[ccp4bb] phase seapration
Hi, i am trying to crystallize a protein. i got phase separation in many conditions. can anybody tell me about phase separation? Is this good or not? My protein concentration is 17mg/ml. shall i increase it? Thanks in advance. parveen
[ccp4bb] Rotation Axis visualisation.
Good morning ccp4bb-ers! I have two protein-protein complex structures, and the orientation of one of the components shifts slightly with respect to the other component between the two structures. If I run superimpose on the shifting component I get this: CROWTHER ALPHA BETA GAMMA 12.41607-9.09294-9.64895 SPHERICAL POLARS OMEGA PHI CHI 73.10930 -78.96756 9.50379 DIRECTION COSINES OF ROTATION AXIS 0.18311-0.93918 0.29055 Angle between rotation axis and Centroid vector93.14726 * Note: Since this angle between rotation axis and Centroid vector is near to 90.0 this may represent a pure rotation *** This is fine - Its what I expected. However. I would like to know how I can graphically represent this axis in Coot/Pymol/CCP4MG? This has probably been asked before, but a quick google of the archives reveals nowt. Can anybody help? Cheers, Dave -- --- David Briggs, PhD. Father Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile --- Anyone who is capable of getting themselves made President should on no account be allowed to do the job. - Douglas Adams
[ccp4bb] pymol movies scripts
Hi all, I'm starting using pymol to generate movies to show my structure. While its seems fairly easy to generate simple movies with rocking or rotating molecules, I have been finding some difficulties understanding how to generate more complex movies. For instance, I'd love to generate a movie in which the molecule rotate along the x axis, then along the y axis, while the surface slowly shows up... or even more complicated scenarios, involving changes in colors of the objects (of course not sudden ones!)... Does anybody have some scripts to share with me, or can point me to some web pages that would explain me how to do that? Thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310 No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.487 / Virus Database: 269.13.22/1013 - Release Date: 9/17/2007 1:29 PM
[ccp4bb] arp/warp in p22121
Dear All, I am trying to build a molecular replacement model in arp/warp in space group P22121. Refmac alone seems to be fine with refining the model in P22121; but arp/warp fails, as far as I can see at the first Refmac refinement stage. In the log-file it says this space group is not supported. I am wondering whether arp/warp needs the Hermann-Mauguin convention space group P21212. I suppose I will need to reindex in P21212 in order to use arp/warp? (the diffraction data were indexed in XDS, scaled in SCALA, and then run through CAD to change the space group from P222 to P22121). I am using arp/warp via the ccp4i interface. Also, arp/warp gives the following message when I load the mtz file cannot extract arp/warp asymmetric unit limits, the job will fail if run. (i did run arp/warp successfully with other mtz-files). Thank you in advance for any comments! Florian
Re: [ccp4bb] arp/warp in p22121
Hi - ARP/wARP only likes standard space groups, like P21212, P22121 is not-standard ... oh well ... (Eleanor is complaining about it for about 13 years ... but never mind that she is right) Just re-index your sg to be P21212 (refl. utilities, reindex, in ccp4i). Choose 'Entering reflection transformation' P22121 to become P21212 you need h=l k=k l=-h set SG to p21212 if you are too lazy redo the Molrep or a nice brain teaser is to apply the correct transformation to your PDB (PDBSET will do that for you) and you are ready to go with ARP/wARP A. PS. depending on cell axes length, and given that convention wants the smaller 21 axis first, the formally correct transformation above might be h=k k=l l=h (in other words if your CURRENT b axis is smaller than your current c axis its the one above. if the CURRENT c axis is smaller than b, the use the one on top) PS2 I think i got the - right, you need to be sure you do not invert the hand - reindex will complain if I was wrong, in which case get rid/add a the '-' sign ;-) On Sep 18, 2007, at 12:28, Florian Schmitzberger wrote: Dear All, I am trying to build a molecular replacement model in arp/warp in space group P22121. Refmac alone seems to be fine with refining the model in P22121; but arp/warp fails, as far as I can see at the first Refmac refinement stage. In the log-file it says this space group is not supported. I am wondering whether arp/warp needs the Hermann-Mauguin convention space group P21212. I suppose I will need to reindex in P21212 in order to use arp/warp? (the diffraction data were indexed in XDS, scaled in SCALA, and then run through CAD to change the space group from P222 to P22121). I am using arp/warp via the ccp4i interface. Also, arp/warp gives the following message when I load the mtz file cannot extract arp/warp asymmetric unit limits, the job will fail if run. (i did run arp/warp successfully with other mtz-files). Thank you in advance for any comments! Florian
Re: [ccp4bb] arp/warp in p22121
Dear Florian, ARP/wARP supports 65 space groups where proteins crystallise and it indeed uses the Hermann-Mauguin convention as given in the International Tables. The space group P22121 (number 3018 in the CCP4 symop.lib) is not supported by ARP/wARP. The standard for it would be number 18, P21212. The easiest is to re-index your data. The error message 'cannot extract asymmetric unit limits' should then also disappear. Victor PS. Actually, Tassos has already replied while I was typing this message. Florian Schmitzberger wrote: Dear All, I am trying to build a molecular replacement model in arp/warp in space group P22121. Refmac alone seems to be fine with refining the model in P22121; but arp/warp fails, as far as I can see at the first Refmac refinement stage. In the log-file it says this space group is not supported. I am wondering whether arp/warp needs the Hermann-Mauguin convention space group P21212. I suppose I will need to reindex in P21212 in order to use arp/warp? (the diffraction data were indexed in XDS, scaled in SCALA, and then run through CAD to change the space group from P222 to P22121). I am using arp/warp via the ccp4i interface. Also, arp/warp gives the following message when I load the mtz file cannot extract arp/warp asymmetric unit limits, the job will fail if run. (i did run arp/warp successfully with other mtz-files). Thank you in advance for any comments! Florian
Re: [ccp4bb] pymol movies scripts
Go to the Pymol community wiki (www.pymolwiki.org) and install SLERPY, a python plugin that allows you to create multiple scenes and transitions in Pymol. It is possible to create some pretty sophisticated animations using slerpy, including fading transitions of surfaces. If you ray-trace the movie frames, you will need substantial computing power, or patience and several cups of coffee. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] Sebastiano Pasqualato wrote: Hi all, I'm starting using pymol to generate movies to show my structure. While its seems fairly easy to generate simple movies with rocking or rotating molecules, I have been finding some difficulties understanding how to generate more complex movies. For instance, I'd love to generate a movie in which the molecule rotate along the x axis, then along the y axis, while the surface slowly shows up... or even more complicated scenarios, involving changes in colors of the objects (of course not sudden ones!)... Does anybody have some scripts to share with me, or can point me to some web pages that would explain me how to do that? Thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310 No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.487 / Virus Database: 269.13.22/1013 - Release Date: 9/17/2007 1:29 PM
[ccp4bb] REFMAC and Hetroatoms
Hi all i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing refinement with REFMAC i m getting following warnings: I am reading library. Please wait. mon_lib.cif WARNING : residue: CA994 chain:XX different element name: file:C dict:CA WARNING : residue: CL995 chain:Xa different element name: file:C dict:CA how can i rectify this problem thanx in advance vineet gaur
[ccp4bb] Postdoc Position in Protein Crystallography
POSTDOCTORAL POSITION IN PROTEIN CRYSTALLOGRAPHY An NIH-funded POSTDOCTORAL position is available immediately to study the structure and function of (1) ATP-dependent molecular machines [e.g. Cell (2003) 115:229; Mol. Cell (2007) 25:261] and (2) multi-component protein assemblies [e.g. EMBO J. (2000) 19:25]. Diffracting crystals are available for some projects [e.g. Acta Cryst F. (2007) 63:784]. The position requires a doctoral degree in one of the natural sciences. Applications from experienced postdoctoral scholars/staff scientists with experience in protein crystallography will be considered. Applicants must have demonstrated experience with methods used for the crystallization and X-ray crystal structure determination (i.e. MAD/MIR) of proteins and enzymes. Experience with gene cloning and methods used for protein expression and purification are an advantage. The salary for this position will be pegged to the current National Research Service Award (NRSA) stipend for postdoctoral fellows (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-07-057.html) and is in addition to a generous fringe benefit package. Our lab is fully equipped for all aspects of molecular biology, protein chemistry, and X-ray crystallography. To apply for this position, please send a current CV, a brief description of research accomplishments and interests, and contact information of three to four referees to: Dr. Francis Tsai, Associate Professor, Dept. of Biochemistry and Mol. Biology, Baylor College of Medicine, One Baylor Plaza MS:BCM125, Room 315B, Houston, Texas 77030, USA. E-mail: [EMAIL PROTECTED]
[ccp4bb] phaser and percent composition result
the phaser docs/tutorial indicate that phaser calculates what could be called (ensemble) / (sequence) to get a percent composition, however i cannot seem to find the direct result from this in any output (.sol, .sum, .pdb, .log... other?) any tips appreciated as to if this can be found / where it might be. -bryan
[ccp4bb] phaser and percent composition result [ part 2]
i wrote (ensemble) / (sequence) to get a percent composition i forgot to emphasize that i do not mean the Vm or the Z composition, but the composition as one would enter e.g. COMPosition ENSEmble mol1 FRACtional 0.22 or COMPosition SCAttering SCATTERING -bryan
Re: [ccp4bb] REFMAC and Hetroatoms
Dear Vineet, It seems, in your input PDB file the atom level for CA and CL in the last column is C. It should be CA CL respectively. The atom name in the input file and Dictionary doesn't match. all the best Manish Vineet Gaur [EMAIL PROTECTED] wrote: Hi all i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing refinement with REFMAC i m getting following warnings: I am reading library. Please wait. mon_lib.cif WARNING : residue: CA994 chain:XX different element name: file:C dict:CA WARNING : residue: CL995 chain:Xa different element name: file:C dict:CA how can i rectify this problem thanx in advance vineet gaur - Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos more.
Re: [ccp4bb] pymol movies scripts
I used to do that in POVray. you can use any program that writes POV output and can generate all the objects you want. I used to write each object I want to manipulate to a separate file and #declare ed it as a POVray object. Then I wrote a 'master' povray file, that #include d the aforementioned ones and added (with the time variable) the transformations I wanted to have. It is then really simple to e.g. rotate your molecule while you're flying towards the active site and slowly display a surface. The upside is, you have tremendous control, the downside is that it's not really reusable for other projects and the planning (which objects to create, and the writing out of them) takes quite a while. well, and you'll have to look a bit into povray (#declare, #include, transform, texture, camera, clock). I think it's well worth the effort. ah, and be careful, for some graphics programs it is important that you don't move anything between writing ou the objects as they translate your scene into a povray frame. good luck and have fun jens On Tue, 2007-09-18 at 11:22 +0200, Sebastiano Pasqualato wrote: Hi all, I'm starting using pymol to generate movies to show my structure. While its seems fairly easy to generate simple movies with rocking or rotating molecules, I have been finding some difficulties understanding how to generate more complex movies. For instance, I'd love to generate a movie in which the molecule rotate along the x axis, then along the y axis, while the surface slowly shows up... or even more complicated scenarios, involving changes in colors of the objects (of course not sudden ones!)... Does anybody have some scripts to share with me, or can point me to some web pages that would explain me how to do that? Thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310 No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.487 / Virus Database: 269.13.22/1013 - Release Date: 9/17/2007 1:29 PM
[ccp4bb] Seeking Linux experts' adivice
Hi, All, After lunching pymol, if I drag the Xterm window produced by PYMOL using mouse, my computer will suddenly freeze, the keyboard seems no longer functioning. The only thing I can do is to re-boot my Linux system. This problem makes it almost impossible for me to use PYMOL on my LINUX box(CENTOS 4 i386). I have had the same problem when using COOT, ccp4i. Relacing the keyboard and mouse with new ones can not solving this problem. Thanks for your help Yanming
