[ccp4bb] error on installing arp/warp
Hi all, Something wrong has happened when I install arp/warp7.1 in my CentOS machine. What it told me during the installation is as below: [r...@lenovo6 arp_warp_7.1]# ./install.sh ARP/wARP installer is checking your c-shell... c-shell is installed on your machine at /bin/csh Your login shell is: /bin/bash Checking permissions for /dev/null- OK Checking availability of sed command - OK Checking availability of tail command - OK Checking availability of awk command - OK Checking decimal separator- OK Checking ARP/wARP directory path - OK Checking ARP/wARP directory structure - OK Checking java installation- installed version is "1.6.0" Checking java version number - OK Checking python installation - installed version is 2.4.3 Checking python version number- OK Python executables are available in /local/prog/arp_warp_7.1/byte-code/python-2.4 Checking operating system name- Linux Checking processor type - i686 ARP/wARP version 7.1 executables for this platform are available in /local/prog/arp_warp_7.1/bin/bin-i686-Linux Installing script and data files for: bin-athlon-Linux bin-i386-Darwin bin-i686-Linux bin-ia64-Linux bin-powerpc-Darwin bin-x86_64-Linux Checking CCP4 & ARP/wARP installation - OK Checking refmac5 installation - installed version is 5.5.0109 Checking refmac5 version number - OK if: Badly formed number. Has anyone have encountered the same problem and what should I do to solve that completely? Any suggestion will be greatly appreciated. Jian -- Jian Wu Ph.D. Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921217 Email: prote...@gmail.com
[ccp4bb] Amazing B-factor
Dear all, Recently we have collected one set of data which is processed to 2.9A and 3.0A and the Wilson-B values are 50.1 and 59.1, respectively. As for the completeness of the highest shell is only 66% in 2.9A (80% in 3.0A), we use the dataset with 3.0A for phasing and refinement. Everything is OK during phasing. Routinely, we use CNS (rigid, minimize and bgroup) for primary refinement and the R and freeR values go to 31.1 and 34.1. Surprisingly, the B-factor is 137.2. I have modified the B-factor to a fixed value (59.1 A^2) in the searching model coordinate file, however it changed to 127.6 after 'rigid' and subsequently to 131.9 after 'minimize'. In all the scripts above I used the default option "anisotrpic" at "overall B-factor correction". I don't know whether it is right to use this option at low resolution, so I have tried the other two options "no" and "isotropic". In the 1st choice, the B-factor is seemingly reasonable (55~59) but the R and freeR are very high (45.9 and 51.9). In the 2nd choice, the B-factor, R and freeR values are between those of the other two options (111.3, 40.6, and 45.3). I want to know what cause these surprising changes especially for B-factor value. Any suggestion is appreciated. Jian Wu -- Jian Wu Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921117 Email: prote...@gmail.com
[ccp4bb] Amazing B-factor
Dear all, Recently we have collected one set of data which is processed to 2.9A and 3.0A and the Wilson-B values are 50.1 and 59.1, respectively. As for the completeness of the highest shell is only 66% in 2.9A (80% in 3.0A), we use the dataset with 3.0A for phasing and refinement. Everything is OK during phasing. Routinely, we use CNS (rigid, minimize and bgroup) for primary refinement. -- Jian Wu Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921117 Email: prote...@gmail.com
[ccp4bb] Need help for solving a tough problem of phasing
Dear all, I have determined a structure with the resolution 2.0A and the spacegroup P3121 from crystals grown at 4 degree. This apo-form structure is composed of an N-terminal (a/b)8 TIM barrel (~300 AA) and two C-terminal domains (~100 AA) which are named as Sub1 and Sub2. Meanwhile, I have also got crystals at 20 degree. Although the diffraction of these crystals is not good, I could confirm that the spacegroup has changed to C2. Recently, I have collected several datasets from crystals with different substrates at 20 degree. All of them have relative low resolution from 3.5A to 2.8A and completeness from 80% to 90% and have the same spacegroup and almost the same cell parameters. Considering that the biological unit is dimer and the C-terminal domains have high flexibility, I use both monomer and dimer forms of the TIM barrel as the search models when I do MR in the best dataset (2.8A resolution and 85% completeness). I use three programs CNS, Molrep, and Phaser and they all could find the same optimal solution which contains a dimer and about 68% solvent in one asymmetric unit. After several rounds of refinement, the R and freeR have dropped to 35.6 and 41.6, respectively and the density fit well at the TIM barrel region. Between the symmetric molecules exists a lot of discontinuous positive peaks which have no obvious secondary structure patterns. All the information above show that something unknown is not determined in this structure. I superpose the full-length dimer to the determined TIM barrel dimer but find that the C-terminal domains have severe conflict with the symmetric molecules at this packing form. I continue the MR using the TIM barrel, Sub1, Sub2, or Sub1+Sub2 as search models with fixed TIM barrel dimer, however no right solutions are obtained. I also do the MR with the full-length monomer and dimer forms but there are still no right solutions. Then I have tried the other datasets, however I get the same results. Now I am trying to build the model manually. Because of the discontinuous densities, it is hard to finish the building work at a relatively short time and I think it is not a right way to cut the knot. I don't know how and what to do next. Could anyone give me a reasonable method to solve this tough problem? Any suggestion is appreciated. Jian Wu -- Jian Wu Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921117 Email: prote...@gmail.com
[ccp4bb] Faculty positions in Structural Biology at IBCB, SIBS, CAS
*Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences* *中国科学院上海生命科学研究院生物化学与细胞生物学研究所*** * * *Faculty positions in Structural Biology: Associate or Full Professor* Institute of Biochemistry and Cell Biology (IBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) ( http://www.sibcb.ac.cn) has begun an initiative to develop an internationally renowned research program in Structural Biology* *to complement and strengthen the existing programs in biological sciences. As part of this initiative, we are inviting applications for up to five faculty positions in *Structural Biology* at the rank of *Associate or Full Professor*. Applicants should have a Ph.D. or an equivalent degree, postdoctoral experience, demonstrated excellence in research, and potential of developing independent outstanding research work. The successful candidates will be expected to develop vigorous, extramurally funded research programs and to contribute to graduate and postdoctoral training programs. The positions come with excellent laboratory space and substantial startup funds. Competitive salary, housing subsidy, and fringe benefit package will be commensurate with experience. IBCB has long-standing expertise in biochemistry, molecular biology, cell biology, and protein science and provides a highly interactive and dynamic research environment, state-of-the-art research support facilities, and one of the best Ph.D. graduate programs in China. Opportunities for participation in intra- and inter-institute collaborative and interdisciplinary research are excellent. The IBCB campus is located in downtown Shanghai with easy access to many social, cultural, and sport events. Applicants should send curriculum vitae with a complete list of publications, a concise summary of past research accomplishments and future research plans, and three letters of references to: Mr. Banghe Mao, Faculty Search Committee, IBCB, SIBS, CAS, 320 Yue-Yang Road, Shanghai 200031, China or electronically to [EMAIL PROTECTED] (Tel. 086-21-54921006 and Fax: 086-21-54921011). Applications will be accepted until positions are filled. Interviews may be conducted at any time upon arrangement. IBCB is an equal opportunity employer. Jianping Ding Professor of Structural Biology Institute of Biochemistry and Cell Biology (IBCB) Shanghai Institutes for Biological Sciences (SIBS) Chinese Academy of Sciences (CAS) Tel: 0086-21-54921619 Fax: 0086-21-54921116 Email: [EMAIL PROTECTED] 招聘Science广告-StructuralBiology.doc Description: MS-Word document
[ccp4bb] Question about the percentages of occupancy for dual conformations.
Dear all, If I have a set of high-resolution data in which there is an important residue having apparent dual conformations, my question is: how or where could I test and calculate the percentages of occupancy for the dual conformations? Any suggestion is welcome. Yours, Jian -- Jian Wu Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921117 Email: [EMAIL PROTECTED]
[ccp4bb] Missing scatter deffinition in CNS
Dear all, I am refining a structure in which there is an fluorine atom in the inhibtor. When I go on the energy minimization in CNS, an unusual error happened to this atom: Program version= 1.1 File version= 1.1 CONNECt: selected atoms form 9 covalently disconnected set(s) list of isolated (non-covalently bonded) atoms: --none-- list of isolated (non-covalently bonded) di-atomic molecules: --none-- %XRASSOC-ERR: missing SCATter definition for ( $RX4 300 FAF ) chemical=FPAF %XRASSOC error encountered: missing SCATter definition for SELEcted atoms. (CNS is in mode: SET ABORT=NORMal END) * ABORT mode will terminate program execution. * Program will stop immediately. I have check the topology file, the paramter file, and the scatter.lib file, but found nothing is unusual in these files. Had anyone ever encountered this problem before? Any suggestion would be welcome and thank you in advance! Best Regards, Jian Wu -- Jian Wu Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921117 Email: [EMAIL PROTECTED]
[ccp4bb] Have a trial
-- Jian Wu Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921117 Email: [EMAIL PROTECTED]
[ccp4bb] Have a trial
[ccp4bb] Can I change the e-mail address
Dear Administrator, The e-mail I am using now is very small. Whether or not and how can I change this address to my another larger e-mail address ([EMAIL PROTECTED]) for receiving the ccp4bb? Thank you! Jian Wu -- Jian Wu Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921117 Email: [EMAIL PROTECTED]
