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[modeller_usage] Questions about alignment and stereo clashes
To : "modeller_usageATsalilab.org " <modeller_usageATsalilab.org >Subject : [modeller_usage] Questions about alignment and stereo clashesFrom : "Li,Haoxi" <hl2500ATchem.ufl.edu >Date : Mon, 30 Mar 2020 18:15:43 +0000Accept-language : en-USArc-authentication-results : i=1; mx.microsoft.com 1; spf=pass smtp.mailfrom=chem.ufl.edu; dmarc=pass action=none header.from=chem.ufl.edu; dkim=pass header.d=chem.ufl.edu; arc=noneArc-message-signature : i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-SenderADCheck; bh=jFBvBKM2C/NMWZjUpgh9t7YzXCT9QII2qQqpA4s6nYs=; b=BxzmTKdgam/qlj3aRGXxJ0t7Uwc7ncCrKY2EvAv/sOWSWunphW6IqKqQUacR/5fr7+gaMMgQYzwEy6eUhyIWpc6i8lRYGQ8CsRtveRl3N3l8Th7pNsiO51mDN4USPNHuaTNtem0JMg4L/J+l3UcdmG4OdJBsEqJVOYJzLZA/94wJIsfxvc+YpjBW16hPyLYVr+YjhWYuL1GiZUYAKefMxTgX6cxt2Bt3yV2XHtvaoCUVrrPHk1tjGOlqY293uDdU6KHg3bHskv7kmP+mNk7/wA4OCPQXDEABMsFhhRy4kySRFqmxuH2jFOnkCzJIaOF091jo3Q+e3IiNWEvgEGGBzw==Arc-seal : i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none; b=oIdqB9GFHAtK6LPaOy0Z5lQWPauSYcgapr1GPYPG0bRg1jxAYlDGoUwsM8KNd+eVtcPZmOw8Z3caSgxDpfIcBwoUC10Oxs7GEoHQ/K+VNFXnKpbdXaK0H/4FDWbYf9K3rFiFBilbyvSukSfYurEGDEjkIwPzGUv497qDQyRjf1342RD5YGFImU2Lt9VHo4Y/Afnah+RRIwSiqmIwdJkUZ39SWAhFmTBf8g4qPYkl769M9T8gBY37fU8xvg6fa3oGQ7OrwrAvqq/b3Uu788dUL46XEN3gFeY4KAo/AJyz+7XwTHqZYS4lj7wC8j6msmocE9RfMtoZdgaZWRTk1Id/yQ==
Dear Modeller Users,
Hope this email finds you well! I’m recently working on homology modeling of Dopamine D1 receptor. Can I ask two questions?
1. Am I able to use the sequence alignment from external sources, like Blast?
2. When the model was built, I found many stereo clashes in the structure. Is this normal? Is there any way that I can fix the stereo clashes?
Thank you so much,
Haoxi