you'll need to delete. Make sure the flanking nucleotides of DNA can already be regularised/refined with coot (a version dependent issue i think) otherwise it won't link the BRU properly. Alan On 23/10/2011 21:03, zhang yu wrote: Hi, My DNA chain has a internal modification of 5-Bromo-2′-deoxyuridine (5BrdU). I had a problem when I tried to model 5BrdU into my DNA chain by coot. I will appreciate it very much if someone can solve it for me. What I did... 1. Generate the cif dictionary and export the pdb for 5BrdU in Jligand. 2. Load the pdb and cif into coot 4. Merge the monomer into my molecule. Change and renumber 5BrdU (Chain G and resi 15). 3. Run Real-space refine in coot The problem... Real-space refine fits the monomer into density quite well, but coot only makes bond (P-O) between 5BrdU and its upstream nt (14), doesn't make bonds between 5BrdU and its downstream nt (16). Whenever I refine it, it seems coot just treats 5BrdU and nt 16 as in different chain, push two atoms away(P in nt16 and O3 in nt15 ), and doesn't connect them. Did I miss something when I generate cif dictionary or at other steps? Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand
Hi, My DNA chain has a internal modification of 5-Bromo-2′-deoxyuridine (5BrdU). I had a problem when I tried to model 5BrdU into my DNA chain by coot. I will appreciate it very much if someone can solve it for me. What I did... 1. Generate the cif dictionary and export the pdb for 5BrdU in Jligand. 2. Load the pdb and cif into coot 4. Merge the monomer into my molecule. Change and renumber 5BrdU (Chain G and resi 15). 3. Run Real-space refine in coot The problem... Real-space refine fits the monomer into density quite well, but coot only makes bond (P-O) between 5BrdU and its upstream nt (14), doesn't make bonds between 5BrdU and its downstream nt (16). Whenever I refine it, it seems coot just treats 5BrdU and nt 16 as in different chain, push two atoms away(P in nt16 and O3 in nt15 ), and doesn't connect them. Did I miss something when I generate cif dictionary or at other steps? Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand
Hi Sabine, Thanks for your suggestions. I checked the cif file of BrdU. the hydrogen of the 3'O of the BrdU is defined as HO3' in BrdU cif file, in stead of 3'OH. The standard dNTP cifs define it as HO3' too. In PDB, there is no atoms for hydrogen, as I excluded them. The BrdU is defined as UBP as I named in my cif file (under 'data_comp_list') Any suggestion? I attached my cif and pdb of BrdU, could you take a look at it? Do you have any suggestion of program generating cif for non-standard nucleotides? Thanks Yu 在 2011年10月23日 下午3:50，Sabine Schneider sabine.schnei...@mytum.de写道： Hi Yu, A few things which caused this happened to me with other non-standart nucleotides: - the hydrogen of the 3'O of the BrdU is defined as 3'OH in the cif file - order of the atoms in the pdb file ie compare the position of the 3'OH with the standard dNTP in the PDB - is the 3BrdU defined as 'DNA' in the cif file? (under 'data_comp_list') Maybe that helps! Sabine On 10/23/2011 09:03 PM, zhang yu wrote: Hi, My DNA chain has a internal modification of 5-Bromo-2′-deoxyuridine (5BrdU). I had a problem when I tried to model 5BrdU into my DNA chain by coot. I will appreciate it very much if someone can solve it for me. What I did... 1. Generate the cif dictionary and export the pdb for 5BrdU in Jligand. 2. Load the pdb and cif into coot 4. Merge the monomer into my molecule. Change and renumber 5BrdU (Chain G and resi 15). 3. Run Real-space refine in coot The problem... Real-space refine fits the monomer into density quite well, but coot only makes bond (P-O) between 5BrdU and its upstream nt (14), doesn't make bonds between 5BrdU and its downstream nt (16). Whenever I refine it, it seems coot just treats 5BrdU and nt 16 as in different chain, push two atoms away(P in nt16 and O3 in nt15 ), and doesn't connect them. Did I miss something when I generate cif dictionary or at other steps? Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 UBP.pdb Description: Protein Databank data UBP.cif Description: CIF chemical test
[ccp4bb] I/sigma for h+k=2n+1 and h+k=2n
Hi, I had a dataset which is P21 but with a pseudo-translational symmetry of (1/2, 1/2 ,0). Theoretically the dataset should show systematic weak spots of h+K= 2n+1 compared to h+k= 2n. Is that correct? I would like to have a close look at the reflections. for example, the average I/sigma for reflections with h+k=2n+1 and reflections with h+k=2n. Which software could do this job? A brief tutorial is appreciated. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] I/sigma for h+k=2n+1 and h+k=2n
Hi Thanks for all the replies. I ran TRUNCATE in CCP4 and got what I want. I will try other options later. Thank you again. Yu 2011/7/26 Esko Oksanen esko.oksa...@helsinki.fi Yu, There is a parity analysis in dataman (a USF program) for example. You have to take into account that the sigmas are generally estimated assuming a unimodal intensity distribution, which is no longer true in the pseudo-symmetric case. In practice this means that the sigmas of the strong reflections tend to be underestimated (generally not a problem really) and those of the weak reflections are overestimated. This can be avoided to some extent by scaling the h+k = 2n and h+k = 2n+1 reflections separately. I ended up writing a small python script to do this from XDS output and scaling separately (see Oksanen et al. (2006) Acta Cryst. D62 1369-1374). Of course it would be even better if the scaling program would directly take into account the bimodal distribution... HTH, Esko On 26.7.2011, at 15.51, zhang yu wrote: Hi, I had a dataset which is P21 but with a pseudo-translational symmetry of (1/2, 1/2 ,0). Theoretically the dataset should show systematic weak spots of h+K= 2n+1 compared to h+k= 2n. Is that correct? I would like to have a close look at the reflections. for example, the average I/sigma for reflections with h+k=2n+1 and reflections with h+k=2n. Which software could do this job? A brief tutorial is appreciated. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 Esko Oksanen, PhD Post-doctoral Fellow (EMBO) Groupe Synchrotron, Institut de Biologie Structurale J.P. Ebel 41, rue Jules Horowitz F-38027 GRENOBLE Cedex 1 FRANCE tel. +33 4 38 78 95 96 mob. +33 6 84 15 14 88 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] Non-crystallography symmetry operator
Hi, Does any one know which software could calculate and output non-crystallography symmetry operator? I am working on a structure with two molecules in one ASU, and two identical subunits in each of one molecule. I would like to know the non-crystallography operator of the two molecules, and also NCS operator of two subunits in the same molecules. Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Non-crystallography symmetry operator
Thanks for all the reply. I am able to use phenix.find_ncs find NCS operators for all the chains. But it doesn't give a NCS matrix between whole molecules in ASU. Is that right or I missed something? In SUPERPOSE of CCP4, How to ask the program to calculate the NCS operator? It asks me to input two structures and will output another pdb file. Yu 2011/7/25 Frederic VELLIEUX frederic.velli...@orange.fr You need to specify which format (i.e. for which program) since the conventions used are different. I personally use suppos which provides a rotation matrix plus translation vector. Row by row for the matrix. Some programs use a column by column approach, the transpose of the rotation matrix, or a set of 3 angles (with several conventions possible) Message du 25/07/11 19:24 De : zhang yu A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Non-crystallography symmetry operator Hi, Does any one know which software could calculate and output non-crystallography symmetry operator? I am working on a structure with two molecules in one ASU, and two identical subunits in each of one molecule. I would like to know the non-crystallography operator of the two molecules, and also NCS operator of two subunits in the same molecules. Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] coot torsion angle restraint
Hi, I am confused by the torsion angle restraint for real space refinement in coot. Is the Torsion angel restraint for side chain or for main chain? Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Denzo/HKL2000 for Pilatus 6M detector
We could use HKL2000 for Pilatus 6M detector a few months ago in our lab. We upgraded our HKL2000 to Version 0.98.701 and asked a new license file to include Pilatus 6M detector. Yu 2011/7/20 Petr Leiman petr.lei...@epfl.ch Dear all, What is the status of Denzo/HKL2000 availability/support for the Pilatus 6M detector? Thank you, Petr -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Dear Duangrudee Thank you for your information. Is there any hardware requirement for the stereo in coot and pymol with Zalman monitor? It seems that Hign-End Nvidia graphic cards (Quadro FX 3800, FX 4800 ) are not necessary. Yu 2011/5/8 Duangrudee Tanramluk nano...@gmail.com Dear Yu, Pymol also has a Zalman option. The monitor comes with 2 pair of light-weight polarized glasses, i.e. one for clipping on your prescription glasses and another regular one. If you have the Zalman monitor and its polarised glasses, you can see this .gif movie in 3D on google chrome, just click on the picture to see in full size. http://nanonan.wordpress.com/2011/03/14/making-zalman-3d-stereoscopic-movie-with-pymol/ May be you can use this movie for trial with other 120 Hz monitor/glasses. Hope it helps, Duangrudee Duangrudee Tanramluk, Ph.D. Institute of Molecular Biosciences, Mahidol University Puttamonthon 4 Road, Salaya, Nakhon Pathom 73170 THAILAND -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Dear colleagues, Sorry to present the stereo issue to the board again. Since my old SGI CRT monitor only has 75 HZ refresh rate, the flickering in stereo mode bothered me a lot. Recently, I want to update my old CRT to 120 HZ LCD. I have a Nvidia Quadro FX3800 in my workstation. I would like to make sure some issues before I make the upgrade. 1. Can I apply the previous stereo emitter (Purchased from Real D, Model #E-2) to 120HZ LCD? Although the company told me this emitter is not compatible with LCD, could some one tell me why? Is it true that the Nvidia 3D vision is the only solution for the stereo in LCD? 2. Nvidia supply two kinds of 3D emitters. One of them is 3D vision, while the other one is 3D vision pro. Which one is sufficient for crystallographier user? (3D vision pro is much more expensive than 3D vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Dave, thanks. There is an option for Zalman stereo in Coot. Could Zalman stereo also display properly in Pymol? Yu 2011/5/6 Dave Roberts drobe...@depauw.edu I'm very happy with Zalman passive stereo. No hardware requirements beyond Zalman monitor. Monitors cost $500ish for 21 and 700ish for 24. Any video card, any software. Glasses are the same as movie glasses ($2 per pair), no batteries, no flicker. Very nice really. Dave Sent from my iPhone On May 6, 2011, at 11:27 AM, zhang yu ccp4f...@gmail.com wrote: Dear colleagues, Sorry to present the stereo issue to the board again. Since my old SGI CRT monitor only has 75 HZ refresh rate, the flickering in stereo mode bothered me a lot. Recently, I want to update my old CRT to 120 HZ LCD. I have a Nvidia Quadro FX3800 in my workstation. I would like to make sure some issues before I make the upgrade. 1. Can I apply the previous stereo emitter (Purchased from Real D, Model #E-2) to 120HZ LCD? Although the company told me this emitter is not compatible with LCD, could some one tell me why? Is it true that the Nvidia 3D vision is the only solution for the stereo in LCD? 2. Nvidia supply two kinds of 3D emitters. One of them is 3D vision, while the other one is 3D vision pro. Which one is sufficient for crystallographier user? (3D vision pro is much more expensive than 3D vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Jim, thanks. I am using Linux and with a 3-pin stereo bracket hooked to my Nvidia Quadro FX3800. It is ready to go. 2011/5/6 Jim Fairman fairman@gmail.com 1. No you cannot use your old stereo emitter. The 3D Vision Emitter is required for stereo on 120 Hz LCD monitors. You will also need new shutter glasses from Nvidia, but these some with the emitter. I'm not sure the reason, but I'd guess that the older emitter can't transmit the signal at the correct frequency to get 60 Hz to each eye. On a side note, consider which operating system you are running on the system to be used for stereo. You'll need the 3-pin stereo connector if you want to do stereo in Linux. For Windows it isn't required. Some computers that Dell and other manufacturers sell with FX3800 cards don't have one built in, and you will need to buy an adapter that hooks into the video card to provide the port. 2. The normal 3D Vision system uses IR signals to communicate between the emitter and the shutter glasses. 3D Vision Pro uses RF signals for communication between the glasses and the emitter and has a longer range and doesn't require line-of-sight like the IR system (hence the hefty price difference you've noticed). I don't believe the glasses from the normal 3D Vision kit are compatible with the 3D Vision Pro system due to the difference in signaling systems, but I haven't tested this. If you're going to be sitting in front of a monitor doing modeling and don't have alot of IR interference in the same room, the normal 3D Vision version will suffice for your needs. 3D Vision Pro is more geared toward having large meeting rooms and presentation halls equipped so everyone in the room can view 3D on a large screen driven by a 120 Hz DLP projector. 3. I don't wear prescription eye glasses, but I do have long modeling sessions without any discomfort wearing these. They come with several inter-changable nose-pieces so you can pick the one that fits you most comfortably. On Fri, May 6, 2011 at 11:27 AM, zhang yu ccp4f...@gmail.com wrote: Dear colleagues, Sorry to present the stereo issue to the board again. Since my old SGI CRT monitor only has 75 HZ refresh rate, the flickering in stereo mode bothered me a lot. Recently, I want to update my old CRT to 120 HZ LCD. I have a Nvidia Quadro FX3800 in my workstation. I would like to make sure some issues before I make the upgrade. 1. Can I apply the previous stereo emitter (Purchased from Real D, Model #E-2) to 120HZ LCD? Although the company told me this emitter is not compatible with LCD, could some one tell me why? Is it true that the Nvidia 3D vision is the only solution for the stereo in LCD? 2. Nvidia supply two kinds of 3D emitters. One of them is 3D vision, while the other one is 3D vision pro. Which one is sufficient for crystallographier user? (3D vision pro is much more expensive than 3D vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Copy NCS chain in coot
Dear Javier, Thanks for your reply. I am using coot 0.6.1, and I could copy molecules with names besides A only if chains are already present in both NCS. For chains which are only present in one NCS , I did find out a way to copy to the other NCS by using 'Find NCS ligand' , although it is not a ligand. For example, there are already chain A - chain D in the first NCS, and chain E-chain H in the second NCS. I build chain 'M' from the scratch in the first NCS, and I want to copy it to its NCS mate. 1. Change the master chain to chain A Draw-NCS ghost control-change to chain A 2. go to Extension-NCS-NCS ligands-, In upper dialog box, Protein with NCS, Fill the master chain ID to A. In the lower dialogue box Molecules contain ligands, choose the right molecule and Fill 'M' and 'residue ranges'. Coot will give a few positions to fit the chain, just choose the right one. Yu 2011/3/31 Javier Garcia gar...@ysbl.york.ac.uk Dear Zhang yu, I also found that same problem recently. I think is a small bug from Coot. It will only copy NCS if the molecule's name you want to copy is molecule A. So maybe will work if you rename your built chain as A. Good luck! Javier On 31/03/11 00:16, zhang yu wrote: Dear all, I have two fold NCS in ASU. I could find phase by molecular replacement, but I have to build other chains by myself, since the model is not complete. During model building in coot, I built one chain in one NCS, and I merged this chain into the previous molecule. Now it is the chain M'. When I tried to directly copy this chain to its NCS mate, It didn't work. I followed the instruction posted before http://www.mail-archive.com/coot@jiscmail.ac.uk/msg01984.html;. What I did is 1. Change the master chain to chain M Draw-NCS ghost control-change to chain M (The terminal said 'there are no ghosts when I change the master chain to chain M) 2. go to Extension-NCS-copy chain-, coot ask to fill the master chain ID, and I typed M Nothing happened. Could someone tell me what is the correct procedure to do it ? Bye the way, for those chains present in both NCS maps, I modified one chain and applied the change to its NCS mate by using the same above procedure, and it worked. Thanks -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] Copy NCS chain in coot
Dear all, I have two fold NCS in ASU. I could find phase by molecular replacement, but I have to build other chains by myself, since the model is not complete. During model building in coot, I built one chain in one NCS, and I merged this chain into the previous molecule. Now it is the chain M'. When I tried to directly copy this chain to its NCS mate, It didn't work. I followed the instruction posted before http://www.mail-archive.com/coot@jiscmail.ac.uk/msg01984.html;. What I did is 1. Change the master chain to chain M Draw-NCS ghost control-change to chain M (The terminal said 'there are no ghosts when I change the master chain to chain M) 2. go to Extension-NCS-copy chain-, coot ask to fill the master chain ID, and I typed M Nothing happened. Could someone tell me what is the correct procedure to do it ? Bye the way, for those chains present in both NCS maps, I modified one chain and applied the change to its NCS mate by using the same above procedure, and it worked. Thanks -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Molecular replacement question
Maybe there is a domain shift of your protein compared to the model. If this is the case, try to do the MP with successive domains. 2010/9/13 Paul Holland pholl...@umd.edu Hello fellow crystallographers, I am trying molecular replacement for a protein crystal dataset that has very high sequence similarity to the search model with several predicted flexible loop regions; however, all attempts at finding a solution have not produce very ideal starting solutions using Phaser and Molrep (CC = 0.3 and Z-score = 5). I am very confident that the unit cell parameters are C2 84.027 120.565 108.272 90.00 104.71 90.00, and there appears to be no evidence of twinning. The Matthews calculation predicts from anywhere from 2-4 monomers in the ASU, and calculation of the SRF in Molrep does not identify any peaks in higher order symmetry except for the expected crystallographic two-fold for C2. Below is the table from the calculated SRF in molrep. Any advice would be greatly appreciated. #thetaphichi alpha beta gamma Rf Rf/sigma Sol_RF 1 0.000.000.000.000.000.00 870.5 21.59 Sol_RF 258.61 -10.17 180.00 169.83 -117.23 10.17 162.5 4.03 Sol_RF 366.02 -0.00 180.00 180.00 -132.030.00 161.1 4.00 Sol_RF 458.42 -9.54 180.00 170.46 -116.859.54 159.8 3.96 Sol_RF 5 149.840.00 180.00 -180.00 60.320.00 156.0 3.87 Sol_RF 658.96 -5.52 180.00 174.48 -117.915.52 151.5 3.76 Sol_RF 765.59 20.95 180.00 20.95 131.18 159.05 143.9 3.57 Sol_RF 890.00 -98.96 180.000.00 180.00 17.92 142.9 3.55 Sol_RF 956.53 15.78 180.00 15.78 113.07 164.22 142.0 3.52 Sol_RF 1071.10 -19.94 180.00 160.06 -142.20 19.94 141.6 3.51 Sol_RF 1171.28 29.78 180.00 29.78 142.55 150.22 140.4 3.48 Sol_RF 1265.22 -15.88 180.00 164.12 -130.44 15.88 139.2 3.45 Sol_RF 1368.84 -0.00 180.00 180.00 -137.670.00 138.0 3.42 Sol_RF 1432.51 -180.00 180.00 -180.00 65.02 -0.00 137.9 3.42 Sol_RF 1575.02 -28.84 180.00 151.16 -150.04 28.84 134.7 3.34 Sol_RF 1671.69 -20.99 180.00 159.01 -143.37 20.99 133.0 3.30 Sol_RF 1792.13 101.46 179.93 102.35 -175.74 79.42 130.9 3.25 Sol_RF 18 107.89 144.73 179.79 145.06 -144.22 35.61 128.8 3.19 Sol_RF 1987.45 -78.19 180.00 101.81 -174.90 78.19 128.1 3.18 Sol_RF 2038.570.69 30.36 102.66 -18.79 -78.71 122.4 3.04 Sol_RF 2126.77 174.59 176.58 172.68 53.523.49 120.5 2.99 Sol_RF 22 116.66 178.08 175.143.49 126.48 187.32 120.5 2.99 Sol_RF 2375.56 -41.35 180.00 138.65 -151.12 41.35 119.8 2.97 Sol_RF 2466.12 36.35 180.00 36.35 132.24 143.65 116.6 2.89 Sol_RF 2583.87 71.62 180.00 71.62 167.74 108.38 114.7 2.85 Sol_RF 2669.24 -12.37 180.00 167.63 -138.48 12.37 112.3 2.79 Sol_RF 2759.75 15.26 172.297.64 119.07 157.12 112.2 2.78 Sol_RF 28 120.25 -164.74 172.29 22.88 119.07 172.36 112.2 2.78 Sol_RF 2996.68 -70.99 180.00 109.01 -166.63 70.99 110.9 2.75 Sol_RF 3063.23 -44.73 180.00 135.27 -126.47 44.73 108.9 2.70 Cheers, Paul Holland -- Yu Zhang HHMI associate Waksman Institute Rutgers University
Re: [ccp4bb] Fab:Peptide complex crystallization
Hi Christine, Just have a try. When people want to co-crystallize complexes of a protein and small molecular compounds, DMSO is often introduced into the drop, since pharmacologists like to dissolve compounds in DMSO. 2010/7/19 Harman, Christine christine.har...@fda.hhs.gov Hi all, I was wondering if anyone has had any experience with setting up Fab:peptide complexes for crystallization. I have Fab protein and peptide and I am not sure how to add the peptide to the Fab protein. My peptide is hydrophobic and thus not very soluble in standard aqueous buffers and barely soluble in some organics. The Fab protein I have is currently in 100mM Sodium Acetate pH5, 150mM NaCl. My current plan is to dissolve lyophilized peptide first in 10% DMSO and use this stock to add to Fab protein in a 20:1 or 10:1 molar ratio. I am not sure of the effects of residual DMSO on peptide binding to Fab or on crystallization. I have read one paper in which they rave about DMSO as an additive in their crystallization, but that protein was not Fab like at all. Any insight you all might have on this would be greatly appreciated. Thanks in advance, Christine -- Yu Zhang HHMI associate Waksman Institute Rutgers University
